Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA706656 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12906200_1.fastq.gz | Fastqsanger.gz | |||
| SRR12906200_2.fastq.gz | Fastqsanger.gz | |||
| SRR12906201_1.fastq.gz | Fastqsanger.gz | |||
| SRR12906201_2.fastq.gz | Fastqsanger.gz | |||
| SRR12906202_1.fastq.gz | Fastqsanger.gz |
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Project description:We determined the structure, characteristics, and functional significance of the H3mm18 nucleosome, and provide insights into understanding genome regulation.
2022-01-03 | GSE168238 | GEO
Project description:Histone H3mm18 is a non-allelic H3 variant expressed in skeletal muscle and brain in mice. However, its function has remained enigmatic. We found that H3mm18 is incorporated into chromatin in cells with low efficiency, as compared to H3.3. We determined the structures of the nucleosome core particle (NCP) containing H3mm18 by cryo-electron microscopy, which revealed that the entry/exit DNA regions are drastically disordered in the H3mm18 NCP. Consistently, the H3mm18 NCP is substantially unstable in vitro. The forced expression of H3mm18 in mouse myoblast C2C12 cells markedly suppressed muscle differentiation. A transcriptome analysis revealed that the forced expression of H3mm18 affected the expression of multiple genes, and suppressed a group of genes involved in muscle development. These results suggest a novel gene expression regulation system in which the chromatin landscape is altered by the formation of unusual nucleosomes with a histone variant, H3mm18, and provide important insight into understanding transcription regulation by chromatin.
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Project description:Nucleosome is the basic structural unit of chromatin, and its dynamics plays critical roles in the regulation of genome functions. However, how the nucleosome structure is regulated by histone variants in vivo is still largely uncharacterized. Here, by employing Micrococcal nuclease (MNase) digestion of crosslinked chromatin followed by chromatin immunoprecipitation (ChIP) and paired-end sequencing (MNase-X-ChIP-seq), we mapped genome-wide unwrapping states of nucleosomes containing histone variant H2A.Z in mouse embryonic stem (ES) cells. We found that H2A.Z is enriched with unwrapped nucleosomes. Interestingly, the function of +1 H2A.Z nucleosome in transcriptional regulation is correlated with the unwrapping states. We further showed that H2A.Z nucleosomes adjacent the CTCF binding sites (CBS) may adopt an open conformation. We confirmed the unwrapping state of H2A.Z nucleosomes under native condition by re-ChIP of H2A.Z after CTCF CUT&RUN in mouse ES cells. Importantly, we found that depletion of H2A.Z results in increased CTCF binding, indicating dynamic competition between the unwrapped H2A.Z nucleosomal intermediates and CTCF at the CBS. Taken together, our results showed that histone variant H2A.Z regulates transcription and CTCF binding through modulating the nucleosome unwrapping.
2020-04-27 | GSE146082 | GEO
Project description:Linker histones are involved in the formation of higher-order chromatin structure. Although linker histones have been implicated in the regulation of specific genes, it still remains unclear what their principal binding determinants are and how their repressive function in vitro can be reconciled with presumed broad binding in vivo. We generated a full genome, high resolution binding map of linker histone H1 in Drosophila Kc cells, using DamID. H1 binds at similar levels across much of the genome, both in classical euchromatin and heterochromatin. Strikingly, there are pronounced dips of low H1 occupancy around transcription start sites of active genes and at many distant cis-regulatory sites. H1 dips are not due to lack of nucleosomes. Rather, all regions with low binding of H1 show enrichment of the histone variant H3.3 which itself has been linked to high nucleosome turnover. Upon knockdown of H3.3, we find that H1 levels increase at sites previously not covered with H1 with a concomitant increase in nucleosome repeat length. These changes are independent of transcriptional changes. Our results show that the H3.3 protein counteracts association of H1 at genomic sites with high rates of histone turnover. This antagonism provides a mechanism to keep diverse genomic sites in an open chromatin conformation. For this study, we generated DamID profiles of histone H1 and RpII18 in Drosophila Kc167 cells. Additionally, we generated H1 profiles in cells treated with RNAi against white, H3.3B, or H3.3A and H3.3B. Nucleosome occupancy profiles were generated in untreated cells and cells treated with RNAi against white or H3.3A and H3.3B. Profiles of expression changes were generated for H3.3B RNAi and H3.3A and H3.3B RNAi. DamID experiments for H1 and RpII18 were performed in Drosophila cell cultures. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Formaldehyde-assisted isolation of regulatotry elements (FAIRE) was performed in Drosophila Kc167 cells. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing over non-crosslinked genomic DNA. Nucleosome positioning profiles were made by hybridizing mononucleosomal DNA over MNase digested purified genomic DNA on 380k NimbleGen arrays with 10 bp probe spacing. Expression profiles were made as H3.3 RNAi over white RNAi cohybridizations on spotted INDAC long oligo arrays. Every experiment was done in duplicate in the reverse dye orientation.
2010-06-23 | E-GEOD-16882 | biostudies-arrayexpress
Project description:Linker histones are involved in the formation of higher-order chromatin structure. Although linker histones have been implicated in the regulation of specific genes, it still remains unclear what their principal binding determinants are and how their repressive function in vitro can be reconciled with presumed broad binding in vivo. We generated a full genome, high resolution binding map of linker histone H1 in Drosophila Kc cells, using DamID. H1 binds at similar levels across much of the genome, both in classical euchromatin and heterochromatin. Strikingly, there are pronounced dips of low H1 occupancy around transcription start sites of active genes and at many distant cis-regulatory sites. H1 dips are not due to lack of nucleosomes. Rather, all regions with low binding of H1 show enrichment of the histone variant H3.3 which itself has been linked to high nucleosome turnover. Upon knockdown of H3.3, we find that H1 levels increase at sites previously not covered with H1 with a concomitant increase in nucleosome repeat length. These changes are independent of transcriptional changes. Our results show that the H3.3 protein counteracts association of H1 at genomic sites with high rates of histone turnover. This antagonism provides a mechanism to keep diverse genomic sites in an open chromatin conformation. For this study, we generated DamID profiles of histone H1 and RpII18 in Drosophila Kc167 cells. Additionally, we generated H1 profiles in cells treated with RNAi against white, H3.3B, or H3.3A and H3.3B. Nucleosome occupancy profiles were generated in untreated cells and cells treated with RNAi against white or H3.3A and H3.3B. Profiles of expression changes were generated for H3.3B RNAi and H3.3A and H3.3B RNAi.
2009-10-15 | GSE16882 | GEO
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Project description:Probing the rice genome for novel histone coding genes revealed a genera specific, histone H4 variant with several variations in N-terminal tail sequence motifs, expressing in a tissue-specific manner. Genetic perturbation of the H4 variant in rice led to defects in growth and fertility. Probing the chromatin binding sites of the H4 variant with a custom antibody revealed its binding at specific genes and its knockout led to mis-expression of stress-associated genes. Stress-challenged plants showed loss of the H4 variant and re-distribution of other H4 linked histone marks. In vitro reconstituted rice nucleosomes with H4 variant histones displayed atypical properties in terms of stability, intra-nucleosome binding and structure, when compared to the canonical nucleosomes.
2025-02-10 | GSE229602 | GEO
Project description:Probing the rice genome for novel histone coding genes revealed a genera specific, histone H4 variant with several variations in N-terminal tail sequence motifs, expressing in a tissue-specific manner. Genetic perturbation of the H4 variant in rice led to defects in growth and fertility. Probing the chromatin binding sites of the H4 variant with a custom antibody revealed its binding at specific genes and its knockout led to mis-expression of stress-associated genes. Stress-challenged plants showed loss of the H4 variant and re-distribution of other H4 linked histone marks. In vitro reconstituted rice nucleosomes with H4 variant histones displayed atypical properties in terms of stability, intra-nucleosome binding and structure, when compared to the canonical nucleosomes.
2025-02-10 | GSE229601 | GEO
Project description:Probing the rice genome for novel histone coding genes revealed a genera specific, histone H4 variant with several variations in N-terminal tail sequence motifs, expressing in a tissue-specific manner. Genetic perturbation of the H4 variant in rice led to defects in growth and fertility. Probing the chromatin binding sites of the H4 variant with a custom antibody revealed its binding at specific genes and its knockout led to mis-expression of stress-associated genes. Stress-challenged plants showed loss of the H4 variant and re-distribution of other H4 linked histone marks. In vitro reconstituted rice nucleosomes with H4 variant histones displayed atypical properties in terms of stability, intra-nucleosome binding and structure, when compared to the canonical nucleosomes.
2025-02-10 | GSE229599 | GEO
Project description:Nucleosome positions were determined in wild type cells, cells lacking Isw2 or Ume6, and cells containing a hybrid Chd1-Ume6 chimeric remodeler Matched MNase digests from W303 strain variants during log growth (OD600=0.4-0.6) were subject to paired-end sequencing for nucleosome mapping. For effects of the engineered fusion remodeling protein, a catalytically inactive (ATPase dead D513N) variant was included as a control.
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