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Epigenetics in Healthand Disease

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Epigenetics in Healthand Disease

Igor Kovalchuk, Ph.D., MDOlga Kovalchuk, Ph.D., MD

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Library of Congress Cataloging-in-Publication Data

Kovalchuk, Igor.Epigenetics in health and disease / Igor Kovalchuk, Olga Kovalchuk. — 1st ed.

p. cm.Includes index.ISBN 978-0-13-259708-1 (hardcover : alk. paper)1. Epigenetics—History. 2. Epigenetics—Health aspects. 3. Pathology, Cellular. 4. Cells—Morphology. I. Kovalchuk, Olga, MD. II. Title. QH430.K68 2012571.9’36—dc23

2012007714

Dedicated to Anna.

Contents

1 Historical Perspective . . . . . . . . . . . . . . . . . . . . .1

2 Chromatin Dynamics and Chromatin Remodeling in Animals . . . . . . . . . . . . . . . . . . . . . . . . . . . .19

3 Chromatin Dynamics and Chromatin Remodeling in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49

4 DNA Methylation as Epigenetic Mechanism . . . . .75

5 Histone Modifications and Their Role in Epigenetic Regulation . . . . . . . . . . . . . . . . . . .119

6 Realm of Non-Coding RNAs—From Bacteria toHuman . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .147

7 Non-Coding RNAs Involved in EpigeneticProcesses—A General Overview . . . . . . . . . . .177

8 Non-Coding RNAs Across the Kingdoms—Bacteria and Archaea . . . . . . . . . . . . . . . . . . .203

9 Non-Coding RNAs Across the Kingdoms—Protista and Fungi . . . . . . . . . . . . . . . . . . . . . .223

10 Non-Coding RNAs Across the Kingdoms—Animals . . . . . . . . . . . . . . . . . . . . . . . . . . . . .267

11 Non-Coding RNAs Across the Kingdoms—Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .297

12 Non-Coding RNAs—Comparison of Biogenesisin Plants and Animals . . . . . . . . . . . . . . . . . . .327

13 Paramutation, Transactivation, Transvection, andCosuppression—Silencing of HomologousSequences . . . . . . . . . . . . . . . . . . . . . . . . . . .343

14 Bacterial Adaptive Immunity—Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) . . . . . . . . . . . . . . . . . . . . . .385

15 Gene Silencing—Ancient Immune Response and a Versatile Mechanism of Control over the Fate of Foreign Nucleic Acids . . . . . . . . . . .409

viii Epigenetics in Health and Disease

16 Epigenetics of Germline and Epigenetic Memory . . . . . . . . . . . . . . . . . . . . . . . . . . . . .435

17 Epigenetics of Health and Disease—Cancer . . .465

18 Epigenetics of Health and Disease—Behavioral Neuroscience . . . . . . . . . . . . . . . . . . . . . . . .499

19 Epigenetics of Health and Disease—Diet and Toxicology, Environmental Exposures . . . . . . . .523

20 Epigenetics and Technology—Hairpin-Based Antisensing . . . . . . . . . . . . . . . . . . . . . . . . . .555

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .577

Acknowledgments

We would like to thank Zoe Migicovsky, Corinne Sidler, Alena Babenko,Melanie Kalischuk, Andriy Bilichak, Stephanie Wickersham, Joel Stim-son, Aki Matsuoka, and Munima Alam for helping us in writing this book,collecting literature, and checking chapters for comprehension. Specialthanks to Valentina Titova for the tremendous help in proofreading thebook.

About the Authors

Igor Kovalchuk, Ph.D., MD, is Professor and Board of GovernorsResearch Chair at the Department of Biological Sciences, University ofLethbridge (Alberta, Canada). He edits Frontiers in Plant MicrobeInteraction, Frontiers in Epigenomics, and other journals. As principalinvestigator in the university’s Plant Biotechnology laboratory, he studiesgenetic and epigenetic regulation of plant response to stress, includingthe transgenerational effects of stress and microevolution of plant stresstolerance/resistance.

Olga Kovalchuk, Ph.D., MD is Professor and Board of GovernorsResearch Chair and CIHR Chair in Gender and Health at the Universityof Lethbridge and a member of the editorial boards of MutationResearch—Fundamental and Molecular Mechanisms of Mutagenesis andEnvironmental and Molecular Mutagenesis. She researches the role ofepigenetic dysregulation in carcinogenesis; epigenetic regulation of can-cer treatment responses; radiation epigenetics and role of epigeneticchanges in genome stability and carcinogenesis; radiation-induced oncogenic signaling; and radiation-induced DNA damage, repair, andrecombination.

Historical perspective

Genetics can be broadly defined as the science studying the mecha-nisms of inheritance in general and genes in particular. Epigeneticscan be, in part, defined as the branch of biology dealing with themechanisms of inheritance. In contrast to genetics, epigeneticsinvolves the control of gene expression that is not accompanied byany changes in DNA sequence. Epigenetics deals with the mecha-nisms of heredity which do not involve modifications of DNAsequence and are reversible in nature.

Success of a certain population depends on the fine balancebetween the ability to retain a given genotype in the stable environ-ment and the ability to evolve by modification in response to substan-tial environmental changes. Changes in the genome can be dual innature; they might deal with stable physical changes in DNAsequence leading to mutations and reversible chemical modificationsof nucleotides or chromatin structure leading to epimutations. Muta-tions are the basis of genetic changes.

This book introduces you to the concept of epigenetics and epige-netic regulation. The book discusses processes of evolution in light ofcurrent understanding of the role of epigenetics and describes therole of epigenetic regulations in the growth and development ofsomatic cells, tissue differentiation, and the maintenance of epige-netic states in various cells of the same organisms. Furthermore, thebook provides an introduction to an in-depth understanding of therole of epigenetics in the mechanisms of inheritance and interactionwith the environment. The chapters also describe the role of epige-netics in health and disease. Finally, the book introduces you to the

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concepts of silencing, co-suppression, and paramutations, and dis-cusses the role of epigenetics in these processes.

This book is aimed primarily at students beginning to study epi-genetics, whether at the undergraduate or graduate level. It may alsobe essential reading for research scientists in the field of epigenetics,genome stability, stress tolerance and adaptation, transgenerationeffects, genome evolution, and other related fields, as well as anyonewho simply wishes to know more about the field of epigenetics.

The mechanisms of environmental influences on the phenotypicappearance of organisms and inheritance were developed nearly twocenturies ago and represented a prominent part of the descriptive workperformed by Jean-Baptiste Lamarck and Charles Darwin. Althoughtheir ideas were often viewed as too preliminary and naïve, it was thoseideas that laid a solid and important foundation for the development ofthe field of epigenetics. Epigenetics has a lot to do with an organism’sinteraction with the environment; therefore, it is important to reviewhow our understanding of the interactions between the organism’sgenome, surroundings, and phenotype has developed over time.

The French biologist Jean-Baptiste Lamarck (1744–1829), who iscredited with the first use of the word “biology,” was the first scientistwho proposed a theory of evolution. He used the term transformationrather than evolution to suggest that organisms change and transformas the result of “a new need that continues to make itself felt.” His firstreference to evolution as a process of less complex species becomingmore complex appeared in 1800 in his Floreal lecture. Within next 20years, Lamarck published three important works (Recherches sur l’or-ganisation des corps vivants, 1802; Philosophie Zoologique, 1809;Histoire naturelle des animaux sans vertèbres (in seven volumes,1815–1822) in which he developed his ideas of evolution and formu-lated the laws that described evolution as a process. Lamarck writes:

Law 1: Life, by its own forces, continually tends to increasethe volume of every body which possesses it and to enlargethe size of its parts up to a limit which it brings about itself.Law 2: The production of a new organ in an animal bodyresults from the appearance of a new want or need, whichcontinues to make itself felt, and from a new movementwhich this want gives birth to and maintains. Law 3: The

1 • Historical perspective 3

development of the organs and their strength of action areconstantly in proportion to the use of these organs. Law 4:All that has been acquired, impressed upon, or changed inthe organization of individuals during the course of their lifeis preserved by generation and transmitted to the new indi-viduals that come from those which have undergone thosechanges.

Lamarck used these laws to explain the two forces he saw as com-prising evolution; a force driving animals from simple to complexforms, and a force adapting animals to their local environments anddifferentiating them from each other.

Lamarck is remembered primarily for his belief in the inheri-tance of acquired characteristics and the use and disuse model bywhich, according to Lamarck, organisms develop their characteris-tics. The theory of evolution developed by Lamarck is frequentlyreferred to as Lamarckism or Lamarckian evolution. This theory isalso often referred to as soft inheritance. The term was first sug-gested by Ernst Mayr to explain the ideas of Lamarck and ÉtienneGeoffroy Saint-Hilaire (1772–1844) and to contrast those ideas withthe modern idea of inheritance, which Mayr referred to as hardinheritance. Geoffroy, a French naturalist and a colleague ofLamarck, defended Lamarck’s idea of the influence of the environ-ment on species evolution. He further developed Lamarck’s idea sug-gesting that the environment causes a direct induction of organicchange that is the transmutation of species in time.

Perhaps the first attempt at rejection of soft inheritance wasmade by the English surgeon William Lawrence (1783–1867) in1819. He stated that “The offspring inherit only connate peculiaritiesand not any of the acquired qualities” (Lawrence and William, 1819).The inheritance of acquired characteristics was also rejected by theGerman biologist August Weismann (1834–1914). In the 1880s, heperformed an experiment in which he cut off the tails of 22 genera-tions of mice, thus proving that the loss of tail cannot be inherited.Furthermore, in 1893, Weismann proposed his own theory of inheri-tance. He discovered that the cells that produce the germ plasm(now known as gametes) separate from somatic cells at an early stageof organismal development. Weissman could not understand how


somatic and gametic cells communicated with each other, andtherefore, he declared that the inheritance of acquired characteristicswas impossible. He further suggested that the organism’s body (thesomatoplasm) exists for only one generation, whereas the hereditarymaterial, which he called germ plasm, is immortal and passed fromgeneration to generation. Although being rather naïve and futuristic,this view led to an important suggestion: Nothing that happens tosomatic cells may be passed on with the germ plasm. Thus, this modelunderlies the modern understanding of inheritance in whichgermlines are main cells passing hereditary information from onegeneration to another. At the same time, because this model sug-gested that the germ plasm is a self-sufficient substance that is notinfluenced by the environment, it represented a unilateral under-standing of evolutionary processes.

Another theory of evolution was synthesized and described by theEnglish biologist and social philosopher Herbert Spencer. In 1857, hepublished his theory of evolution in his essay “Progress: Its Law andCause.” Spencer characterized the process of evolution as “evolutionof complexity”; he suggested that evolution was a process in whichsimple organisms always evolved into more complex ones, therefore,evolution itself was progressive in nature. Currently, this view of evo-lution is considered to be misleading; it is generally accepted thatspecies evolve in response to the environment in the process of natu-ral selection that does not have directionality. The absence of the log-ical explanation of natural selection did not allow Spencer’s theory ofevolution to become more prominent. At the same time, it wasSpencer who popularized the term evolution itself. Moreover, afterreading Darwin’s The Origin of Species, published just two years afterSpencer’s essay, Spencer attempted to use Darwin’s theory for expla-nation of the role of evolution in society. Moreover, he also tried toincorporate it into his own theory of evolution, coining the now-com-mon phrase survival of the fittest.

In 1859, Charles Darwin published the work “On the Origin ofSpecies by Means of Natural Selection, or the Preservation ofFavoured Races in the Struggle for Life” (Darwin, 1859) (commonlyknown as The Origin of Species) that became a foundation of evolutionary biology and a reason for plenty of scientific discussions.


Darwin’s theory suggested that species in the population evolvethrough a process of natural selection. His book offered multipleexamples of how the diversity of life on our planet arose by commondescent with modification through a branching pattern of evolution.Darwin proposed that within a certain species, individuals that areless fit for their particular environment are less likely to survive andreproduce compared to those that are well-adapted and have bettersurvival and reproductive potential. The more successful individualsleave more progeny, and thus pass their heritable traits to the nextgeneration. As a result, a certain part of population adapts to thechanged environment and eventually might become a separatespecies. One important thing to note here is that the environmentplays a critical role in shaping species’ evolution. Darwin accepted aversion of the inheritance of acquired characteristics proposed earlierby Lamarck.

Later on, Darwin set forth his provisional hypothesis describingthe mechanisms of heredity. In 1868, he presented this idea in hiswork The Variation of Animals and Plants under Domestication(Darwin, 1868). The theory of pangenesis suggests that each individ-ual cell of an organism not only experiences environmental changesand responds to them but also generates molecules that accumulatein germ cells. Darwin believed that these molecules, which he calledgemmules (Darwin, 1868; Darwin, 1971), are capable of contribut-ing to the development of new traits and organisms. Nowadays, it is astriking fact that small non-coding RNAs such as microRNAs(miRNAs) and small interfering RNAs (siRNAs) generated bysomatic cells are indeed able to travel within the organism reachingthe gametes and potentially influencing the phenotypic appearanceof progeny.

1-1. Ontogeny and phylogenetics

Ontogeny (ontogenesis, morphogenesis) is a branch of sciencedescribing the development of an organism from the fertilized eggto its adult form.

Phylogenetics (phylogenesis) is the study of evolutionary related-ness among various groups of organisms.


Neo-Darwinism is a comprehensive theory of evolution, fre-quently called the Modern Synthesis, that combines Mendeliangenetics with Darwinian natural selection as a major factor in evolu-tion and population genetics. The term Neo-Darwinism was first usedby George Romanes (1848–1894) in 1895 to explain that evolutionoccurs solely through natural selection as it was proposed by AlfredRussel Wallace (1823–1913) and August Weismann. Neo-Darwinismsuggests that evolution occurs without mechanisms involving theinheritance of acquired characteristics based upon interactions withthe environment. Thus, this modernized Darwinism accepted someideas developed by Darwin’s original theory of evolution via naturalselection, but at the same time it separated them from Darwin’shypothesis of pangenesis and the Lamarckian view of inheritance.

Historically, many scientists tried to prove or disprove Darwin’stheory of pangenesis. Francis Galton (1822–1911), a cousin of Dar-win, conducted many experiments that led him to refute the pangen-esis theory. Initially, he accepted the theory, and, in consultation withDarwin, he tried to detect how gemmules were transported in theblood. In his very simple hypothesis, he suggested that if gemmuleswere transferred to gametic cells though the blood then blood trans-fusion between various breeds of animals would generate new traitsin progeny. In a long series of experiments initiated around 1870, hetransfused the blood between dissimilar breeds of rabbits and foundno evidence of characteristics transmitted by blood transfusion.

Darwin challenged the validity of Galton’s experiment. He wrotein 1871:

Now, in the chapter on Pangenesis in my “Variation of Ani-mals and Plants under Domestication,” I have not said oneword about the blood, or about any fluid proper to any circu-lating system. It is, indeed, obvious that the presence of gem-mules in the blood can form no necessary part of myhypothesis; for I refer in illustration of it to the lowest ani-mals, such as the Protozoa, which do not possess blood or anyvessels; and I refer to plants in which the fluid, when presentin the vessels, cannot be considered as true blood.

Until the end of the nineteenth century, Darwin’s theory of pan-genesis was accepted by many scientists. The work of Gregor Johann


Mendel on plant hybridization fundamentally changed scientists’understanding of the mechanism of inheritance. Although Mendelpublished his work in 1866, it was not until 1900 that his ideas werere-examined. Upon re-discovering the significance of Mendel’s work,a new era of Mendelian genetics began in which scientists completelyrejected the possibility of the transmission of information fromsomatic cells to gametes and thus to progeny. It was a real pushbackfor Lamarck’s theory of evolution.

Many scientists still considered the possibility of environmentallyinduced heritable changes. The Russian scientist Ivan Michurin(1855–1935), one of the founders of scientific agricultural selection,also assumed that genotypes could change upon environmental pres-sure. He worked on hybridization of plants of similar and differentorigins, developing strategies for overcoming species incompatibilityupon hybridization and cultivating new methods in connection withthe natural course of ontogenesis (1922–1934). He was also inter-ested in directing the process of predominance, evaluation, and selec-tion and in working out methods of acceleration of selectionprocesses. In the early twentieth century, he proved that the domi-nant traits in generation of hybrids depend on heredity, ontogenesis,and phylogenesis of the initial cell structure as well as on individualfeatures of hybrids. Michurin was a true follower of Lamarck andDarwin, and he firmly believed that natural selection could be influ-enced by external factors, with man being the most influential one.

In the not-too-distant past, the ideas of Lamarck and Michurinseemed to be pseudo-scientific and impossible to believe in. Butrecently, a breakthrough publication describing changes in thegenetic make-up of grafted plants appeared that became an eye-opener, suggesting many new possibilities for transmission of geneticmaterial. Sandra Stegemann and Ralph Bock showed that transfer ofgenetic material from stock to scion is possible upon grafting oftobacco plants (Stegemann and Bock, 2009). The results of the studydemonstrated that recipient plants acquired tolerance to an antibioticin the same manner as donor plants, and they also confirmed thetransfer of genetic material from a donor to a recipient. Although it isstill unclear whether the acquisition of antibiotic resistance occurs viaplastid transfer through plasmodesmata or via the transfer of a largeportion of the plastid genome from a donor cell to a recipient cell, it


can be definitely considered as an example of changes not only in phe-notypic appearance but also in the genetic make-up of a grafted plant.

The emergence of epigenetics as science was closely linked to thestudy of evolution and development. Nowadays, we know that chro-mosomes are associated with both genetic and epigenetic regulation,thus driving the developmental processes. Despite the early discoveryof chromosomes by Walther Flemming (1843–1905), the founder ofcytogenetics, in 1879, it took many more experiments to links chromo-somes to function, phenotypes, and developmental programming.The experiments by Edmund Wilson (1856–1939), Theodor Boveri(1862–1915), Walter Sutton (1877–1916), and later on Thomas HuntMorgan (1866–1944) provided several evidences that chromosomeswere indeed involved in developmental processes, and changes inchromosomes resulted in changes in phenotype. The Boveri-Suttonchromosome theory suggested that Mendelian laws of inheritancecould be applied to chromosomes and chromosomes might thus beunits of inheritance. Morgan’s work in Drosophila showed that theinheritance of many genes was linked to the X chromosome; amongthem were genes coding for eye color. This and other works enabledhim to become the first scientist to receive a Nobel Prize (1933) for hiswork in genetics. The report by Watson and Crick (1953) describingDNA structure and proposing the mode of DNA replication furtherreinforced the notion that DNA is the cell’s genetic material. Althoughthe studies of chromosome morphology indicated that somatic cellscontained all of the chromosomes, it was not clear why the somaticcells of different tissues had different phenotypic appearance, raisingdoubts whether somatic cells actually did carry all the genes and notonly those that were necessary for their growth and development.

Although investigations of epigenetic regulation of an organism’sdevelopment and cell fate were being actively pursued throughoutthe twentieth century, the actual name “epigenetics” did not emergeuntil 1942 when Conrad Hal Waddington (1905–1975) used it todescribe how genes might interact with their surroundings to pro-duce a phenotype. Waddington described several essential concepts,including canalization, genetic assimilation, and epigeneticlandscape. The concept of canalization in Waddington’s understand-ing was the capacity of the organisms of a given population to pro-duce the same phenotype regardless of the extent of genetic and


environmental variations. He assumed that this robustness came as aresult of evolution, shaping the developmental processes to perfec-tion. Waddington’s idea of genetic assimilation suggested that anorganism responds to the environment in such a way that theacquired phenotype would become part of the developmentalprocess of the organism.

To demonstrate that the phenomenon exists, Waddingtoninduced an extreme environmental reaction in the developingembryos of the fruit fly Drosophila. When exposed to ether vapor, asmall percentage of the Drosophila embryos developed a second tho-rax. It was obvious that bithorax embryos represent an abnormal phe-notype. Waddington continued selection of bithorax mutant embryos,and after about 20 generations of selection, he obtained Drosophilaflies that developed bithorax without being exposed to ether vapor.Waddington suggested that in this particular case, selection led to theproduction of the desired effect, which became canalized, and, as aresult, bithorax appeared regardless of environmental conditions.Thus, Waddington’s experiments demonstrated that Lamarckianideas of inheritance of acquired characteristics could, at least in prin-ciple, be true. Finally, the epigenetic landscape, as suggested byWaddington, represents is a programmed cell fate where develop-mental changes would occur with increasing irreversibility, much likemarbles rolling down a small-ridged slope toward the lowest elevationpoint. Nowadays, the term epigenetic landscape refers to the cer-tain area of a chromatin in the cell with specific cytosine methylationand histone modifications involved.

During the past 50 years, the scientific community has witnesseda lot of rises and falls in an interest in epigenetics. Perhaps, the nextimportant discovery in the area of epigenetics was Alexander Brink’sreport on the phenomenon of paramutation. In 1956, Brinkdescribed a somewhat puzzling and controversial phenomenon of theinheritance phenotype associated with the of Red 1 (r1) locus inmaize (Brink, 1956). It was observed that the spotted seed allele (R-st) was able to transform the R-r (purple color seeds) phenotypeallele into a colorless seed phenotype in subsequent generations. As aresult of the cross, all of the F2 generation plants showed reducedanthocyanin in seeds, which was contrary to the expected segregationratios according to the Mendelian law. The phenomenon that he


proposed to be called paramutation involved heritable transmissionof epigenetically regulated expression states from one homologoussequence to another. For a more detailed description of paramuta-tions in plants and animals, see Chapter 13, “Paramutation, Transacti-vation, Transvection, and Cosuppression: Silencing of HomologuousSequences.”

In her early work, Barbara McClintock (1902–1992) also sug-gested that the chromosomal position effect might influence on thebehavior of mutable loci in maize. She assumed that the observed dif-ference in mutability ratios of suppressor elements in maize had themechanism similar to the earlier described phenomenon of position-effect variegation. The latter term was first brought up by HermannJoseph Muller (1890–1967) and was meant to describe the effect ofchromosomal position on gene expression. Having observed grosschromosomal rearrangements, Muller noted changes in gene expres-sion, and the genes that were brought into the area of heterochro-matin expressed poorly. McClintock noted that some controllingelements, such as Spm, would suppress gene expression rather thanmutate a gene; she also noticed that the suppression of gene expres-sion would take place not only at the locus where the elements hadbeen inserted but also at the neighboring loci.

The work of David Nanney (published in 1958) showed that thecytoplasmic history of conjugating parents had an impact upon themating-type determination of resulting progeny in Tetrahymena(Nanney, 1958). This phenomenon was suggested to be of epige-netic nature.

In the early 1960s, Mary Lyon and Walter Nance presented themechanism of another epigenetically regulated process, X-chromo-some inactivation. It was suggested that inactivation of the mam-malian female X chromosome occurred before the 32-cell stage of theembryo. However, there was no clear assumption that this processwas indeed of epigenetic nature. The fact that no changes wereobserved at the level of DNA allowed Riggs (1975) and Holliday andPugh (1975) to propose that DNA methylation could be a mechanismof X-chromosome inactivation.


In the 1970s, Hal Weintraub’s work on the expression of globingenes revealed an influence of chromosomal location on the transcrip-tional activity. His observations were the source from which the sugges-tion came that the chromatin structure might regulate gene expression.

In the early 1980s, it became clear that there was an apparentcorrelation between the level of cytosine methylation at GpG DNAsequences and the level of gene transcription. Moreover, the mitoticheritability of DNA methylation patterns was also shown. Later on,by the mid-1980s, the influence of nuclear content on thegenetic/phenotypic make-up of the organism was also revealed. It wasfound out that not only the DNA sequence of paternal or maternalalleles had an effect on the phenotype, but the origin of a particularchromosome itself could influence the phenotype. Thus, it was sug-gested that besides the DNA sequence, the chromosome also carriedadditional information.

In the 1990s, scientists presented more discoveries in the area ofepigenetics, coming from studies of various organisms including proto-zoa, fungi, Drosophila, plants, and animals. In plants, it was found thatthe transgene coding for chalcone synthase (Chs) had various degreesof suppression of expression gene expression. It was perhaps the firstwell-documented event of gene silencing (Napoli et al., 1990).

In trypanosomes, it was discovered that silencing of the group ofVariable Surface antigen Genes (VSG) is maintained by the incorpo-ration of a novel base, β-D-glucosylhydroxymethyluracil (Borst et al.1993). Because trypanosomes do not have the mechanism of cytosinemethylation, it was suggested that the insertion of the modified basewould also serve as a gene-silencing mechanism. Significant progresswas made in understanding the mechanisms of X inactivation. A por-tion of the human X chromosome was identified to function as the Xchromosome inactivation center; later on, the gene Xist was identi-fied that appeared to be coding for a non-coding RNA expressedonly in an inactive X chromosome (Willard et al., 1993). The analysisof the expression of the neighboring gene Igf2 and H19 pair provideda further understanding of the mechanism underlying chromosomalimprinting. The genes were mutually exclusively expressed depend-ing on the maternal or paternal origin of the chromosome; if the Igf2gene was expressed from the paternal chromosome, then the H19


gene was repressed, whereas if the H19 gene was expressed from thematernal chromosome, the Igf2 gene was repressed. Methylationanalysis of the locus identified high frequency of occurrence ofmethylated CpGs. Therefore, it was proposed that methylation con-trolled the access to the enhancer element that functioned mutuallyexclusively for both genes. Indeed, in mice, it was found that amutant impaired in the function of a 5-methyl-cytosine DNA methyl-transferase lost the imprinting of the gene pair in ES cells.

The role of epigenetic regulation in control over gene expressionwas also demonstrated by the experiments on fungi. Gene duplicationin Neurospora crassa often resulted in the occurrence of two events:frequent mutations and hypermethylation of both gene copies, a phe-nomenon known as repeat-induced point mutation (RIP). Fur-thermore, for the first time, it was shown that cytosine methylation inNeurospora could occur at non-CpG sites. A similar phenomenonwas observed in Drosophila; the duplication of the brown genetranslocated near heterochromatin increased the level of repressionin the active copy. Because in Drosophila, cytosine methylation is notused as a process of gene expression regulation, there should be a dif-ferent repression mechanism. The research in this direction resultedin the development of the concept of chromosomal boundary ele-ments, the areas of the chromosome that contained a 300 bp nucle-ase-resistant core surrounded by nuclease hypersensitive sites thatwere first described in Drosophila. It was suggested that such ele-ments allow the separation of a chromatin domain along the chromo-some, thus leading to differential areas of chromosome compactionand gene expression. In yeasts, the Sir2, Sir3, and Sir4 proteins (silentinformation regulator proteins) were identified that were proposed tocontrol repressive states near heterochromatic regions. The evidencethat Sir3 and Sir4 interacted with the tails of histones H3 and H4 fur-ther confirmed the importance of both these proteins and histones inthe maintenance of the chromatin state. By the end of the 1990s, his-tone-modifying enzymes such as acetylases and deacetylases wereidentified, and the MeCP2 protein complex that was able to bind tomethylated DNA and histone deacetylases were described.

One more important discovery made in the late 1990s was thedescription of the phenomenon of RNA interference. A series of work by Craig Mello and Andrew Fire culminated in the famous


publication in Nature (Fire et al., 1998) that described the ability ofdouble-stranded RNA molecules to inactivate the expression of genesin C. elegans; the effect of interference was evident in both injectedanimals and progeny. Because just a few molecules per cell were suf-ficient to trigger the effect, the authors suggested the existence of anamplification component, currently known as a mechanism thatinvolves the function of RNA-dependent RNA polymerase. Theimportance of this work for studying organism development, thetherapy of various human diseases, as well as for the development ofbiotechnology and basic science was recognized with the Nobel Prizeawarded to Mello and Fire in 2006.

In 1990, Robin Holliday defined epigenetics as “the study of themechanisms of temporal and spatial control of gene activity duringthe development of complex organisms” (Holliday, 1990). Today, thedefinition of epigenetics has been changed; it is now described as thestudy of the mechanisms of inheritance and control of gene expres-sion that do not involve permanent changes in the DNA sequence.Such changes occur during somatic cell division and sometimes canbe transmitted transgenerationally through the germline.

The last ten years were marked by the most prominent achieve-ments in epigenetic research. In 2000, it was discovered that the Sir2protein of yeasts was in fact a histone deacetylase. Studies of the het-erochromatin states, replication processes, the activity of the Sir3protein in yeast, and the heterochromatin protein (HP1) in mammalsshowed that heterochromatin was not in a solid inert stage reversibleonly during replication but rather in an active equilibrium stage ofprotein exchange between the nuclear soluble compartment and het-erochromatin itself, regardless of cell cycle status.

By the early 2000s, most of the histone modifications and theenzymes that catalyze them were discovered, and it was believedthat besides histone methylation, all other modifications such asacetylation, phosphorylation, ubiquitination, and so on werereversible. Thus, various histone methylation states were regarded asa permanent epigenetic mark of chromatin status and werereversible only during replication. The results of studies by Cuthbertet al. (2004) and Henikoff et al. (2004) raised the possibility that his-tone methylation could be reversible, and their suggestions were metwith true enthusiasm. In his works, Cuthbert demonstrated that


peptidylarginine deaminase was able to remove single methylationevents at the arginine amino acid of histone H3 (Cuthbert et al.,2004). Henikoff et al. (2004) showed that H3.3, a histone H3 variant,was able to replace histone H3 in a transcription-dependent andreplication-independent manner, opening the possibility for moreflexible regulation of methylation after the process transcription wasover.

Another breakthrough was the discovery that nuclear organiza-tion and silencing at telomeres were not necessarily completely inter-related. The experiment showed that if telomeres and the associatedsilencing complex were released from the periphery of the nucleusand were able to move throughout the nucleus, the silencing attelomeres was established with similar efficiency (Gasser et al.,2004). This is truly exciting—it suggests that chromatin compart-mentalization and gene silencing processes are not rigid and prede-fined states; there indeed exists an active exchange between thenuclear pools of proteins and small RNAs that are able to establish acertain chromatin state at any given locus regardless of its nuclearlocation.

A curious phenomenon was reported for Arabidopsis; it was onthe borderline of epigenetic regulation and described a non-Mendelian inheritance. An hth mutant is homozygous for the muta-tion in the HOTHEAD (HTH) gene that encodes a flavin adeninedinucleotide-containing oxidoreductase involved in the creation ofthe carpel during the formation of flowers. It was reported that in theprogeny of the hth mutant, the percentage of the frequency ofappearance of the HTH phenotype and HTH genomic sequence was~15% (Lolle et al., 2005). It was first proposed that reversion wastriggered by RNA synthesized by HTH/hth parents and stored in theprogeny hth/hth plants. Four alternative explanations have been pro-posed: Two of them were in part similar to an original explanationmade by Lolle et al. (2005) and dealt with template-directed geneconversion; the third one offered the process of mutation accumula-tion followed by selection; and the fourth one involved chimerism.Later on, two publications seemed to put everything in place: Peng etal. (2006) and Mercier et al. (2008) reported that the hth mutantshowed a tendency toward outcrossing and recovered a normalgenetic behavior when grown in isolation. Despite the fact that


Arabidopsis is an extreme self-pollinator (less than 0.1% of outcross-ing), in the hth plants the frequency of outcrossing among neighbor-ing plants was ~12%. This can be an excellent alternative explanationfor the apparent genetic instability of hothead mutants.

Now that the genome sequences of model organisms such as C.elegans, Drosophila, Arabidopsis, human, mice, rice, and so on areavailable, more and more investigators have attempted to understandthe organization of the genome and chromatin and explain the mech-anisms of inheritance, maintenance of genome stability, and regula-tion of gene expression. What has become clear is that thesemechanisms are both genetic and epigenetic in nature. As it wasrecently put by Daniel E. Gottschling (“Epigenetics: from phenome-non to field” in Epigenetics; eds. C.D. Allis, T. Jenuwein, D. Rein-berg), it was time to move “above genetics”—a literal meaning ofepigenetics as several important genomes have already beensequenced.

There are multiple examples of the influence of environment onthe genetic and epigenetic make-up of the organism. The phenomenaof stress-induced transposon activation, non-targeted mutagenesis,stress-induced communication between cells and organisms, and evi-dences of transgenerational changes induced by stress are just somerepresentations of epigenetic effects of the environment on theorganism.

The non-linear response to DNA damaging agents is one of themost interesting examples of an epigenetically controlled process. Ithas already been known that a higher dose of mutagen does not nec-essarily result in a higher level of damage to DNA. In fact, low dosesof ionizing radiation often lead to disproportionally high levels ofDNA damage. Doses of ionizing radiation that are believed to have anegligible effect on a cell often exert dramatic influence on DNAdamage and cell viability.

In the past, cell-to-cell communication between neighboringcells as well as communication between cells of different tissues andorgans in multicellular organisms were considered Lamarckian/Darwinian and thus improbable. There are multiple examples ofphysiological cell-to-cell communications in simple and complexorganisms involving hormonal signaling, neurotransmission, and so


on. Moreover, it is believed that damaged tissues are able to commu-nicate with non-damaged tissues—a phenomenon known asbystander effect. The phenomenon of bystander effect has alsobeen observed between whole living organisms.

Can organisms communicate memory of stress across genera-tions? According to Darwin, organisms evolve from the pool of indi-viduals with spontaneous changes/mutations through the process ofnatural selection. The process of mutagenesis is believed to be ran-dom, and the majority of mutations are deleterious. The rare muta-tions that become beneficial under certain environmental conditionshave a chance to be fixed in a population. Because mutagenesis doesnot occur frequently, the fixation of desired traits would take placevery rarely. In contrast, processes of acclimation and adaptation arerapid ones that allow organisms to acquire protection against stress ina single generation after stress exposure. These processes cannot beexplained by the laws of Mendelian genetics. In this book, you findmultiple examples demonstrating the inheritance of stress memory invarious organisms across generations.

This chapter attempted to explain what epigenetics is, how it isinvolved in the regulation of growth and development of the organ-ism, how it controls interactions of the organism with the environ-ment, and what roles epigenetics plays in the mechanisms ofinheritance and evolutionary processes.

There have been many more important discoveries in the field ofepigenetics, and we apologize to all those authors whose work,though relevant, is not mentioned in this chapter because of limita-tions of space.

ReferencesBorst et al. (1993) Control of antigenic variation in African trypanosomes.Cold Spring Harb Symp Quant Biol. 58:105-14.Brink RA. (1956) A genetic change associated with the R locus in maizewhich is directed and potentially reversible. Genetics 41:872-879.Cuthbert et al. (2004) Histone deimination antagonizes arginine methyla-tion. Cell 118:545-53.


Darwin CR. (1871) Pangenesis. Nature. A Weekly Illustrated Journal ofScience 3:502-503.Darwin CR. (1859) On the Origin of Species by Means of Natural Selection,or the Preservation of Favoured Races in the Struggle for Life (1st ed.),London: John Murray.Darwin CR. (1868) The variation of animals and plants under domestication.London: John Murray. 1st ed., 1st issue.Fire et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806-11.Gasser et al. (2004) The function of telomere clustering in yeast: the circeeffect. Cold Spring Harb Symp Quant Biol. 69:327-37.Henikoff et al. (2004) Epigenetics, histone H3 variants, and the inheritanceof chromatin states. Cold Spring Harb Symp Quant Biol. 69:235-43.Holliday R. (1990) Mechanisms for the control of gene activity during devel-opment. Biol Rev Camb Philos Soc, 65:431-471.Lawrence, William FRS. (1819) Lectures on physiology, zoology and thenatural history of man. London: J. Callow, p. 579.Lolle et al. (2005) Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis. Nature 434:505-9.Mercier et al. (2008) Outcrossing as an explanation of the apparent uncon-ventional genetic behavior of Arabidopsis thaliana hth mutants. Genetics180:2295-7.Nanney DL. (1958) Epigenetic factors affecting mating type expression incertain ciliates. Cold Spring Harb Symp Quant Biol. 23:327-35.Napoli et al. (1990) Introduction of a Chimeric Chalcone Synthase Geneinto Petunia Results in Reversible Co-Suppression of Homologous Genes intrans. Plant Cell 2:279-289.Peng et al. (2006) Plant genetics: increased outcrossing in hothead mutants.Nature 443:E8.Stegemann S, Bock R. (2009) Exchange of genetic material between cells inplant tissue grafts. Science 324:649-651.

Index

21U-RNAs, 267, 271-2736S RNA, 208-209

AA-to-I editing, humans/plants, 165-166A-type lamins, 22aberrant RNA (aRNA), 236acetylation, histones, 121

animals, 126plants, 137-138

acetyltransferases, plant histones, 137ACF (chromatin-assembly factor)

complex, 31actin-related proteins (ARPs), 23-25activation of translation, 282-283activation-induced cytosine

deaminase (AID), 99active chromatin states, 55active demethylation, 99-101, 110-113active state, gene promoters, 122AD (Alzheimer’s disease), 508-510adaptive immunity of bacteria,

CRISPRs, 385-387array structure, 387-389evolutionary context, 403-404function, 390-399incorporation of new sequences

into loci, 400-401potential functions, 402-403remaining questions, 404-405

adenine methylation, 90Adomet (S-adenosylmethionine), 90AGAMOUS-LIKE19 gene, 63AGL19 gene, 63AGO (ARGONAUTES), 298, 420

Agouti locus, 524AGRIKOLA (Arabidopsis Genomic

RNAi Knockout Line Analysis), 565ahpRNA (artificial hpRNA), 556, 561AID (activation-induced cytosine

deaminase), 99air pollution, influence on

phenotypes, 529-534algae-chloroplasts containing

protists, ncRNAs, 233-236alleles, 348allelic interactions

co-suppression, 380-381paramutation, 344-345

animals, 372-379epigenetic regulation, 354-361fungi, 371historical view, 345-347models, 361-370plants, 347-354, 370-371tandem repeats, 362-365

transvection, 379-380Alleman, Mary, 356allotetraploidization, 348Alu elements, 199Alzheimer’s disease (AD), 508-510animals

applications of hairpin RNAi, 569-570

chromatin structure, 125characterization of histone

modification by distributionin nucleus, 135-137

histone acetylation/deacetylation, 126

histone methylation/demethylation, 127-129

577

histone phosphorylation, 130-131

histone ubiquitination, 131-132histone variants, 133-134

development, miRNAs, 291-292epigenetic reprogramming, 440

gametes, 441-446histone-mediated inheritance,

452-453inheritance of disease, 454-456methylation-mediated

inheritance, 448-452protamine-mediated

inheritance, 447-448sRNA-mediated inheritance,

453-454histone modifications, 125

acetylation/deacetylation, 126characterization by

distribution in nucleus, 135-137

methylation/demethylation,127-129

phosphorylation, 130-131ubiquitination, 131-132variants, 133-134

methylation, 92active and passive mechanisms

of demethylation, 99-101de novo methylation, 93-97maintenance, 98-99

ncRNAs, 267C. elegans, 267-274comparison to plants, 327-340Drosophila melanogaster,

274-283paramutation, 372

RNAs involved in phenotypicepigenetic inheritance, 374-379

whitetail phenotype sample,372-374

antisense ncRNAs, 180antisense technology, 555-558

animal applications, 569-570chimeric hairpins, 559components of hairpin, 560-561inducible hairpin RNAi, 562-563limitations, 573mammal applications, 570-573targeting conserved sequences,

558-559tissue-specific, 562

antisense transcript-derived RNAs(nat-siRNAs), 232

apolipoprotein B RNA-editingcatalytic component 1(APOBEC1), 99

apoptosis, regulation by tRNAs, 153aptamer FC RNA, transcription

prevention, 248aptamer region (riboswitches), 204Arabidopsis. See also plants

active chromatin states in, 55Arabidopsis thaliana, 234AtSYD and AtBRM proteins, 66-67DCL proteins, 310DDM1 protein, 68PIE1 protein, 64-66PRC complexes in, 54seed development genes, 49SNI1 protein, 67-68summer-annual state, 55, 61-63winter-annual state, 55-61

Arabidopsis Genomic RNAiKnockout Line Analysis(AGRIKOLA), 565

Archaea, ncRNAs, 217-220Argonaute protein, 196ARGONAUTES (AGO), 298aRNA (aberrant RNA), 236ARPs (actin-related proteins), 23-25array structure, CRISPRs, 387-389artificial hpRNA (ahpRNA), 556, 561asthma, 530AtBRM protein, 66-67AtMBD protein, 69-70ATPases, in chromatin-remodeling

complexes, 25-26CHD complexes, 33-35INO80 complexes, 35-36ISWI complexes, 31-33SWI/SNF proteins, 26-27, 30-31

ATRX syndrome, 507AtSWP1 protein, 62AtSYD protein, 66-67

BB-type lamins, 22b1 locus, paramutation in plants,

351-354B2 RNA, transcription prevention, 248

578 index

bacteriaadaptive immunity, CRISPRs,

385-387array structure, 387-389evolutionary context, 403-404function, 390-399incorporation of new

sequences into loci, 400-401potential functions, 402-403remaining questions, 404-405

crRNAs, 396methylation, 75

CcrM, 86-89Dam (DNA adenine

methyltransferase), 78-87ncRNAs, 203

cis- and trans-encoded smallRNAs, 209-215

CRISPRs, 216-217protein-binding ncRNAs,

207-209riboswitches, 204-206

phages, 387regulation of virulence, 84

bacteriophage-insensitive mutants(BIMs), 400

BAF complex, 27, 30-31BAP (Brahman-associated

proteins), 27barrier insulators, 41behavioral neuroscience, influence

of epigenetic changes, 499chromatin remodeling, 500classical experiments of Meaney

and Szyf, 503-505DNA methylation and the brain, 499histone modifications, 500ncRNAs, 501-502neurodegenerative disorders,

508-516neurodevelopmental disorders,

506-507psychiatric disorders, 516-517

benzene, 550BFCs (bioactive food components),

epigenetic effects, 536DNA methylation, 536-538histone modifications, 538-539influence of compound

concentration, 540-541miRNAs, 539-540

bidirectional ncRNAs, 180

BIMs (bacteriophage-insensitivemutants), 400

bioactive food components (BFCs),epigenetic effects, 536DNA methylation, 536-538histone modifications, 538-539influence of compound

concentration, 540-541miRNAs, 539-540

biogenesisncRNAs

comparison of plants toanimals, 327-340

gRNAs, 197-199lncRNAs, 178-182miRNAs, 184-190piRNAs, 192-195RNase III-type

endonucleases, 195siRNAs, 190-192small ncRNAs, 183

plants, 298biomarkers, cancer, 480-482bivalent state, gene promoters, 122black carbon, 530blood transfusions, 6Bock, Ralph, 7boundary elements, 12Boveri, Theodor, 8Boveri-Sutton chromosome theory, 8BPTF proteins, 32Brahma-associated proteins (BAP), 27brain

chromatin remodeling, 500DNA methylation, 499histone modifications, 500ncRNAs, 501-502

BRG1 proteins, 30Brink, Alexander, 9, 345BRTF protein, 38BRU1 protein, 51bystander effects, 16, 543-545

CC nucleotides, insertion/deletion,

167-168C-to-U editing, 163-165C. elegans (Caenorhabditis

elegans), 267as model for biological function of

ncRNAs, 273-274ncRNAs, 267-273

index 579

C3 (chromosome conformationcapture) methodology, 364

ca-siRNAs (cis-acting nat-siRNAs), 308Caenorhabditis elegans

(C. elegans), 267CAF1 protein, 51Cajal body, 154Cajal body-specific RNAs

(scaRNAs), 154canalization, 8cancer

defined, 465influence of epigenetic changes, 465

DNA methylation, 468-483histone modifications, 484-492therapeutic interventions,

492-493stages of development, 466

canonical nucleosomes, 125carcinogenesis, 465carcinogens, epigenetic effects,

548-550cas genes (CRISPR-associated

genes), 387-389CASS (CRISPR-Cas system), 217CcrM (cell cycle-regulated

methylase), 78, 86-89CECR2-containing remodeling

factor (CERF) complex, 32Celera Genomics, 523cell cycle

histone deposition during, 141-142regulation, 88-89

cell cycle-regulated methylase. SeeCcrM

cell cycle-regulatedmethyltransferases, 88

cell-to-cell communication, 15CERF (CECR2-containing

remodeling factor) complex, 32Chandler, Vicki, 356chaperones (histone), 121CHARGE syndrome, 34CHD (chromodomain and helicase-

like domain) ATPases, 26, 33-35CHD1 proteins, 33-34CHD3 proteins, 34CHD4 proteins, 34CHD7 proteins, 34chemical carcinogens, epigenetic

effects, 548-550chimeric hairpins, 559chimerism, 14

Chlamydomonas reinhardtii, 233CHRAC (chromatin accessibility

complex), 31chromatin

architecture, 20-23compaction, 19-20defined, 119modifiers, cancer and, 484-487parachromatin, 363remodeling, 20

Alzheimer’s disease, 509brain, 500complexes, 25-36effector proteins, 36-41in plant development, 49-70insulator proteins, 41-44nuclear ARPs (actin-related

proteins) in, 23-25structure in animals, 125

characterization of histonemodification by distributionin nucleus, 135-137

histone acetylation/deacetylation, 126

histone methylation/demethylation, 127-129

histone phosphorylation, 130-131

histone ubiquitination, 131-132histone variants, 133-134

structure in trypanosomes, 123-125chromatin accessibility complex

(CHRAC), 31chromatin-assembly factor (ACF)

complex, 31chromatin-remodeling complexes,

developmental roles, 25CHD complexes, 33-35INO80 complexes, 35-36ISWI complexes, 31-33SWI/SNF proteins, 26-27, 30-31

chromodomain and helicase-likedomain (CHD) ATPases, 26, 33-35

CHROMOMETHYLASE (CMT3), 102

chromosomal imprinting, 11chromosome conformation capture

(3C) methodology, 364chromosome territories (CTs), 20, 135chromosomes

boundary elements, 12in developmental processes, 8

580 index

ciliatesepigenetic reprogramming, 436-440ncRNAs, 223-229

cis natural antisense transcripts (cis-NATs), 181

cis-acting nat-siRNAs (ca-siRNAs), 308cis-acting ncRNAs, 170cis-encoded ncRNAs, 209-211cis-nat-siRNAs, 306cis-NATs (cis natural antisense

transcripts), 181, 276cloning vectors (hairpins), 564closed non-permissive chromatin, 484CMT3 (CHROMOMETHYLASE),

102co-suppression, 236, 297, 380-381,

409-411Coe, Edward, 346Coffin-Lowry syndrome, 507Commonwealth Scientific and

Industrial Research Organization(CSIRO), 564

communication, cell-to-cell, 15conjugation, 385

defined, 386repression of, 83-84

cortical inheritance, ciliates, 436CpG dinucleotide pairs, 92CpG islands, 92CRISPR RNAs (crRNAs), 391, 396CRISPR-associated (cas) genes. See

cas genes, 387-389CRISPR-Cas complexes, 388CRISPR-Cas system, 416CRISPR-Cas system (CASS), 217CRISPRs (clustered regularly

interspaced short palindromicrepeats), 216-217bacterial adaptive immunity, 385-405comparison to piRNAs, 395comparison to RNAi pathway, 391defined, 385inheritance, 404related proteins, 389-390

cross-protection, 410crRNAs (CRISPR RNAs), 391, 396cryptic unstable transcripts (CUTs),

250-251CSIRO (Commonwealth Scientific

and Industrial ResearchOrganization), 564

CsrB RNA, 207CsrC RNA, 207

CT-IC (interchromatin compartmentmodel), 21

CTCF proteins, 42-43CTs (chromosome territories), 20, 135CUTs (cryptic unstable transcripts),

250-251cytosine methylation, 11

animals, 92active and passive mechanisms

of demethylation, 99-101de novo methylation, 93-97maintenance, 98-99

fungi, 91-92non-symmetrical methylation, 110plants, 101

active and passivedemethylation, 110-113

de novo DNA methylation,104-108

maintenance, 108-110methyltransferases involved,

102-104symmetrical methlation, 92

DDam (DNA methyltransferase), 75,

78-79, 468DNA repair, 81maintenance and inheritance of

DMPs, 85-87organization of nucleoid region, 80regulation of bacterial virulence, 84regulation of gene expression, 78repression of conjugation, 83-84role in DNA replication, 80transposition, 82-83

Darwin, Charles, 2, 4-6, 16DCL (Dicer-like) proteins, 195DCL1 protein, 301, 417DCL2 protein, 417DCL3 protein, 417DCL4 protein, 417DCLs (DICERs), 298DDM1 protein, 68-70ddRNAi (DNA-directed RNAi), 556DdRP (DNA-dependent RNA

Polymerases), 238de novo DNA methylation, 93-97

germline cells, 97plants, 104-108

de novo methyltransferases(DNMTs), 92-93

index 581

deacetylation, 126, 137-138deletion

C or G nucleotides, 167-168uridines (editing), 162-163

demethylation, 127-129developmental functions, ncRNAs in

plants, 319-320developmental stages of cancer, 466diagnostic markers, miRNAs and

cancer, 491diagnostic value of epigenetics,

492-493dicer proteins, 409dicer-independent small interfering

RNAs (disiRNAs), 247-248Dicer-like (DCL) proteins, 195DICERs (DCLs), 298Dictyostelium discoideum, 230diet, epigenetic effects, 536-541differentially methylated regions

(DMRs), 95, 449dimorphic bacterium, 88direct IR exposure, epigenetic

changes, 542-543disease and health, influence of

epigeneticsbehavioral neuroscience, 499-517cancer, 465-493chemical carcinogens, 548-550diet, 536-541environmental exposures, 523-535radiation-induced changes, 542-548

disease inheritance, 454-456disiRNAs (dicer-independent small

interfering), 247-248DMPs (DNA methylation patterns),

79, 85-87DMRs (differentially methylated

regions), 95, 449DNA damaging agents, non-linear

response to, 15DNA methylation, 113-114

Alzheimer’s disease, 508-509animals, 92-97

active and passive mechanismsof demethylation, 99-101

maintenance, 98-99bacteria, 75-78


methyltransferase), 78-87

brain, 499cancer, 468-470

as a biomarker, 480-482detection and analysis of

methylomes, 482-483hypermethylation, 476-480hypomethylation, 470-476

correlation to histonemodifications, 142-143

defined, 75effects of bioactive food

components, 536-538eukaryotes, 90-91fungi, 91-92Huntington’s disease, 513Multiple Sclerosis, 515-516non-symmetrical, 110Parkinson’s disease, 512plants, 101



epigenetic reprogramming, 456maintenance, 108-110methyltransferases involved,

102-104schizophrenic patients, 517symmetrical, 92

DNA methylation patterns (DMPs),11, 79, 85-87

DNA methyltransferase. See DamDNA pairing model, 361DNA repair, 81DNA replication, 80DNA unscrambling, 227DNA viruses, 417DNA-dependent RNA Polymerases

(DdRP), 238DNA-directed RNAi (ddRNAi), 556DNMTs (de novo

methyltransferases), 92-93DOMAINS REARRANGED

METHYLTRANSFERASE 2(DRM2), 102

DOMAINS REARRANGEDMETHYLTRANSFERASE 3(DRM3), 161

double-strand breaks (DSBs), 112double-stranded RNA-binding

domains (dsRBDs), 166, 276

582 index

double-stranded RNA-bindingproteins (DRBs), 419

double-stranded RNAs (dsRNAs),159, 177, 556gene silencing, 412viruses, 416

DRAGs (dsRNA-activated genes), 248DRBs (double-stranded RNA-

binding proteins), 419DRD1 protein, 69-70DRM2 (DOMAINS

REARRANGEDMETHYLTRANSFERASE 2), 102

DRM3 (DOMAINSREARRANGEDMETHYLTRANSFERASE3), 161

Drosophila melanogaster. See alsochromatin, methylationantagonistic functions of trxG and

PcG proteins, 28-29BAP (Brahma-associated proteins)

in, 27CHD1 proteins in, 33CHD7 proteins in, 34gypsy insulators in, 44histone modification, 119ISWI complexes in, 31-32ncRNAs, 274-283protein insulators in, 42-43

DSBs (double-strand breaks), 112dsRBDs (double-stranded RNA-

binding domains), 166, 276dsRNA-activated genes (DRAGs), 248dsRNA-induced transcriptional

program, 248-249dsRNAs (double-stranded RNAs),

159, 177, 556gene silencing, 412viruses, 416

Dutch Hunger Winter, 526

EE. coli dam, gene expression, 78editing

A-to-I editing, 165-166C-to-U editing in humans, 163-165flagellated protists, 161-163role of gRNAs, 197-199

effector complexes, 124effector proteins, 36-41, 121EFS/SDG8 protein, 58egg cell, 107

embryoblast, 94embryonic stem cells (ESCs), 29ENCODE (Encyclopedia Of DNA

Elements), 171endo-siRNAs (endogenous siRNAs),

276-279endosperm cells, 106enhancer blocking, 41environmental exposures, influence

on phenotypes, 523-524air pollution, 529-534prenatal environment, 525-527psychological environment, 527-529twin models to study environmental

effects, 534-535enzymes, histone-modifying, 485-487epigenetic landscape, 8-9epigenetic memory, 435

reprogramming in animals, 440gametes, 441-446histone-mediated inheritance,

452-453inheritance of disease, 454-456methylation-mediated

inheritance, 448-452protamine-mediated

inheritance, 447-448sRNA-mediated inheritance,

453-454reprogramming in ciliates, 436

cortical inheritance, 436homology-dependent

inheritance, 436-440reprogramming in plants, 456

DNA methylation in gametes, 456

gene imprinting, 458-459histone modifications, 457-458passing to progeny, 459-460

epigenetic regulation, 354-361epigenetic somatic inheritance, 435epigenetics

defined, 1, 13health and disease

behavioral neuroscience, 499-517

chemical carcinogens, 548-550diet, 536-541environmental exposures,

523-535radiation-induced changes,

542-548

index 583

historical background, 2-16influence on health and disease,

465-493technology, 555-573

epimutations, 1epistasis, 357epistatic interaction, 357esBAF complex, 29-31ESCs (embryonic stem cells), 29establishment of paramutation, 345eukaryotes, methylation, 90-91evolution, historical background, 2-8evolutionary conservation, plant

miRNAs, 303-304evolutionary context, CRISPRs,

403-404exo-siRNAs (exogenous siRNAs),

274-276expression

E. coli dam gene, 78genes, influence of histone

modifications, 122-123platform (riboswitches), 204

Ffamilies

DNMTs (de novomethyltransferases), 93

plant histone acetyltransferases, 137famine, epigenetic effects, 526FAS1 gene, 51FIE (fertilization independent

endosperm) genes, 53Fire, Andrew, 12FIS (fertilization independent seed)

genes, 54flagellated protist, editing with

gRNAs, 161-163flagellates, ncRNAs, 229-230FLC expression

in summer annuals, 61-63in winter annuals, 57-61repression of, 59-61

Flemming, Walther, 8flowering (in plants), chromatin

remodeling in, 55-64AGL19 genes, 63Snf2-like genes, 64-70summer-annual state, 61-63winter-annual state, 57-61

flowering locus t (FT) floralintegrator, 56

fragile X syndrome, 507Friedrich’s ataxia, 507FT (flowering locus t) floral

integrator, 56functional genomics, 564functional groups (ncRNAs), 150-152functions

CRISPRs, 390-403miRNAs and cancer, 490ncRNAs, 178-183

animals, 267-283Archaea, 217-220cis- and trans-encoded

ncRNAs, 209-215comparison of plants to

animals, 327-340CRISPRs, 216-217fungi, 236-249gRNAs, 197-199mammals/humans, 283-292miRNAs, 184-189piRNAs, 192-195plants, 297-323protein-binding ncRNAs,

207-209protozoa, 223-229riboswitches, 204-206RNase III-type

endonucleases, 195siRNAs, 190-192yeasts, 249-261

rRNAs, 155-161VSRs (viral suppressors of RNA

silencing), 426-430fungi

methylation, 91-92ncRNAs, 236-242

disiRNAs, 247-248dsRNA-induced

transcriptional program,248-249

milRNAs, 245-247MSUD, 243-245qiRNAs, 242-243

paramutation, 371future, ncRNAs, 170-171

GG nucleotides, insertion/deletion,

167-168Galton, Francis, 6

584 index

gametes. See also germlinecells, 4epigenetic reprogramming, 441-446transgenerational inheritance of

epigenetic states, 441gemmules, 5gene activation, DNA

hypermethylation and cancer, 477-478

gene expressioninfluence of histone modifications,

122-123ncRNA-mediated regulation in S.

cerevisiae, 254-257regulation

co-suppression, 380-381paramutation, 343-379role of CcrM, 88role of Dam, 78transvection, 379-380

gene imprinting, epigeneticreprogramming in plants, 458-459

gene promoters, 122gene silencing, 11, 343. See also

RNAi (RNA interference)at telomeres, 14co-suppression, 380-381hairpin-based antisensing, 555-557

animal applications, 569-570chimeric hairpins, 559components of hairpin, 560-561inducible hairpin RNAi,

562-563limitations, 573mammal applications, 570-573plant applications, 563-569targeting conserved sequences,


history of, 410-413protection of plants against

viruses, 413PTGS as antiviral mechanism,

413-415purpose of, 413RdDM pathway, 312-317summary of ncRNAs involved, 327TGS (transcriptional gene

silencing), 421-423trans-silencing, 359transgenerational inheritance

(epigenetic states)reprogramming in animals,

440-456

reprogramming in ciliates,436-440

reprogramming in plants, 456-460

transitive silencing, 423-426VIGS (virus-induced gene

silencing), 416-421viral suppressors, 426-430

generative cell, 105genetic assimilation, 8genetics, 1genomic imprinting, 95, 356, 470genotoxic carcinogens, 549Geoffroy Saint-Hilaire, Étienne, 3germ plasm, 3germline. See also gametes

cells, de novo DNA methylation,97, 105-108

genome, ciliates, 223GINA (Global Initiative in Asthma)

scores, 531GlmY RNAs, 208GlmZ RNAs, 208global genome hypomethylation

(cancer cells), 470Global Initiative in Asthma (GINA)

scores, 531glycosylases, 111Gottschling, Daniel E., 15grafted plants, 7gRNAs (guide RNAs)

A-to-I editing, 165-166C-to-U editing in humans, 163-165editing in flagellated protists,

161-163editing of miRNA/siRNA, 197-199insertion/deletion of C or G

nucleotides, 167-168reasons for RNA editing, 168-169

groups, ncRNAs, 150-152guide RNAs. See gRNAsguide strand, 191, 421gypsy insulators, 44

HH2AX histone variant, 133H2AZ histone variant, 133H3 histone variants, 134H3K acetylation, 121, 134H3K27me, histone methylation, 139H3K36me, histone methylation, 140

index 585

H3K4me, histone methylation, 138H3K9me, histone methylation, 140Hagemann, Rudolf, 346hairpin RNAi construct, 555-558

animal applications, 569-570chimeric hairpins, 559components, 560-561inducible hairpin RNAi, 562-563limitations, 573mammal applications, 570-573plant applications, 563-569targeting conserved sequences,


hairpin RNAs (hpRNAs), 279, 556,570-571

haplotypes, 348hard inheritance, 3HAT (histone acetyl transferase)

enzymes, 121hc-siRNAs (heterochromatic

siRNAs), 308HD (Huntington’s disease), 513-514HDAC (histone deacetylase)

enzymes, 121health and disease, influence of

epigeneticsbehavioral neuroscience, 499-517cancer, 465-493chemical carcinogens, 548-550diet, 536-541environmental exposures, 523-535radiation-induced changes, 542-548

Heat-shock RNA1 (HSR1 RNA), 291HEN1 protein, 420heterochromatic siRNAs

(hc-siRNAs), 308Hfq RNA-binding protein, 214HGPS (Hutchinson-Gilford

progeria), 23HGT (horizontal gene transfer),

385-386histone acetyl transferase (HAT)

enzymes, 121histone code, 124histone core, 119histone deacetylase (HDAC)

enzymes, 121histone-mediated inheritance, 452-453histones

acetylation, 121, 135chaperones, 121defined, 119

H2AX, 133H2AZ, 133in chromatin compaction, 19methylation, 13modifications, 119

Alzheimer’s disease, 509animals, 125-137brain, 500cancer, 484-492effects of bioactive food

components, 538-539epigenetic reprogramming,

457-458gene expression states, 122-123Huntington’s disease, 513Parkinson’s disease, 512plants, 137-143transcription regulation,

120-122trypanosomes, 123-125

phosphorylation, 130-131ubiquitination, 131-132

historical background of epigeneticsresearch, 2-16

historyncRNAs, 148-149of gene silencing, 410-413paramutation, 345-347RNA, 148-149

Holliday, Robin, 13homologous recombination, 67, 134homology-dependent inheritance,

ciliates, 436-440homology-dependent silencing,

ciliates, 224horizontal gene transfer (HGT),

385-386horizontal inheritance, CRISPR

elements, 404HOTAIR RNA (Hox antisense

intergenic RNA), 291HOTHEAD (HTH) gene, 14Hox antisense intergenic RNA

(HOTAIR RNA), 291HP1 protein, 37hpRNAs (hairpin RNAs), 279, 556,

570-571HR (hypersensitive response),

423-424HSR1 RNA (Heat-shock RNA), 291humans

A-to-I editing, 165-166C-to-U editing, 163-165

586 index

ncRNAs, 283HOTAIR RNA, 291HSR1 RNA, 291miRNAs, 283-292piRNAs, 288-290siRNAs, 287-288Xist and Tsix RNAs, 290

Huntington’s disease (HD), 513-514Hutchinson-Gilford progeria

syndrome (HGPS), 23hypermethylation, cancer

gene activation, 477-478mechanisms, 479-480miRNA genes, 478-479mutagenic potential, 476

hypersensitive response (HR), 423-424

hypomethylation, cancer, 470development and progression,

474-476loss of imprinting, 473mechanisms, 473-474oncogenes, 472-473repetitive sequences, 471

IIAP (intracisternal A-particle)

retrotransposons, 448IC (imprinting center), 455ICD (interchromosome domain)

model, 21ICRs (imprinting control regions),

94-95, 443ICs (interchromatin compartments),

20, 135IES (internally eliminated

sequences), 224, 437IGS (intergenic spacer), 156imitation switch (ISWI) ATPases, 26,

31-33imprinted genes, 442imprinting center (IC), 455imprinting control regions (ICRs),

94-95, 443inactive state, gene promoters, 122incorporation of new sequences,

CRISPR loci, 400-401indirect IR exposure, epigenetic

changes, 543-548inducible hairpin RNAi, 562-563inheritance

DMPs (DNA methylationpatterns), 85-87

hard inheritance, 3histone-mediated, 452-453historical background, 3-8methylation-mediated, 448-452non-Mendelian mechanism, 440of stress memory, 16phenotypic epigenetic inheritance,

374-379protamine-mediated, 447-448soft inheritance, 3sRNA-mediated, 453-454transgenerational, 435

reprogramming in animals,440-456

reprogramming in ciliates,436-440

reprogramming in plants, 456-460

INO80 ATPases, 26, 35-36insertion

C or G nucleotides, 167-168uridines (editing), 162-163

insulator proteins, 41-44integrons, 385interchromatin compartment model

(CT-IC), 21interchromatin compartments (ICs),

20, 135interchromosome domain (ICD)

model, 21intergenic ncRNAs, 180intergenic spacer (IGS), 156internal lamins, 22internal ribosome entry site

(IRES), 285internally eliminated sequences

(IES), 224, 437intracisternal A-particle (IAP)

retrotransposons, 448intronic ncRNAs, 180invasion and metastases (cancer), 472inversely amplified responses,

co-suppression, 380ionizing radiation (IR) exposure,

epigenetic changes, 542-548IR (ionizing radiation) exposure,

epigenetic changes, 542-548IRES (internal ribosome entry

site), 285ISWI (imitation switch) ATPases, 26,

31-33

index 587

J–K–LKaiso protein, 40kinetic model, 168Knudson’s “two-hit” cancer

hypothesis, 466

Lamarck, Jean-Baptiste, 2-3lamin-associated polypeptides

(LAPs), 23lamins, 23LAPs (lamin-associated

polypepetides), 23lariats, 189lateral gene transfer, 386Lawrence, William, 3Lewis, Edward B., 379LHP1 protein, 69-70LHP1/TFL2 protein, 54like heterochromatin protein 1

(LHP1)/terminal flower 2 (TFL2), 54limitations, hairpin-mediated

RNAi, 573lncRNAs (long ncRNAs), 310

biogenesis and function, 178-183categories, 179-180modes of action, 182transcriptional repression, 181

LOI (loss of imprinting), cancer, 473long ncRNAs. See lncRNAslong siRNAs (lsiRNAs), 308loss of imprinting (LOI), cancer, 473lsiRNAs (long siRNAs), 308lunasin, 541Lyon, Mary, 10

MMAC (macronucleus), 437macronucleus (MAC), 437Macronucleus Destined Segments

(MDSs), 437maintenance

DMPs (DNA methylationpatterns), 85, 87

DNA methylation, 98-99, 108-110methyltransferase, 92paramutation, 345

malignant cells, 465mammals/humans

applications of hairpin RNAi, 570-573

BAF complex, 27, 30-31

CHD1 proteins in, 34CHD7 proteins in, 34HP1 protein in, 37INO80 complexes in, 35-36ISWI complexes in, 32-33MBD3 proteins in, 40ncRNAs, 283

HOTAIR RNA, 291HSR1 RNA, 291miRNAs, 283-292piRNAs, 288-290siRNAs, 287-288Xist and Tsix RNAs, 290

NURD complexes in, 34protein insulators in, 42-43

manipulation of biosyntheticpathways, plant applications forhairpin-based RNAi, 566-567

maternal diet (prenatalenvironment), epigenetic effects,525-527

Mattick, John, 149maturation, tRNAs, 153maxicircle molecules, 162Mayr, Ernst, 3MBD (methylbinding domain),

39, 469MBD1 protein, 39MBD2 protein, 39MBD3 protein, 40MBD4 protein, 40McClintock, Barbara, 10MCSs (multiple cloning sites), 564MDSs (Macronucleus Destined

Segments), 437Meaney, Michael, 503-505mechanisms (epigenetic), DNA

methylationanimals, 92-101bacteria, 75-89eukaryotes, 90-91fungi, 91-92plants, 101-113

MeCP1 protein complex, 39MeCP2 protein complex, 39MED1 protein, 40meiotic silencing by unpaired DNA

(MSUD), 243-245meiotic transsensing, 243meiotic transvection, 243meiotic unannotated transcripts

(MUTs), 257-258Mello, Craig, 12

588 index

memoryepigenetic, 435

animals, 440-456ciliates, 436-440plants, 456-460

formation, 499Mendel, Gregor Johann, 7, 148MET1 (METHYLTRANSFERASE 1),

102metals, exposure to, 550metameres, 362metastasis, miRNAs and cancer,

491-492methyl-CpG-binding domain (MBD)

proteins, 469methylated DNA, binding to, 39methylation

Alzheimer’s disease, 508-509animals, 92

active and passive mechanismsof demethylation, 99-101

de novo methylation, 93-97maintenance, 98-99

bacteria, 75CcrM, 86-89Dam (DNA adenine

methyltransferase), 78-87brain, 499cancer, 468-470

as a biomarker, 480-482detection and analysis of

methylomes, 482-483hypermethylation, 476-480hypomethylation, 470-476

defined, 75effects of bioactive food

components, 536-538eukaryotes, 90-91fungi, 91-92histones

animals, 127-129plants, 138

Huntington’s disease, 513Multiple Sclerosis, 515-516non-symmetrical, 110plants, 101



epigenetic reprogramming, 456maintenance, 108-110methyltransferases involved,

102-104

schizophrenic patients, 517symmetrical, 92

methylation-mediated inheritance,448-452

methylbinding domain (MBD), 39Methylome DB study, 517methylomes, detection and analysis,

482-483METHYLTRANSFERASE 1

(MET1), 102methyltransferases, plant

demethylation, 102-104mi-RISC, 302MIC (micronucleus), 437Michurin, Ivan, 7micRNA (mRNA-interfering

complementary RNA), 204micronucleus (MIC), 437microRNAs. See miRNAsmilRNAs (miRNA-like small RNAs),

245-247minicircle molecules, 162miRISC (miRNA-RISC), 302miRNA recognition elements

(MREs), 187miRNA-like small RNAs (milRNAs),

245-247miRNA-mediated translational

inhibition, 332-335miRNA-responsive element

(MRE), 302miRNA-RISC (mi-RISC), 302miRNA/AGO ribonucleoprotein

(miRNP), 186miRNAs (microRNAs), 183

Alzheimer’s disease, 510biogenesis and function, 184-189

comparison of plants toanimals, 329-332

mirtrons, 189-190C. elegans, 268-270cancer and, 488

diagnostic and prognosticmarkers, 491

function, 490metastasis, 491-492oncogenes, 489tumor-suppressors, 489-490

DNA hypermethylation and cancer,478-479

Drosophila melanogaster, 281-282editing by gRNAs, 197-199effects of bioactive food

components, 539-540

index 589

Huntington’s disease, 514mammals/humans, 283-287, 291-292Multiple Sclerosis, 516Parkinson’s disease, 513plants, 301-304psychiatric pathologies, 517regulation, 188

miRNP (miRNA/AGOribonucleoprotein), 186

mirtrons, miRNA biogenesis, 189-190mismatch repair (MMR), 81MMR (mismatch repair), 81models

biological function of ncRNAs, 273-274

heterochromatin-independent/dependent generation andamplification siRNAs, 260

MSUD, 244paramutation, 361

physical interaction, 368-370RNA, 366-368

quelling, 240scan RNA, 225stuttering, 167translational inhibition, 284-287twins model, 534-535use and disuse model, 3

Modern Synthesis, 6modes of action, lncRNAs, 182modifications, histones, 119

Alzheimer’s disease, 509animals, 125-137brain, 500cancer, 484-492effects of bioactive food

components, 538-539gene expression states, 122-123Huntington’s disease, 513Parkinson’s disease, 512plants, 137-143transcription regulation, 120-122trypanosomes, 123-125

MOM1 protein, 69-70Morgan, Thomas Hunt, 8MRE (miRNA-responsive

element), 302MREs (miRNA recognition

elements), 187mRNA-interfering complementary

RNA (micRNA), 204MS (Multiple Sclerosis), 514-516

MSUD (meiotic silencing byunpaired DNA), 243-245

MTases, 75CcrM, 86-89Dam (DNA adenine

methyltransferase), 78-87Muller, Hermann Joseph, 10multiple cloning sites (MCSs), 564Multiple Sclerosis (MS), 514-516mutagenesis, 16mutations, 1MUTs (meiotic unannotated

transcripts), 257-258

NNance, Walter, 10Nanney, David, 10nat-siRNAs (natural antisense

transcripts short interferingRNAs), 232, 306-309, 417, 557

National Human Genome ResearchInstitute (NHGRI), 171

natural antisense transcripts shortinterfering RNAs (nat-siRNAs),232, 306-309, 417, 557

natural selection, 5-7ncRNAs (non-coding RNAs), 11,

147-149algae-chloroplasts containing

protists, 233-236animals. See animalsArchaea, 217-220bacteria. See bacteriabrain, 501-502cis- and trans-acting, 170criteria for classification, 150-152fungi. See fungifuture directions, 170-171gRNAs, 161-169history, 148-149homology-dependent inheritance in

ciliates, 439-440mammals/humans. See

mammals/humansplants. See plantsprotozoa. See protozoaRNase P, 169role in epigenetic processes, 177-199rRNAs, 155-161snoRNAs, 154-155snRNAs, 153

590 index

SRP ribonucleoprotein complex, 169summary of, 338-340tmRNA, 170tRNAs, 152-153yeasts

S. cerevisiae, 249-258S. pombe, 258-261

Neo-Darwinism, 6NER (nucleotide excision repair), 110neurodegenerative disorders,

influence of epigenetic changesAlzheimer’s disease, 508-510Huntington’s disease, 513-514Multiple Sclerosis, 514-516Parkinson’s disease, 511-513

neurodevelopmental disorders,influence of epigenetic changes,506-507

neurological processes, influence ofepigenetic changeschromatin remodeling, 500classical experiments of Meaney

and Szyf, 503-505DNA methylation and the brain, 499histone modifications, 500ncRNAs, 501-502neurodegenerative disorders,

508-516neurodevelopmental disorders,

506-507neuron development, 499neuronal plasticity, 499Neurospora crassa, 236Neurospora RNAi pathway model, 240NHGRI (National Human Genome

Research Institute), 171non-coding RNAs. See ncRNAsnon-CpG methylation, 109-110non-genotoxic carcinogens, 549non-Mendelian mechanism of

inheritance, 440non-paramutagenic alleles, 344non-processive DNA

methyltransferases, 96non-RM MTases


methyltransferase), 78DNA repair, 81maintenance and inheritance

of DMPs, 85-87regulation of bacterial

virulence, 84-85

repression of conjugation, 83role in DNA replication, 80transposition, 82

NONCODE classification (ncRNAs),150-152

nonlinear responses, co-suppression, 380

NoRC (nucleolar-remodelingcomplex), 32

NORs (nucleolus organizer regions), 155

NRP1 protein, 51NRP2 protein, 51nuclear architecture, epigenetics of,

20-23nuclear ARPs (actin-related

proteins), 23-25nucleoid, 80-81nucleolar-remodeling complex

(NoRC), 32nucleolus organizer regions

(NORs), 155nucleosomes, 19, 119-122nucleotide excision repair

(NER), 110NURD (nucleosome-remodeling and

histone deacetylase) complexes, 34NURF (nucleosome-remodeling

factor) complex, 31

Ooncogenes, 472-473, 489ontogenesis, 7ontogeny, 5open permissive chromatin, 484organ development (plants),

chromatin remodeling in, 52-55organization, nucleoid region, 80The Origin of Species (Darwin), 4OxyS RNA, 214Oxytricha

homology-dependent inheritance,438-439

RNA-mediated epigeneticinheritance, 228

Ppachytene piRNAs, 289palindromic CRISPR repeats, 389PAME (proto-spacer adjacent motif

end), 401

index 591

PAMs (proto-spacers adjustingmotifs), 401

pANDA vector, 564pangenesis, 5-6parachromatin, 363paramecium, silencing, 224paramutable alleles, 344paramutagenecity, 358paramutagenic alleles, 344paramutation, 9, 343

animalsRNAs involved in phenotypic

epigenetic inheritance, 374-379

whitetail phenotype, 372-374epigenetic regulation, 354-361fungi, 371historical view, 345-347models, 361

physical interaction, 368-370RNA, 366-368

plants, 347b1 locus in maize, 351-354importance and significance,

370-371R1 locus in maize, 348-351

tandem repeats, 362-365parasite-derived resistance (PDR), 411parental imprinting control regions,

94-95Parkinson’s disease (PD), 511-513passenger strand, 191passive demethylation, 110-113passive DNA demethylation, 99-101passive DNA replication-dependent

demethylation, 86pathogen resistance, plant

applications for hairpin-basedRNAi, 567-569

pathogen-derived resistance (PDR), 411

PcG (polycomb group) proteinsantagonistic functions of, 28-29cancer and, 487-488

PcG (Polycomb-group) proteincomplexes, 52-55, 128

PD (Parkinson’s disease), 511-513PDR (pathogen-derived

resistance), 411penetrance, 345peripheral lamins, 22permissive state, gene promoters, 122pFGC vector, 564

PGCs (polycistronic gene clusters), 124

PGCs (primordial germ cells), 94, 441phage transduction, 385phages (bacterial), 387pHANNIBAL cloning vector, 564phosphorylation, histones, 130-131photoperiod-independent early

flowering 1 (PIE1) protein, 64-66phylogenesis, 7phylogenetics, 5physical interaction model,

paramutation, 368-370PIE1 protein, 64-66Pikaard, Craig, 315piRNAs (PIWI-interacting RNAs),

97, 183, 267biogenesis and function, 192-195C. elegans, 271-273comparison to CRISPRs, 395Drosophila melanogaster, 279-281mammals/humans, 288-290

PIWI (P-element-induced wimpytestis)-interacting RNAs. SeepiRNAs

PIWI-interacting RNAs. See piRNAspKANNIBAL cloning vector, 564pKNOCKOUT vector, 564plants

A-to-I editing, 165-166applications of hairpin RNAi, 563

functional genomics, 564manipulation of biosynthetic

pathways, 566-567pathogen resistance, 567-569removal of undesirable

traits, 565biogenesis, 298chromatin remodeling in, 49

flowering, 55-64organ development, 52-55RAM (root apical meristem), 51SAM (shoot apical meristem),

50-52seed development, 49-50Snf2-like genes, 64-70

epigenetic reprogrammingDNA methylation in

gametes, 456gene imprinting, 458-459histone modifications, 457-458passing to progeny, 459-460

grafting, 7

592 index

histone modificationsacetylation/deacetylation,

137-138correlation to DNA

methylation, 142-143deposition during cell cycle,

141-142methylation, 138variants, 140-141

methylation, 101active and passive

demethylation, 110-113de novo DNA methylation,

104-108maintenance, 108-110methyltransferases involved,

102-104ncRNAs, 297-300

comparison to animals, 327-340functions, 319-323long ncRNAs, 310miRNAs, 301-304RdDM and gene silencing,

312-317redundant mechanisms for

ncRNA production, 310-311siRNAs, 304-310

paramutation, 347b1 locus in maize, 351-354importance and significance,

370-371R1 locus in maize, 348-351

protection against viruses, 413-415transgenesis, 347

pluripotency, esBAF complex and,29-31

pollen siRNAs, 309-310pollution, influence on phenotypes,

529-534PollV, as component of RdDM

pathway, 315-317PolV, as component of RdDM

pathway, 315-317polycistronic gene clusters

(PGCs), 124polycomb group (PcG) proteins

antagonistic functions of, 28-29cancer and, 487-488

polycomb repressive complex 1(PRC1), 28, 128

polycomb repressive complex 2(PRC2), 28, 128

Polycomb-group (PcG) proteincomplex, 52-55, 128

position-effect variegation, 10post-transcriptional gene silencing

(PTGS), 177, 297, 410as antiviral mechanism, 413-415fungi, 236

post-traumatic stress disorder(PTSD), 527

PRC complexes, repressive statesand, 53-55

PRC1 (Polycomb RepressiveComplex 1), 28, 128

PRC2 (Polycomb RepressiveComplex 2), 28, 128

PRC2-MEA complex, 54pre-miRNAs (precursor-miRNAs),

184, 281, 297pre-pachytene piRNAs, 289pre-tRNAs (precursor tRNAs), 153precursor tRNAs (pre-tRNAs), 153precursor-miRNAs (pre-miRNAs),

184, 281, 297prenatal environment, influence on

phenotypes, 525-527PREs (PcG response elements), 28primal small RNAs (priRNAs), 260primary miRNAs, 557primary paramutation, 352primary siRNAs, 270-271primary transcript (pri-miRNA), 184primordial germ cells (PGCs), 94, 441priRNAs (primal small RNAs), 260pRNAs (RNA products), 208Processing (P) bodies, 188prognostic markers, miRNAs and

cancer, 491promotional stage of

carcinogenesis, 465protamine-mediated inheritance,

447-448protection

bacteriaCRISPRs, 385-405stress responses, 386-387

plants, 413-415protein-binding ncRNAs, bacteria,

207-209proteins

CRISPR-related, 389-390in chromatin remodeling

chromatin-remodelingcomplexes, 25-36

effector proteins, 36-41insulator proteins, 41-44

ncRNA biogenesis, 338-340

index 593

PcG (polycomb group), cancer and,487-488

plant biogenesis, 298RAMPs (Repeat-Associated

Mysterious Proteins), 389TrxG (trithorax group), cancer and,

487-488protists, editing flagellated protists

with gRNAs, 161-163proto-spacer adjacent motif end

(PAME), 401proto-spacers adjusting motifs

(PAMs), 401protozoa, ncRNAs

ciliates, 223-229flagellates, 229-230pseudopodia-containing protists,

230-233pseudopodia-containing protists,

ncRNAs, 230-233psychiatric disorders, influence of

epigenetic changes, 516-517psychological environment,

influence on phenotypes, 527-529PTGS (post-transcriptional gene

silencing), 177, 297, 410as antiviral mechanism, 413-415fungi, 236

PTSD (post-traumatic stressdisorder), 527

Q–RqiRNAs, 242-243quelling, 236, 240, 410-411

R1 locus, paramutation in plants,348-351

ra-siRNAs (repeat-associatedsiRNAs), 308

radiation-induced epigenetic changesdirect IR exposure, 542-543indirect IR exposure, 543-548

RAM (root apical meristem),chromatin remodeling in, 51

RAMPs (Repeat-AssociatedMysterious Proteins) family, 389

RdDM (RNA-directed DNAmethylation), 102, 159, 423

RdDM pathway, gene silencing, 312-317

RDRC (RNA-dependent RNApolymerase complex), 258

RdRP (RNA-dependent RNApolymerase), 191, 270, 298, 337, 557

recessive mutation, 354redundant mechanisms, ncRNA

production in plants, 310-311regulation

apoptosis, 153bacterial virulence, 84cell cycle, 88-89gene expression

CcrM, 88co-suppression, 380-381Dam, 78paramutation, 343-379S. cerevisiae, 254-257transvection, 379-380

paramutation, 354-361transcription, 120-122

regulatory RNAsalgae-chloroplasts containing

protists, 233-236animals, 267-283

comparison to plants, 327-340Archaea, 217-220bacteria, 203-217fungi, 236-249mammals/humans, 283-292plants, 297-323

comparison to animals, 327-340protozoa, 223-233yeasts, 249-261

relative frequency, RM systems incell population, 76

repair of DNA, 81Repeat-Associated Mysterious

Proteins (RAMPs) family, 389repeat-associated siRNAs

(ra-siRNAs), 308repeat-counting mechanisms,

paramutation, 362-365repeat-induced point mutation

(RIP), 12replication, 80Replication Protein A, 238repression

of conjugation, 83-84of FLC expression, 59-61

repressive states, PRC complexesand, 53-55

response to stressbacteria, 386-387ncRNAs in plants, 320-323

594 index

restriction-modification (RM)system, 76, 387

restrictive state, gene promoters, 122Rett syndrome (RTT), 506reverse genetics, 564Ribonuclease P (RNase P), 169ribosomal RNAs (rRNAs), 149,

155-161riboswitches, 204-206, 223RIP (repeat-induced point

mutation), 12RISC (RNA-Induced Silencing

Complex), 183, 302, 410, 558RITS (RNA-Induced Transcriptional

Silencing Complex), 183, 308RM (restriction-modification)

system, 76, 387RNA

editing, 168-169history of, 148-149paramutation model, 366-368phenotypic epigenetic inheritance,

374-379silencing, viral suppressors, 426-430thermometers, 205

RNA Dependent RNA Polymerases(RDRs), 298

RNA interference. See RNAiRNA polymerases (RNAPs),

69-70, 167RNA products (pRNAs), 208RNA-based model, paramutation, 361RNA-dependent RNA polymerase

complex (RDRC), 258RNA-dependent RNA polymerases

(RdRPs), 191, 337RNA-directed DNA methylation

(RdDM), 102, 159, 423RNA-Induced Silencing Complex

(RISC), 183, 410RNA-Induced Transcriptional

Silencing Complex (RITS), 183, 308RNA-mediated epigenetic

inheritance, 228RNAi (RNA interference pathway),

12, 178, 268, 409comparison to CRISPR, 391hairpin RNAi construct, 555-558

animal applications, 569-570chimeric hairpins, 559components, 560-561inducible hairpin RNAi, 562-563limitations, 573

mammal applications, 570-573plant applications, 563-569targeting conserved sequences,


history of silencing, 410-413protection of plants against

viruses, 413purpose of, 413siRNAs in C. elegans, 270-271

RNAPs (RNA polymerases), 167RNase III-type endonucleases, 195RNase P (Ribonuclease P), 169roles, biogenesis and function of

ncRNAs, 177comparison of plants to animals,

327-340gRNAs, 197-199lncRNAs, 178-182miRNAs, 184-190piRNAs, 192-195RNase III-type endonucleases, 195siRNAs, 190-192small ncRNAs, 183

Romanes, George, 6root apical meristem (RAM),

chromatin remodeling in, 51RPA1, 238rRNAs (ribosomal RNAs), 149,

155-161RTT (Rett syndrome), 506Rubinstein-Taybi syndrome, 507

SS-adenosylmethionine (SAM or

Adomet), 90S. cerevisiae (Saccharomyces

cerevisiae), ncRNAs, 249cryptic site origination, 253CUTs, 250-251MUTs, 257-258regulation of gene expression,

254-257short sense ncRNAs upstream of

mRNA sites, 251, 253S. pombe (Schizosaccharomyces

pombe), ncRNAs, 249, 258-261Saccharomyces cerevisiae. See

S. cerevisiaeSAGOs (secondary Argonautes), 270SAM (S-adenosylmethionine), 90

index 595

SAM (shoot apical meristem),chromatin remodeling in, 50-52

SAR (systemic acquired resistance),423-424 transitive silencing, 423-424

scan RNA model, 225scan RNAs (scnRNAs), 225scaRNAs (Cajal body-specific

RNAs), 154schizophrenia, 517Schizosaccharomyces pombe

(S. pombe), 249, 258-261scnRNA-mediated elimination of

genomic sequences, 227scnRNAs (scan RNAs), 225sdRNAs, 152second-hand smoke exposure, 524secondary Argonautes (SAGOs), 270secondary nat-siRNAs, 307secondary paramutation, 352secondary siRNAs, 270-271seed development, chromatin

remodeling in, 49-50seed regions, 187self-renewal process of cells, 571sense ncRNAs, 180shoot apical meristem (SAM),

chromatin remodeling in, 50-52short hpRNAs (shRNAs), 556, 569-573short interfering RNAs. See siRNAsshort interspersed element

(SINE), 199shRNAs (short hpRNAs), 556, 569-573sigma (s) factor, 208signal recognition particle (SRP), 169silencing (gene). See gene silencingSINE (short interspersed

element), 199siRNAs (small interfering RNAs),

183, 297, 413, 556biogenesis and function, 190-192,

335-338C. elegans, 270-271Drosophila melanogaster

endo-siRNAs, 276-279exo-siRNAs, 274-276

editing by gRNAs, 197-199mammals/humans, 287-288plants

nat-siRNAs, 306-309pollen siRNAs, 309-310trans-acting siRNAs, 304-306

qiRNAs, 242

SKB1 protein, 62Skipper retrotransposon, 232slicing, 420small interfering RNAs. See siRNAssmall ncRNAs

biogenesis and function, 178-183miRNAs, 183-190piRNAs, 183, 192-195siRNAs, 183, 190-192

small nuclear ribonucleic acid(snRNAs), 153

small nuclear ribonucleoproteins(snRNPs), 154

small nucleolar RNAs (snoRNAs),154-155

small RNAs (sRNAs), 62-63, 203smoke (tobacco), 549Snf2-like genes, 64-70SNF2H proteins, 33SNF2L proteins, 32SNI1 protein, 67-68snoRNAs (small nucleolar RNAs),

154-155snRNAs (small nuclear ribonucleic

acids), 153snRNPs (small nuclear

ribonucleoproteins), 154SOC1 (suppressor of overexpression

of CO) floral integrator, 56socioeconomic status, influence on

phenotypes, 524soft inheritance, 3somatic cells, 4somatic genome, 224somatoplasm, 4SOS DNA damage response, 386soy, 541Spencer, Herbert, 4sperm cells, 105spliRNAs, 152sRNA-mediated inheritance, 453-454sRNAs (small RNAs), 62-63, 203SRP (signal recognition particle), 169SRP ribonucleoprotein complex, 169stages, cancer development, 466stalked cells, 88Stegemann, Sandra, 7stress

influence on phenotypes, 527-529memory, 16response

bacteria, 386-387ncRNAs in plants, 320-323

596 index

structure, RNase III-typeendonucleases, 195

stuttering model, 167summer annuals, 55summer-annual state, 61-63suppression. See gene silencingsuppressor of overexpression of CO

(SOC1) floral integrator, 56survival of the fittest, 4Sutton, Walter, 8swarmer cells, 88SWI/SNF (SWITCH/SUCROSE

NONFERMENTING) ATPases,26-27, 30-31, 52

SWI/SNF chromatin-remodelingATPase, 52

symmetric cytosine methylation, 92systemic acquired resistance (SAR),

423-424Szyf, Moshe, 503-505

TT-boxes, 205ta-siRNAs (trans-acting siRNAs),

304-306tandem repeats, paramutation,

362-365targeting Alu elements, 199tasiRNAs, 276technology, influence on epigenetics,

555-573telomeres, silencing at, 14terminator structures, 205TEs (transposable elements), 97Tetrahymena termophila, 225TGS (transcriptional gene silencing),

159, 343, 410, 421-423theory of evolution, 3therapeutic interventions, cancer,

492-493TIF1b protein, 37tiRNAs, 152tissue-specific hairpin RNAi, 562tmRNA, 170tobacco smoke, 549toxin-antitoxin systems, 211trans-acting ncRNAs, 170, 256trans-acting siRNAs (ta-siRNAs),

304-306trans-encoded ncRNAs, 212-215trans-nat-siRNAs, 306

trans-NATs, 276trans-silencing, 358-359transcription

factories, 21-23regulation, 120-122

transcriptional antitermination, 205transcriptional gene silencing (TGS),

159, 343, 410, 421-423transcriptional repression, 181transcriptional-repression domain

(TRD), 39transcriptionally silent information

(TSI), 159transduction, 386transfer RNAs (tRNAs), 149-153transformation, 385-386transgenerational inheritance

(epigenetic states), 435, 546-548reprogramming in animals, 440-456reprogramming in ciliates, 436-440reprogramming in plants, 456-460

transgenes, 347transgenesis, plants, 347transitive silencing, 423-426transitivity, 419translation activation, ncRNAs,

282-283translational inhibition

mi-RNA-mediated, 332-335models, 284-287

transposable elements (TEs), 97transposition, 82-83transvection, 368, 379-380TRD (transcriptional-repression

domain), 39TREs (trxG response elements), 28tRFs (tRNA fragments), 153trithorax group (TrxG) proteins,

cancer and, 487-488tRNA fragments (tRFs), 153tRNAs (transfer RNAs), 149, 152-153trophoectoderm, 94TrxG (trithorax group) proteins

antagonistic functions of, 28-29cancer and, 487-488plant organ development, 52-55

Trypanosoma brucei, 229trypanosomes, 11, 123-125TSI (transcriptionally silent

information), 159Tsix RNAs, 181, 290tumor-suppressors, miRNAs, 489-490

index 597

twins model, 534-535“two-hit” cancer hypothesis

(Knudson), 466type I antitoxin proteins, 211type I RM systems, 76type II antitoxin proteins, 211type II RM systems, 76type III antitoxin proteins, 211type III RM systems, 76

U–VUAS (upstream activating

sequence), 84ubiquitination, histones, 131-132UHRF1 protein, 41uridines, insertion/deletion editing,

162-163use and disuse model, 3

variants, histonesanimals, 133-134plants, 140-141

The Variation of Animals and Plantsunder Domestication (Darwin), 5

vegetative cell, 105Venter, Dr. Craig, 523vernalization, 56-57

FLC repression, 59-61steps in, 61

vernalization 1 (VRN1) protein, 57vernalization insensitive 3 (VIN3)

protein, 57vertical inheritance, CRISPR

elements, 404VIGS (virus-induced gene silencing),

409, 416-421, 567VIN3 (vernalization insensitive 3)

protein, 57viral suppressors of RNA silencing

(VSRs), 427viRNA RISC complexes

(vi-RISC), 419viRNAs (virus-derived small RNAs),

409, 417viroids, 568virulence, bacteria, 84virus-derived small RNAs (viRNAs),

409, 417virus-induced gene silencing (VIGS),

409, 416-421, 567

virusesprotection against, 413-415silencing suppressors, 426-430

VRN1 (vernalization 1) protein, 57VRN2-PRC2 complex, 60VSRs (viral suppressors of RNA

silencing), 427

W–ZWaddington, Conrad Hal, 8Wallace, Alfred Russel, 6Watson and Crick, proposed model

of DNA structure, 148Weintraub, Hal, 11Weismann, August, 3, 6white tail phenotype, paramutation

example, 372-374WICH complex (WSTF (Williams-

Beuren syndrome transcriptionfactor)-ISWI chromatinremodeling), 32

Williams-Beuren syndrome, 33Wilson, Edmund, 8winter annuals, 55winter-annual state, 57-61

Xi (X chromosome inactivation), 10-11, 22

Xist RNAs, 181, 290

yeasts, ncRNAsS. cerevisiae, 249-258S. pombe, 258-261

598 index

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