chromosomes and chromatine structural arrangement of genetic information
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Chromosomes and chromatine
structural arrangement of genetic information
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Chromatin (Walther Flemming 1882)
= DNA + associated proteins
euchromatin x heterochromatin
heterochromatin facultative x constitutive
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Chromatin(DNA + associated proteins)
Genetic information = DNA sequence (change = mutation)
- protein-coding, regulatory, RNA-coding-
Epigenetic information (less stable, depends on location)
- transcriptional activity, access of interacting proteins
transcriptionally active x transcriptionally inactive decondensed, accessible x compact, unaccessible
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• DNA methylation• histone posttranslational modifications mutually interconnected! • histone types
Epigenetic modifications of chromatin- epigenetic information can be mitotically and meiotically herritable (e.g. some changes in gene activity)- no change in primary DNA sequence - modifications of chromatin components:
euchromatin heterochromatin
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Varying composition:- histone variants (isoforms): CenH3, H3.3, H2A.Z- posttranslational modifications of histone proteins
Nucleosomeoctamer of histones (small alcaline proteins): 2 x H2A, 2 x H2B, (2 x H3, 2 x H4) + 147 bp DNA
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Structure of 30nm fibreSolenoid or ZigZag?
- still unclear
solenoid
Li and Reinberg 2011
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• LBARs (loop basement attachment regions) - organize chromosomes to huge loops (distances 20kb až 100kb)
• MARs (matrix attachment regions) alt. SARs (scaffold attachment reg.)
– harboring regions surrounding coding sequences to nuclear protein matrix
– AT rich, colocalize with „insulators“(sequences that prevent spreading of heterochromatin)
– distances between 3 - 100kb
Higher structural order of chromatine- hypothetically loops with actively transcribed genes- insufficiently understood
example of hypothetical arrangement
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Interconnections betweeen nucleosomes
- linker sequence between: length = multiple of 10 bp (20 to
90 bp)
- average (most frequent) length - differences among species, tissues, …
(20 bp yeast, 30 bp Arabidopsis, 40 bp mammels)
- internucleosomal fragmentation yields: 167 – 237 bp ( frequent length of repeats)
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Interconnections betweeen nucleosomes
Direct interactions - N-ends of H4 interact with H2A.H2B bodies in parallel fiber- presence of H2A.Z variant probably prevents parallel
interaction
Linker histone H1 - alcaline both ends (amino and carboxy) interaction with both histones and DNA- stabilization of higher structures (30nm), phosphorylated during cell cycle- length of linker sequence:
longer - require H1, more compact – heterochromatin
shorter – H1 less important, more decondensed, active chromatin
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Nucleosome position
• arrangement on DNA is not random (but is changable)
- DNA sequence- DNA methylation- histone modification/types- DNA transcription
• regulation / modulation of transcription- „unstable nucleosom region“ (earlier „nucleosom-free region“) in front of transcription start site (mainly constitutively expressed genes) –
- unstable nucleosomes with H3.3 and H2A.Z histones
- surrounded with stably situated nucleosomes with H2A.Z- nukleosomes help to define exons (central location even without transcription!)
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Histone code
- covalent posttranslatinal modifications (PTM)- modifications mainly on N-ends (out of core)- high complexity- „epigenetic instruction“ to manage with DNA
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Some histone PTMs are mutually interconnected and have multiple functions
e.g. H2A phosphorylation – injured DNA labelling,but also role in regulation of transcription and spiralizationand in PCD
Rossetto et al. 2012
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Histone code
Phosphorylation – predominantly short-time transient label, various functions
Acethylation – predominantly „executive modification“ for weakening interaction with DNA
- K-Ac – specific interaction of bromodomain proteins
Methylation – signal role ( stabile), both repressive and activating (~
depends on position)
- K-Me – specific interaction with chromodomain and TUDOR-
like domain proteins
- key role in regulation of DNA methylation
and chromatine activity
- H3K9me2, H3K4me3, H3K27me3
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Reproduction of nucleosomes after replication- histone tetramers (H3/H4) and dimers (H2A.H2B) not divided between sister strands! - one strand – „parental histons“ (Asf1) de novo deposition (CAF1, Asf1) - H2A.H2B incorporated even later (post replication)
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Chromosomes
NOR: 18S- 5,8S- 26S rDNA
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Caryotype – number, types and sizes of chromosomes
Flow caryotype(FISH labelling)
Doležel et al. 1999
Classical caryotype (metaphase)
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Chromosome number and sizes Number: 2 - 600
Size: 2,4 Mb Genlisea
30 Mb Arabidopsis
800 Mb Triticum
What are the consequences?
- different linkage groups (various gene recombination)
- limited hybrid fertility, …
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Chromosome number differs between species
• Extreme chromosome numbers – Haplopappus gracilis: 2n = 4– Sedum suaveolens: 2n = cca 640
• Luzula sp.: – 2n = 6 až 66– holocentric chromosomes– Chromosom size differes up to 60x
(Cullis, Plant genomics and proteomics, 2004)
L. pilosa
L. elegans
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B chromosomes in plants
- non-pair chromosomes in some species (1500 species – maize)
- usually no protein-coding genes
- usually negatively affect fitness (fertility)
- not present in all individuals in population
- parazitic DNA (?)
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Chromosome number and genome size
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TelomeresDNA-protein structures serving to maintain stability of chromosomal ends
Repetitive sequences synthetized by telomerase after replication(TTTAGGG)n in Arabidopsis
Some plants have typical mammalian sequence: (TTAGGG)n
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Telomerase - RT with an RNA template
repeat number depends on:- species- developmental stage- cell type - chromosome (within a cell)
Keeping telomere length
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- attachement of chromatids- defined by presence of histone CenH3 - CenH3 – kinetochore – spindel fibers
Types:- point (125 bp, yeast Saccharomyces) - holocentric chromosomes (CenH3 along whole chr.)
e.g. Luzula – allows fragmentation- classical – region of different length formed
with heterochromatin (repeats, TE)= epigenetically defined
(neocentromeres)- various strenth in hybrids
Centromeres
Chromosomes: ((telocentric, acrocentric, metacentric,submetacentric))
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Crossing of WT Arabidopsis with a line carrying modified (weaker) CenH3 issues in haploid progeny
– inefficient segregation of chromosomes (elimination)
Ravi and Chan 2010
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Rabl’s arrangement of chromosomes in interphase nuclei
centromeres and telomeres localized in oposite sites(chrom. size above 500 Mb)
WHY?
Chromosomal territoriesRegions in nucleus occupied with certain chromosome(postmitotic decondensation 2 hours, 2.5 fold increse)
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Cremer and Cremer 2010
Experimental confirmation of chromosomal territories
- laser injury, detection of reparation
- specific labelling of chromosomes (FISH)
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Sex chromosomes in plants
Sexuality in various taxons of plants evolved independently and repeatedly (5 % species, in about 75 % plant families)
- Marchantia, Gingo, Silene, Rumex, Hop, Poplar …
- sex determination (single locus or more loci)
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Sex chromosomes in plantsMorphological classification of sex chromosomes- homomorphic
- heteromorphic
- polymorphic – more than two types:
e.g. Rumex acetosa: male XY1Y2, female XX
Humulus lupulus var. cordiflorus: male X1X2Y1Y2, female X1X1X2X2
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Evolution of sex chromosomesFormation of sex chromosome and single sex individuals
– primary mutations causing male and female sterility in loci in strong genetic linkage (intermediarily usually gynodioecy)
model: female (XX) – an allele (in locus A) necessary for development of male sex organs is non-functional in X-chromosome ancestor
(recessive allele)
male XY – an allele (in locus B, linked with locus A) is mutated to suppress formation of female sex organs (dominant allele), this allele is linked with functional allele in locus A
Evolutionary young – homomorphic (recombination only partially limited)
Degenerations (inversions, TE amplification, deletions) - heteromorphic
Splitting or translocations can issue in polymorhic
Polyploidy complicates formation of sex chromosomes