Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome compaction and individualization
Ontology highlight
ABSTRACT:
ORGANISM(S): Xenopus laevis
PROVIDER: GSE164434 | GEO | 2021/07/07
REPOSITORIES: GEO
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Project description: Not available
| S-EPMC8416026 | biostudies-literature
Project description:Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome compaction and individualization
| PRJNA690708 | ENA
Project description:As a key structural component of the chromatin of higher eukaryotes, linker histones (H1s) are involved in stabilizing the folding of extended nucleosome arrays into higher-order chromatin structures and function as a gene-specific regulators of transcription in vivo. The H1 C-terminal domain (CTD) is essential for high affinity binding of linker histones to chromatin and stabilization of higher-order chromatin structure. Importantly, the H1 CTD is an intrinsically disordered domain that undergoes a drastic condensation upon binding to nucleosomes. Moroever, although phosphorylation is a prevalent posttranslational modification (PTM) within the H1 CTD, exactly where this modification is installed and how phosphorylation influences the structure of the H1 CTD remains unclear for many H1s. Using novel mass spectrometry techniques, we identified six phosphorylation sites within the CTD of the archetypal linker histone Xenopus H1.0. We then analyzed nucleosome-dependent CTD condensation and H1-dependent linker DNA conformation for six full-length H1s in which the phosphorylated serine residues were replaced by glutamic acid residues.
2022-08-12 | PXD032292 | Pride
Project description:The nucleosome plays a central role in genome regulation. Traditional methods for mapping nucleosomes depend on the resistance of the nucleosome core to micrococcal nuclease (MNase). However, the lengths of the protected DNA fragments are heterogeneous, limiting the accuracy of nucleosome position information. To resolve this problem, we removed residual linker DNA by simultaneous digestion of yeast chromatin with MNase and exonuclease III (ExoIII). Paired-end sequencing of mono-nucleosomes revealed not only core particles (145-147 bp), but also intermediate particles in which ~8 bp project from one side (154 bp) or both sides (161 bp) of the nucleosome core. We term these particles "pseudo-chromatosomes" because they are present in yeast lacking linker histone. They are also observed after MNase-ExoIII digestion of chromatin reconstituted using recombinant core histones. We propose that the pseudo-chromatosome provides a DNA framework to facilitate H1 binding. Comparison of budding yeast nucleosome sequences obtained using micrococcal nuclease (MNase-seq) and MNase + exonuclease III (ExoIII) (MNase-ExoIII-seq): wild type cells and hho1-null cells. Nucleosome sequences from native chromatin and H1-depleted chromatin from mouse liver. Nucleosome sequences from a plasmid reconstituted into nucleosomes using recombinant yeast histones or native chicken erythrocyte histones.
2015-09-23 | E-GEOD-65889 | biostudies-arrayexpress
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| S-EPMC1885653 | biostudies-literature
Project description:ABSTRACT: Condensin is a central regulator of mitotic genome structure, with mutants showing poorly condensed chromosomes and profound segregation defects. Here we identify the fission yeast NCT complex, comprising the Nrc1 BET-family tandem bromodomain protein (SPAC631.02), Casein Kinase II (CKII) and several TAFs, as a novel regulator of condensin function (where NCT mutants restore the formation of segregation-competent chromosomes in cells containing defective condensin). Synchronous ChIP-seq shows that NCT and condensin bind similar genomic regions, but only briefly co-localize during the periods of chromosome condensation and decondensation. These results are consistent with a model where NCT targets CKII to chromatin in a cell cycle-directed manner to modulate the activity of condensin during chromosome condensation and decondensation. DATA: Study includes ChIP-seq of fission yeast H3-K4Me3, H3-K36Me3, TBP, Taf7, Nrc1, Cka1 from aynchronous cells; Nrc1 and Cut3 (representing condensin) from four synchronized cell-cycle stages estimated as G2/M, Metaphase, Anaphase and G1/S.
2014-01-10 | E-GEOD-53955 | biostudies-arrayexpress
Project description:Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ~147 bp of DNA wrapped ~1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. Micrococcal nuclease (MNase) digests the linker to yield the chromatosome, containing H1 and ~160 bp, and then converts it to a core particle, containing ~147 bp and no H1. Sequencing of nucleosomal DNA obtained after MNase digestion (MNase-seq) generates genome-wide nucleosome maps that are important for understanding gene regulation. We present an improved MNase-seq method involving simultaneous digestion with exonuclease III, which removes linker DNA. Remarkably, we discovered two novel intermediate particles containing 154 or 161 bp, corresponding to 7 bp protruding from one or both sides of the nucleosome core. These particles are detected in yeast lacking H1 and in H1-depleted mouse chromatin. They can be reconstituted in vitro using purified core histones and DNA. We propose that these "proto-chromatosomes" are fundamental chromatin subunits, which include the H1 binding site and influence nucleosome spacing independently of H1.
2015-09-23 | GSE65889 | GEO
Project description:An emerging theme of gene regulation is the involvement of architectural chromosomal molecules in transcription control. Condensins are critical regulators of mitotic chromosomes, but their interphase chromatin localization and functions remain poorly understood. Here we report that both the condensin I and condensin II complexes exhibit an unexpected, dramatic 17-?-estradiol-induced preferential recruitment to oestrogen receptor ? (ER-?)-bound active enhancers in interphase breast cancer cells, exhibiting non-canonical interaction with ER-? distinct from classic cofactors. Condensins prove to positively regulate ligand-dependent gene and eRNA transcription by modulating a binding equilibrium of enhancer-associated coactivators/corepressors, including p300 and RIP140. This activity was achieved by the condensin-dependent recruitment of an E3 ubiquitin ligase, HECTD1, to active enhancers, where it polyubiquitinates and dismisses corepressor RIP140 to stimulate eRNA transcription. Collectively, our results reveal an important, unanticipated transcriptional role of interphase condensins in modulating enhancer activation, providing new insights into enhancer function in the regulated transcriptional programs
2015-07-15 | GSE62228 | GEO
Project description:An emerging theme of gene regulation is the involvement of architectural chromosomal molecules in transcription control. Condensins are critical regulators of mitotic chromosomes, but their interphase chromatin localization and functions remain poorly understood. Here we report that both the condensin I and condensin II complexes exhibit an unexpected, dramatic 17-β-estradiol-induced preferential recruitment to oestrogen receptor α (ER-α)-bound active enhancers in interphase breast cancer cells, exhibiting non-canonical interaction with ER-α distinct from classic cofactors. Condensins prove to positively regulate ligand-dependent gene and eRNA transcription by modulating a binding equilibrium of enhancer-associated coactivators/corepressors, including p300 and RIP140. This activity was achieved by the condensin-dependent recruitment of an E3 ubiquitin ligase, HECTD1, to active enhancers, where it polyubiquitinates and dismisses corepressor RIP140 to stimulate eRNA transcription. Collectively, our results reveal an important, unanticipated transcriptional role of interphase condensins in modulating enhancer activation, providing new insights into enhancer function in the regulated transcriptional programs
2015-07-15 | GSE62222 | GEO
Project description:Vertebrate condensin I and II molecules are loaded onto the genome to mediate essential changes in chromosome condensation during mitosis, but it is not clear how the two forms of condensin become distributed on chromosomes. We report here that condensin II, the form of condensin present in the nucleus throughout the cell cycle, is loaded at transcriptionally active promoters, migrates through these genes in a transcription-dependent fashion and accumulates in transcription termination regions during interphase. During mitosis, condensin I is recruited to actively transcribed genes and replaces condensin II. We conclude that the two forms of condensin are loaded at different times during the cell division cycle at the promoters of actively transcribed genes. ChIP-Seq data for Condensin II in v6.5 ESCs treated or not with nocodazole
2012-03-14 | E-GEOD-33346 | biostudies-arrayexpress