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H1.4K34ac ChIP-sequencing in MCF-7 cells

ABSTRACT: The linker histone H1 is a key player in chromatin organization, yet our understanding of the regulation of H1 functions by posttranslational modifications is very limited. We provide here the first functional characterization of H1 acetylation. We show that H1.4K34 acetylation (H1.4K34ac) is mediated by GCN5 and is preferentially enriched at promoters of active genes, where it stimulates transcription by increasing H1 mobility and recruiting a general transcription factor. H1.4K34ac is dynamic during spermatogenesis and marks undifferentiated cells, such as induced pluripotent stem (iPS) cells and testicular germ cell tumors. We propose a model for H1.4K34ac as a novel regulator of chromatin function with a dual role in transcriptional activation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE36367 | GEO | 2012/04/15

SECONDARY ACCESSION(S): PRJNA153339

REPOSITORIES: GEO

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H1.4K34ac ChIP-sequencing in MCF-7 cells

Project description:The linker histone H1 is a key player in chromatin organization, yet our understanding of the regulation of H1 functions by posttranslational modifications is very limited. We provide here the first functional characterization of H1 acetylation. We show that H1.4K34 acetylation (H1.4K34ac) is mediated by GCN5 and is preferentially enriched at promoters of active genes, where it stimulates transcription by increasing H1 mobility and recruiting a general transcription factor. H1.4K34ac is dynamic during spermatogenesis and marks undifferentiated cells, such as induced pluripotent stem (iPS) cells and testicular germ cell tumors. We propose a model for H1.4K34ac as a novel regulator of chromatin function with a dual role in transcriptional activation. Examination of H1.4K34ac in the MCF-7 cell line by ChIP-Seq - two replicates of H1.4K34ac IP as two sequencing runs used to produce 1 BED file, one control IP sample.

2012-04-14 | E-GEOD-36367 | biostudies-arrayexpress

The interactome of site-specifically acetylated linker histone H1

Project description:Linker histone H1 plays a key role in chromatin organization and maintenance, however, our knowledge of the regulation of H1 functions by its posttranslational modifications (PTMs) is very limited. In this study, we report on the generation of homogeneously and site-specifically mono- and di-acetylated H1 (H1 Ac) using genetic code expansion. We used these modified histones to identify and comprehensively characterize the acetylation-dependent cellular interactome for linker histone H1 and show that site-specific acetylation results in overlapping, but distinct groups of interacting partners. Intriguingly, H1 acetylation-specific interactors comprise translational initiation factors and are involved in transcriptional regulation, suggesting that acetylation of H1 may indeed act as a regulator of the linker histone H1 by modulation of protein-protein interactions.

2021-07-09 | PXD025832 | Pride

Histone H4K16 acetylation modulates the dynamics of linker H1 and heterochromatin protein HP1 in male X chromosome dosage compensation

Project description:Drosophila dosage compensation is an epigenetic phenomenon in which the transcription of most genes on X-chromosome is enhanced by approximately two folds in males to equalize that in females. In this study, we provide evidence that transcriptional repressors, such as HP1 and linker histone H1, are globally reduced on male X chromosome. We further investigated the role of HP1 and linker H1 on X chromosome dosage compensation using flies with overexpression of HP1 and H1, we demonstrate that these repressors surpress H4K16 acetylation, presence of the elongating RNA Pol II and the transcription of the genes on male X chromosomes. To understand how H1 and HP1 are regulated on male X chromosome, we next explored the relationship between MOF and the two repressors of chromatin. We show that the hyperacetylation of H4K16 induced by MOF resulted in the loss of H1 and HP1 on chromatin and global chromatin decondensation. Our biochemical analysis further shows that the presence of acetylation on histone H4 at lysine 16 directly inhibits the interaction between histone H4 and linker H1. This study therefore provides novel clues on understanding the dynamic regulation of chromatin regulators on male X chromosome dosage compensation.

2017-11-01 | GSE29537 | GEO

Identification and analysis of phosphorylation within Xenopus laevis linker histone H1.0

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

The functional interactome of site-specifically ubiquitylated linker histone H1

Project description:Decoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. While this process is well studied for core histones and many of their PTMs, this is not the case for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the generation of site-specifically mono-ubiquitylated H1.2 via click chemistry and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that the H1 interactome is generally modulated by ubiquitylation and that site-specific ubiquitylation results in overlapping, but distinct interactomes. We further demonstrate that site-specific ubiquitylation of H1 affects the interaction with enzymes relevant for deubiquitylation and deacetylation. We finally show that site-specific ubiquitylation at position K64 impacts H1-dependent chromatosome assembly as well as H1-induced phase separation. In summary, we demonstrate that site-specific ubiquitylation is a general functional regulator for linker histone H1.

2021-07-20 | PXD020686 | Pride

Site-specific ubiquitylation acts as a regulator of linker histone H1

Project description:Decoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. While this process is well studied for core histones and many of their PTMs, this is not the case for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the generation of site-specifically mono-ubiquitylated H1.2 via click chemistry and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that the H1 interactome is generally modulated by ubiquitylation and that site-specific ubiquitylation results in overlapping, but distinct interactomes. We further demonstrate that site-specific ubiquitylation of H1 affects the interaction with enzymes relevant for deubiquitylation and deacetylation. We finally show that site-specific ubiquitylation at position K64 impacts H1-dependent chromatosome assembly as well as H1-induced phase separation. In summary, we propose that site-specific ubiquitylation plays a general regulatory role for linker histone H1.

2021-06-07 | PXD025258 | Pride

Genome-wide maps of linker histone H1 lysine 85 acetylation in HCT116 cells

Project description:We identify acetylation of linker histone H1 lysine 85 as a novel histone acetylation mark, which regulates chromatin structure and genome stability upon DNA damage. By performing a chromatin immunoprecipitation and deep sequencing assay, we identified the genome-wide distribution patterns of H1 lysine 85 acetylation in HCT116 cells. We found that H1K85ac largely bound intergenic regions (53%) and gene bodies (39%), whereas only 7% H1K85ac bound regions 2 kb upstream of the transcription start sites (TSSs). As the proportion of H1K85ac bound to potential promoter regions was not significantly different to that of the random peaks (~6%), these data suggest that H1K85ac may not be mainly involved in general transcriptional regulation.

2018-04-18 | GSE113238 | GEO

Genome-wide maps of chromatin state and gene expression in control and TPA-stimulated pre-B leukemic 697 line

Project description:Linker histone H1 has been correlated with transcriptional inhibition, but the mechanistic basis of the inhibition and its reversal during gene activation has remained enigmatic. We report that H1-compacted chromatin, reconstituted in vitro, blocks transcription by abrogating core histone modifications by p300 but not activator and p300 binding. Transcription from H1-bound chromatin is elicited by H1 chaperone NAP1, which is recruited in a gene-specific manner through direct interactions with activator-bound p300 that facilitate core histone acetylation (by p300) and concomitant eviction of H1 and H2A/H2B. An analysis in B cells confirms the strong dependency on NAP1-mediated H1 eviction for induction of the silent CD40 gene and further demonstrates that H1 eviction, seeded by activator-p300-NAP1 interactions, is propagated over a CTCF-demarcated region through a distinct mechanism that also involves NAP1. Our results confirm direct transcriptional inhibition by H1 and establish a gene-specific H1 eviction mechanism through an activator-p300-NAP1-H1 pathway.

2019-02-06 | GSE126083 | GEO

PELP1 ChIP-chip from MCF-7 cells

Project description:Proline-, glutamic acid-, and leucine-rich protein 1 (PELP1) is a transcriptional coactivator that has previously been shown to collaborate with nuclear receptors. Evidence from other groups suggest that PELP1 may stimulate transcription by displacing the linker histone H1 and/or by recruiting the lysine demethylase KDM1 to demethylate H3K9me2. Also known as modulator of the non-genomic activity of estrogen receptor (MNAR), PELP1 has also been implicated promoting estrogen receptor signaling from the plasma membrane. We recently identified PELP1 a factor that interacts with the macro domain of the histone variant macroH2A1. To determine if PELP1 interacts with macroH2A1 in cells, we performed PELP1 ChIP-chip from MCF-7 cells. The pattern of PELP1 bind across the genome strongly correlates with that previously determined for macroH2A1. This data combined with additional experiments allow us to conclude that macroH2A1 regulates target gene expression in part by recruiting the transcriptional coregulator PELP1. Two PELP1 ChIP-chip biological replicates from MCF-7 human breast cancer cells are included.

2014-04-24 | E-GEOD-22254 | biostudies-arrayexpress

Genome-wide maps of linker histone H1 lysine 85 acetylation in HCT116 cells

Project description:Genome-wide maps of linker histone H1 lysine 85 acetylation in HCT116 cells

| PRJNA450529 | ENA