2002 beyond the central dogma

BIOINFORMATICS Vol. 18 no. 2 2002Pages 223225

EditorialBEYOND THE CENTRAL DOGMA

The central dogma, DNA makes RNA makes protein, haslong been a staple of biology textbooks. More recently,this paradigm has been extended from individual genes towhole genomes by advances in genomic technologies. Forexample, probing of DNA microarrays accomplishes on alarge scale what was previously achieved for single genesusing filter hybridization. High-throughput technology,not breakthrough biology, is becoming synonymous withgenomics.

The longevity of the central dogma has also meantthat basic computational tools for analyzing sequencedata reached maturity before whole genomic sequencesbecame available. For example, gene finding systems wereintroduced over a decade ago (Fields and Soderlund,1990), and the importance of the problem attractedmany computational biologists. As a result of numerousincremental advances made already, diminishing returnsmay be expected for this problem. A similar situationappears to hold for database searching (Schaffer et al.,2001). Thus, the computational tools that are most widelyused now may be difficult to improve upon in the post-genomic era.

Technologies based on textbook biology will continueto generate opportunities in bioinformatics. However,more exciting prospects may come from new discoveriesthat extend or even violate the central dogma. Considerdevelopmental biology. The central dogma says nothingabout the differences between the cells in a human body,as each one has the same DNA. However, recent findingshave begun to shed light on how these differences ariseand are maintained, and the biochemical rules that governthese differences are only being worked out now. Theemerging understanding of developmental inheritance fol-lows a series of fundamental discoveries that have led to arealization that there is more to life than the central dogma.

The central dogma was first challenged by the discoveryof reverse transcription (Baltimore et al., 1970; Teminand Mizutani, 1970). Thought at the time to be peculiarto retroviruses, we now know from large-scale sequenc-ing that our genome contains an order of magnitudemore copies of sequences encoding reverse transcriptasethan sequences encoding all other proteins combined(Lander et al., 2001)! Half of our genome is devoted toretroelements and their remnants, compared to only a fewpercent devoted to gene coding regions. Humans are notalone in having genomes dominated by retroelements.The genomes of many plants are even more infested: forexample, retrotransposons occupy about 80% of the maizegenome (SanMiguel et al., 1996).

With so much genomic territory taken over by selfish el-ements, they are prime candidates for involvement in im-portant genetic processes. One example is the propagationof silencing along the inactivated X chromosome of mam-malian females: abundant LINE-1 retrotransposons wereproposed to act as way-stations (Lyon, 1998). Evidencein support of this idea was obtained by analyzing genomicsequence data (Bailey et al., 2000), an illustration of howthinking about genetic mechanisms creates opportunitiesin bioinformatics. Selfish elements also reveal evolution-ary processes that continue to shape genomes: arguablythe major scientific story of the draft human genome se-quence was the history of retrotransposon evolution (Lan-der et al., 2001), a story missed by others who may havebeen so focused on the genes that they overlooked the junk(Venter et al., 2001).

The success of selfish DNA elements does not meanthat our genomes are entirely at their mercy. A widespreadview is that genomes are protected by an immunity system(Yoder et al., 1997). Among the weapons that are thoughtto help protect genomes, especially in plants, are DNAmethyltransferases, enzymes that mark sequences for si-lencing by covalent modification. Silencing of retrotrans-poson transcription, which must precede reverse transcrip-tion and integration, should be an effective defense againsttheir mobilization. A major unsolved problem has been thebasis for recognition of transposons and their ilk by theDNA methylation machinery. Without obvious sequencecues, it has been difficult to understand how a genome de-fense system protects against invaders. This question goesbeyond DNA methylation: organisms such as the fruit fly,which has an almost unmethylated genome, may effec-tively prevent transposition by packaging retroelements insilent chromatin (van Steensel et al., 2001).

Recently, a surprising solution to the problem ofretroelement recognition has been proposed: RNA in-terference (RNAi). First elucidated in the nematode,where genes could be shut down by introduction ofdouble-stranded RNA, this powerful gene silencingtechnique is now known to utilize enzymatic machinerythat is common to animals and plants (Carthew, 2001).Small interfering RNAs (siRNAs) of only 22-25 bp cantraverse intracellular spaces to enter cells and trigger rapiddegradation of homologous RNAs. The same mechanismunderlies post-transcriptional gene silencing (PTGS) inplants, where unintended post-transcriptional silencingof transgenes has been the bane of genetic engineersfor over a decade. Thus, PTGS appears to be a naturalmechanism for defending against RNA-based invaders.In addition, PTGS may be involved in the recognitionand targeting of genomic DNA sequences: siRNA madein the cytoplasm would be targeted to the nucleus whereit guides a DNA methyltransferase to covalently modify

c Oxford University Press 2002 223

Bertin PaizHighlight

Bertin PaizUnderline

S.Henikoff

its homologous DNA (Matzke et al., 2001). Whereas thecentral dogma begins with DNA, in this hypothesizedRNAi-based process, DNA participates only at the end.

Perhaps the simplest exceptions to the central dogmaare prions, proteins that undergo heritable conforma-tional changes and seed polymeric forms of themselves(Lindquist, 1997). Prions were discovered in the searchfor the infectious agents of scrapie and mad cow disease,and their existence was confirmed by demonstratingprotein inheritance in yeast. Although no nucleic acidcomponent has been reported for scrapie, these searcheswere carried out before the discovery of RNAi, raising thepossibility that siRNA guides that have eluded detectionare causally involved in prion diseases.

RNAi is only the most recent RNA-based phenomenonto grab the attention of biologists. It is widely believedthat an ancestral ribozyme-based RNA world has beenmostly supplanted by protein enzymes (Woese, 2001).In addition to protein synthesis, several RNA-basedprocesses are known: a large structural RNA, Xist, coatsthe inactive X chromosome (Mlynarczyk and Panning,2000), and numerous small RNAs are involved in diverseprocessing reactions (Eddy, 2001). RNA-based regulatorymechanisms have recently been documented, includingtranscription from the opposite strand which represses theXist locus (Mlynarczyk and Panning, 2000), and siRNAswhich repress production of a sperm-specific protein inflies (Aravin et al., 2001). Clearly, the dogmatic view ofRNA as playing merely intermediary roles in the synthesisof protein is becoming increasingly outmoded. Yet theanalysis of genomic sequences to identify non-codingRNAs is still in its infancy (Eddy, 2001).

Genetic mechanisms that challenge the central dogmacontribute to the complexity of eukaryotic organisms.However, when we get down to the nitty-gritty of abiological mechanism, what can emerge is elegant in itssimplicity. Indeed, it now appears that all of the examplesof gene silencing that I have mentioned rely on a simpleon/off code. Recall that DNA comprises less than halfof the chromosome, because it wraps tightly around acore octamer of four histones to form a nucleosome.Each histone has an N-terminal tail that exits from thenucleosome core, and the tail of histone H3 is cova-lently and permanently modified by methylation of twolysine residues, K4 and K9 (Jenuwein and Allis, 2001).Methylation of K4 but not K9 is found on nucleosomesthat are transcriptionally active and methylation of K9but not K4 is found on nucleosomes that are present insilent chromatin. Over the past few months, evidence hasemerged that this simple difference distinguishes activeversus silent chromatin, whether it is constitutively silentchromatin found around centromeres (Jenuwein and Allis,2001) or chromatin found on the inactive but not theactive mammalian X chromosome (Heard et al., 2001).

By heritably affecting DNA accessibility, nucleosomesappear to be ultimately responsible for maintaining differ-ences in gene expression that occur during development.Nucleosomes are ubiquitous components of eukaryoticchromosomes, and so there is reason to expect that thehistone code is a generally applicable. Centromeres,the points on chromosomes that are responsible formitotic movements, are exceptional, being inhabited bynucleosomes containing an H3-like histone that replacesH3 (Henikoff et al., 2001). Centromeric sequences arenotoriously repetitive and diverse, and yet all centromeresand only centromeres contain these specialized nucle-osomes. Centromeres appear to be inherited by thecontinued presence of centromeric nucleosomes, withDNA sequence playing at most a secondary role. Thus,mitosis, a defining feature of eukaryotes, may rely upon aprotein-based inheritance mechanism.

I have little doubt that these exciting developmentswill continue to open up new areas for computationalbiologists willing to look beyond the central dogma.

REFERENCESAravin,A.A., Naumova,N.M., Tulin,A.V., Vagin,V.V., Ro-

zovsky,Y.M. and Gvozdev,V.A. (2001) Double-strandedRNA-mediated silencing of genomic tandem repeats and trans-posable elements in the D. melanogaster genome. Curr. Biol.,11, 10171027.

Bailey,J.A., Carrel,L., Chakravarti,A. and Eichler,E.E. (2000)Molecular evidence for a relationship between LINE-1 elementsand X chromosome inactivation: the Lyon repeat hypothesis.Proc. Natl. Acad. Sci. USA, 97, 66346639.

Baltimore,D. (1970) RNA-dependent DNA polymerase in virions ofRNA tumour viruses. Nature, 226, 12091211.

Carthew,R.W. (2001) Gene silencing by double-stranded RNA.Curr. Op. Cell Biol., 13, 244248.

Eddy,S.R. (2001) Non-coding RNA genes and the modern RNAworld. Nat. Rev. Genet., 2, 919929.

Fields,C.A. and Soderlund,C.A. (1990) gm: A practical tool forautomating DNA sequence analysis. Comput. Appl. Biosci., 6,263270.

Heard,E., Rougeulle,C., Amaud,D., Avner,P., Allis,C.D. and Spec-tor,D.L. (2001) Methylation of histone H3 at Lys-9 is an earlymark on the X chromosome during X inactivation. Cell, 107,727738.

Henikoff,S., Ahmad,K. and Malik,H.S. (2001) The centromereparadox: Stable inheritance with rapidly evolving DNA. Science,293, 10981102.

Jenuwein,T. and Allis,C.D. (2001) Translating the histone code.Science, 293, 10741080.

Lander,E.S., Linton,L.M., Birren,B. and Nusbaum,C. et al. (2001)Initial sequencing and analysis of the human genome. Nature,409, 860921.

Lindquist,S. (1997) Mad cows meet psi-chotic yeast: the expansionof the prion hypothesis. Cell, 89, 495498.

Lyon,M.F. (1998) X-chromosome inactivation: a repeat hypothesis.Cytogenet Cell Genet., 80, 133137.

224










Beyond the central dogma

Matzke,M., Matzke,A.J.M, and Kooter,J.M. (2001) RNA: Guidinggene silencing. Science, 293, 10801083.

Mlynarczyk,S.K. and Panning,B. (2000) X inactivation: Tsix andXist as yin and yang. Curr. Biol., 10, R899R903.

SanMiguel,P., Tikhonov,A., Jin,Y.K., Motshoulskaia,N., Za-kharov,D., Melake-Berhan,A., Springer,P.S., Edwards,K.J.,Lee,M., Avramova,Z. and Bennetzen,J.L. (1996) Nested retro-transposons in the intergenic regions of the maize genome.Science, 274, 765768.

Schaffer,A.A., Aravind,L., Madden,T.L., Shavirin,S., Spouge,J.L.,Wolf,Y.I., Koonin,E.V. and Altschul,S.F. (2001) Improvingthe accuracy of PSI-BLAST protein database searches withcomposition-based statistics and other refinements. NucleicAcids Res., 29, 29943005.

Temin,H.M. and Mizutani,S. (2001) RNA-dependent DNA poly-merase in virions of Rous sarcoma virus. Nature, 226, 12111213.

van Steensel,B., Delrow,J. and Henikoff,S. (2001) Chromatin profil-ing using targeted DNA adenine methyltransferase. Nature Gen.,27, 304308.

Venter,J.C., Adams,M.D., Myers,E.W. and Li,P.W. et al. (2001) Thesequence of the human genome. Science, 291, 13041351.

Woese,C.R. (2001) Translation: in retrospect and prospect. RNA, 7,10551067.

Yoder,J.A., Walsh,C.P. and Bestor,T.H. (1997) Cytosine methyla-tion and the ecology of intragenomic parasites. Trends Genet.,13, 335340.

Steven HenikoffHoward Hughes Medical Institute

Fred Hutchinson Cancer Research CenterSeattle WA 98109-1024, USA

E-mail: [email protected]

225

2002 beyond the central dogma

Documents