Evolutional heterochromatin condensation delineates chromocenter formation and retrotransposon constraint in plants
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PROVIDER: PRJNA975586 | ENA |
REPOSITORIES: ENA
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Project description:Heterochromatic condensates (chromocenters) are critical for maintaining the silencing of heterochromatin. However, it is a riddle why the presence of chromocenters is variable across species. Here, we reveal that variations in the plant heterochromatin protein ADCP1 confer a diversity in chromocenter formation via phase separation. ADCP1 physically interacts with the high mobility group protein HMGA to form a complex and mediates heterochromatin condensation by multivalent interactions. The loss of intrinsically disordered regions (IDRs) in ADCP1 homologues during evolution has led to the absence of prominent chromocenter in various plant species, and introduction of IDR-containing ADCP1 with HMGA promotes heterochromatin condensation and retrotransposon silencing. Moreover, plants in the Cucurbitaceae group have evolved an IDR-containing chimera of ADCP1 and HMGA, which enables formation of chromocenters remarkably. Together, our work uncovers a coevolved mechanism of phase separation in packing heterochromatin and constraining retrotransposons.
2024-06-22 | GSE233265 | GEO
Project description:Histone variants play crucial roles in gene expression, genome integrity and chromosome segregation. However, to what extent histone variants control chromatin architecture remains largely unknown. Here, we show that the previously uncharacterized histone variant H2A.W plays a crucial role in condensation of heterochromatin. Genome-wide profiling of all four types of H2A variants in Arabidopsis shows that H2A.W specifically associates with heterochromatin. H2A.W recruitment is independent of heterochromatic marks H3K9me2 and DNA methylation. Genetic interactions show that H2A.W acts in synergy with CMT3 mediated methylation to maintain genome integrity. In vitro, H2A.W enhances chromatin condensation through a higher propensity to make fiber-to-fiber interactions via its conserved C-terminal motif. In vivo, elimination of H2A.W causes decondensation of heterochromatin and conversely, ectopic expression of H2A.W promotes heterochromatin condensation. These results demonstrate that H2A.W plays critical roles in heterochromatin by promoting higher order chromatin condensation. Since similar H2A.W C-terminal motifs are present in other variant found in mammals and other organisms our findings impact our understanding of heterochromatin condensation in a wide variety of eukaryotic organisms. Two mRNA-seq samples, two bisulfite-seq samples, six ChIP-seq samples.
2014-07-05 | E-GEOD-50942 | biostudies-arrayexpress
Project description:Histone variants play crucial roles in gene expression, genome integrity and chromosome segregation. However, to what extent histone variants control chromatin architecture remains largely unknown. Here, we show that the previously uncharacterized histone variant H2A.W plays a crucial role in condensation of heterochromatin. Genome-wide profiling of all four types of H2A variants in Arabidopsis shows that H2A.W specifically associates with heterochromatin. H2A.W recruitment is independent of heterochromatic marks H3K9me2 and DNA methylation. Genetic interactions show that H2A.W acts in synergy with CMT3 mediated methylation to maintain genome integrity. In vitro, H2A.W enhances chromatin condensation through a higher propensity to make fiber-to-fiber interactions via its conserved C-terminal motif. In vivo, elimination of H2A.W causes decondensation of heterochromatin and conversely, ectopic expression of H2A.W promotes heterochromatin condensation. These results demonstrate that H2A.W plays critical roles in heterochromatin by promoting higher order chromatin condensation. Since similar H2A.W C-terminal motifs are present in other variant found in mammals and other organisms our findings impact our understanding of heterochromatin condensation in a wide variety of eukaryotic organisms.
2014-07-05 | GSE50942 | GEO
Project description:Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis
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Project description:We found PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing.
2018-06-21 | GSE116064 | GEO
Project description:We found PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing.
2018-06-21 | GSE116067 | GEO
Project description:We found PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing.
2018-06-21 | GSE116066 | GEO
Project description:We found PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing.
2018-06-21 | GSE116065 | GEO
Project description:We report that Setd8 is essential for murine erythropoeisis. Setd8 null erythroblasts have severe defects in cell cycle progression, chromatin condensation,and heterochromatin integrity. They also have dysregulated gene expression.
2017-11-28 | GSE83809 | GEO
Project description:Transposable elements have the potential to act as controlling elements to influence the expression of genes. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of the transposable element and influence the chromatin state of neighboring low-copy sequences. This would allow transposable elements to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I transposable elements (retrotransposons) that are present in moderate to high copy numbers and many are found in regions near genes which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into flanking DNA around each family of retrotransposons through profiling of DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. The effects of different retrotransposon families on local chromatin are highly variable. Some LTR families exhibit enrichment of heterochromatic marks within 800-1200 base pairs of the insertion site while other families have very little evidence for spreading of heterochromatic marks. The analysis of chromatin state in genotypes that lack specific insertions suggests that the adjacent heterochromatin results from spreading of silencing rather than insertion-site preferences. Genes that are located near elements that exhibit spreading of heterochromatin tend to be expressed at lower levels than other genes. Our findings suggest that a subset of LTR retrotransposon families may act as controlling elements influencing neighboring sequences while the majority of elements have little effect on flanking sequences Transposable elements comprise a substantial portion of many eukaryotic genomes. These mobile fragments of DNA can result in mutations through insertions into genes but may also affect the regulation of genes they insert near. There is evidence that the majority of transposable elements are epigenetically silenced and in some cases this silencing may affect neighboring sequences. However, evolutionary theory would predict that there would be selective pressures for transposable elements to limit their effects on neighboring genes. The maize genome has a complex organization with many genes flanked by retrotransposons. We profiled the spread of heterochromatin from the retrotransposons into nearby low copy sequences for 150 high copy retrotransposon families. While the manymajority of retrotransposons exhibit little to no spreading of heterochromatin there are a small number ofsome retrotransposon families that influence the chromatin state of surrounding regions. The families may represent bad “neighbors” that spread heterochromatin and influence nearby genes. 6 total samples: 3 replicates of B73 H3k9 and 3 replicates of Mo17 H3k9 3 total samples: mop1 mutant, b73.zmet2 (zmet2.m1 mutant in B73 background) and mo17.zmet2 (zmet2.m1 mutant in Mo17 background)
2012-11-26 | E-GEOD-39460 | biostudies-arrayexpress