Epigenetic chromatin modifications in Brassica genomes

Genome ◽  
2010 ◽  
Vol 53 (3) ◽  
pp. 203-210 ◽  
Author(s):  
Agnieszka Braszewska-Zalewska ◽  
Tytus Bernas ◽  
Jolanta Maluszynska
Keyword(s):  
Dna Methylation ◽  
Ploidy Level ◽  
Genome Structure ◽  
Histone H3 ◽  
Diploid Species ◽  
Brassica Species ◽  
Epigenetic Modifications ◽  
Chromatin Modifications ◽  
Histone H3 Methylation ◽  
Allotetraploid Species

Epigenetic modifications such as histone and DNA methylation are highly conserved among eukaryotes, although the nuclear patterns of these modifications vary between different species. Brassica species represent a very attractive model for analysis of epigenetic changes because of their differences in genome size, ploidy level, and the organization of heterochromatin blocks. Brassica rapa and B. oleracea are diploid species, and B. napus is an allotetraploid species that arose from the hybridization of these two diploids. We found that patterns of DNA and histone H3 methylation differ between Brassica species. The most prominent differences concern the two diploids. DNA methylation was present exclusively in the heterochromatin only in B. rapa. In B. oleracea and B. napus this modification was detected in both euchromatin and heterochromatin. A similar pattern was observed for dimethylation of lysine 9. Dimethylation of lysine 4 is a typical marker of euchromatin in Brassica species, like it is in other plant species. We conclude that the diploid species differ in patterns of analyzed epigenetic modifications and the allotetraploid B. napus has combined patterns from both diploids. Differences in patterns of DNA and histone H3 methylation between Brassica species can be attributed mainly to the genome structure and heterochromatin localization rather than ploidy level.

scholarly journals DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Wendan Ren ◽  
Huitao Fan ◽  
Sara A. Grimm ◽  
Jae Jin Kim ◽  
Linhui Li ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Histone H3 ◽  
Genomic Stability ◽  
Mammalian Genome ◽  
Dna Methyltransferase 1 ◽  
Chromatin Modifications ◽  
Direct Link ◽  
Histone H4 ◽  
Radiation Induced

AbstractDNA methylation and trimethylated histone H4 Lysine 20 (H4K20me3) constitute two important heterochromatin-enriched marks that frequently cooperate in silencing repetitive elements of the mammalian genome. However, it remains elusive how these two chromatin modifications crosstalk. Here, we report that DNA methyltransferase 1 (DNMT1) specifically ‘recognizes’ H4K20me3 via its first bromo-adjacent-homology domain (DNMT1BAH1). Engagement of DNMT1BAH1-H4K20me3 ensures heterochromatin targeting of DNMT1 and DNA methylation at LINE-1 retrotransposons, and cooperates with the previously reported readout of histone H3 tail modifications (i.e., H3K9me3 and H3 ubiquitylation) by the RFTS domain to allosterically regulate DNMT1’s activity. Interplay between RFTS and BAH1 domains of DNMT1 profoundly impacts DNA methylation at both global and focal levels and genomic resistance to radiation-induced damage. Together, our study establishes a direct link between H4K20me3 and DNA methylation, providing a mechanism in which multivalent recognition of repressive histone modifications by DNMT1 ensures appropriate DNA methylation patterning and genomic stability.

scholarly journals H3 Lysine 9 Methylation Is Maintained on a Transcribed Inverted Repeat by Combined Action of SUVH6 and SUVH4 Methyltransferases

2005 ◽  
Vol 25 (23) ◽  
pp. 10507-10515 ◽  
Author(s):  
Michelle L. Ebbs ◽  
Lisa Bartee ◽  
Judith Bender
Keyword(s):  
Dna Methylation ◽  
Chromatin Immunoprecipitation ◽  
Inverted Repeat ◽  
Histone H3 ◽  
Inverted Repeats ◽  
Chromatin Modifications ◽  
Double Stranded Rna ◽  
Repeat Sequences ◽  
Endogenous Genes ◽  
Combined Action

ABSTRACT Transcribed inverted repeats are potent triggers for RNA interference and RNA-directed DNA methylation in plants through the production of double-stranded RNA (dsRNA). For example, a transcribed inverted repeat of endogenous genes in Arabidopsis thaliana, PAI1-PAI4, guides methylation of itself as well as two unlinked duplicated PAI genes, PAI2 and PAI3. In previous work, we found that mutations in the SUVH4/KYP histone H3 lysine 9 (H3 K9) methyltransferase cause a loss of DNA methylation on PAI2 and PAI3, but not on the inverted repeat. Here we use chromatin immunoprecipitation analysis to show that the transcribed inverted repeat carries H3 K9 methylation, which is maintained even in an suvh4 mutant. PAI1-PAI4 H3 K9 methylation and DNA methylation are also maintained in an suvh6 mutant, which is defective for a gene closely related to SUVH4. However, both epigenetic modifications are reduced at this locus in an suvh4 suvh6 double mutant. In contrast, SUVH6 does not play a significant role in maintenance of H3 K9 or DNA methylation on PAI2, transposon sequences, or centromere repeat sequences. Thus, SUVH6 is preferentially active at a dsRNA source locus versus targets for RNA-directed chromatin modifications.

DNA methylation, histone H3 methylation, and histone H4 acetylation in the genome of a crustacean

Genome ◽  
2006 ◽  
Vol 49 (1) ◽  
pp. 87-90 ◽  
Author(s):  
Rita Barzotti ◽  
Franca Pelliccia ◽  
Angela Rocchi
Keyword(s):  
Dna Methylation ◽  
Banding Pattern ◽  
Histone H3 ◽  
Asellus Aquaticus ◽  
Histone H4 ◽  
Y Chromosomes ◽  
Histone H4 Acetylation ◽  
Histone H3 Methylation

In this work, we used antibodies against histone H3 trimethylated at lysine 9 (H3K9m3); against histone H4 acetylated at lysines 5, 8, 12, and 16 (H4ac); and against DNA methylated at 5C cytosine (m5C) to study the presence and distribution of these markers in the genome of the isopod crustacean Asellus aquaticus. The use of these 3 antibodies to immunolabel spermatogonial metaphases yields reproducible patterns on the chromosomes of this crustacean. The X and Y chromosomes present an identical banding pattern with each of the antibodies. The heterochromatic telo meric regions and the centromeric regions are rich in H3K9m3, but depleted in m5C and H4ac. Thus, m5C does not seem to be required to stabilize the silence of these regions in this organism.Key words: DNA methylation, H3 methylation, H4 acetylation, crustacean, Asellus aquaticus.

Histone H3 methylation patterns in Brassica nigra, Brassica juncea, and Brassica carinata species

Genome ◽  
2012 ◽  
Vol 55 (1) ◽  
pp. 68-74 ◽  
Author(s):  
Agnieszka Braszewska-Zalewska ◽  
Alina Dziurlikowska ◽  
Jolanta Maluszynska
Keyword(s):  
Interphase Nucleus ◽  
Tissue Specificity ◽  
Histone H3 ◽  
Brassica Species ◽  
Interphase Nuclei ◽  
Meristematic Tissue ◽  
Post Translational Modifications ◽  
Histone H3 Methylation ◽  
Core Histones ◽  
Methylation Patterns

Core histones are subjected to various post-translational modifications, and one of them, most intensively studied in plants, is the methylation of histone H3. In the majority of analyzed plant species, dimethylation of H3 at lysine 9 (H3K9me2) is detected in heterochromatin domains, whereas methylation of H3 at lysine 4 (H3K4me2) is detected in euchromatin domains. The distribution of H3K9me2 in the interphase nucleus seems to be correlated with genome size, chromatin organization, but also with tissue specificity. In this paper, we present the analysis of the pattern and level of histone H3 methylation for two allotetraploid and one diploid Brassica species. We have found that the pattern of H3K9me2 in interphase nuclei from root meristematic tissue is comparable within the analyzed species and includes both heterochromatin and euchromatin, but the level of modification differs not only among species but even among nuclei in the same phase of the cell cycle within one species. Moreover, the differences in the level of H3K9me2 are not directly coupled with DNA content in the nuclei and are probably tissue specific.

scholarly journals A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jouni Kvist ◽  
Camila Gonçalves Athanàsio ◽  
Michael E. Pfrender ◽  
James B. Brown ◽  
John K. Colbourne ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Histone H3 ◽  
Daphnia Pulex ◽  
Epigenetic Modifications ◽  
The Other ◽  
Gene Expression Level ◽  
Expression Level ◽  
Male And Female ◽  
Phenotypic Differences

Abstract Background Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female Daphnia can be genetically identical, yet display large differences in behaviour, morphology, lifespan and metabolic activity. Our goal was to integrate multiple omics datasets, including gene expression, splicing, histone modification and DNA methylation data generated from genetically identical female and male Daphnia pulex under controlled laboratory settings with the aim of achieving a better understanding of the underlying epigenetic factors that may contribute to the phenotypic differences observed between the two genders. Results In this study we demonstrate that gene expression level is positively correlated with increased DNA methylation, and histone H3 trimethylation at lysine 4 (H3K4me3) at predicted promoter regions. Conversely, elevated histone H3 trimethylation at lysine 27 (H3K27me3), distributed across the entire transcript length, is negatively correlated with gene expression level. Interestingly, male Daphnia are dominated with epigenetic modifications that globally promote elevated gene expression, while female Daphnia are dominated with epigenetic modifications that reduce gene expression globally. For examples, CpG methylation (positively correlated with gene expression level) is significantly higher in almost all differentially methylated sites in male compared to female Daphnia. Furthermore, H3K4me3 modifications are higher in male compared to female Daphnia in more than 3/4 of the differentially regulated promoters. On the other hand, H3K27me3 is higher in female compared to male Daphnia in more than 5/6 of differentially modified sites. However, both sexes demonstrate roughly equal number of genes that are up-regulated in one gender compared to the other sex. Since, gene expression analyses typically assume that most genes are expressed at equal level among samples and different conditions, and thus cannot detect global changes affecting most genes. Conclusions The epigenetic differences between male and female in Daphnia pulex are vast and dominated by changes that promote elevated gene expression in male Daphnia. Furthermore, the differences observed in both gene expression changes and epigenetic modifications between the genders relate to pathways that are physiologically relevant to the observed phenotypic differences.

scholarly journals Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation

2020 ◽  
Vol 117 (31) ◽  
pp. 18439-18447
Author(s):  
Wendan Ren ◽  
Huitao Fan ◽  
Sara A. Grimm ◽  
Yiran Guo ◽  
Jae Jin Kim ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Histone Modifications ◽  
Dna Methyltransferase ◽  
Histone H3 ◽  
Genomic Stability ◽  
Epigenetic Modifications ◽  
Global Dna Methylation ◽  
Replication Foci ◽  
Direct Readout

In mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation.

Caught in conspiracy: cooperation between DNA methylation and histone H3K9 methylation in the establishment and maintenance of heterochromatin

2005 ◽  
Vol 83 (3) ◽  
pp. 385-395 ◽  
Author(s):  
Irina Stancheva
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Rna Interference ◽  
Histone Methylation ◽  
Functional Relationship ◽  
Histone H3 ◽  
H3k9 Methylation ◽  
Complex Interactions ◽  
Histone H3 Methylation ◽  
Intensive Investigation

Heritable patterns of gene expression and gene silencing are determined by chromatin states that either permit or restrict transcription. Restrictive heterochromatin in most eukaryotes is characterized by high levels of DNA methylation and histone H3 methylation at lysine 9. The functional relationship between these two modifications is the focus of intensive investigation in various organisms from fungi to mammals. Complex interactions have been discovered among various components of DNA methylation and histone methylation pathways, proteins involved in the formation of higher-order chromatin structure, chromatin remodelling activities, and RNA interference. This review discusses some aspects of this crosstalk and the cooperation between DNA methylation and histone H3K9 methylation in the establishment and maintenance of heterochromatin.Key words: DNA methylation, H3K9 methylation, heterochromatin.

scholarly journals Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation

2020 ◽  
Author(s):  
Wendan Ren ◽  
Huitao Fan ◽  
Sara A Grimm ◽  
Yiran Guo ◽  
Jae Jin Kim ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Histone Modifications ◽  
Dna Methyltransferase ◽  
Histone H3 ◽  
Genomic Stability ◽  
Epigenetic Modifications ◽  
Global Dna Methylation ◽  
Replication Foci ◽  
Direct Readout

ABSTRACTIn mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation.

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