Independent manipulation of histone H3 modifications in individual nucleosomes reveals the contributions of sister histones to transcription
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ABSTRACT:
PROVIDER: PRJNA412313 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4429110.fastq.gz | Fastqsanger.gz | |||
| SRR4429120.fastq.gz | Fastqsanger.gz | |||
| SRR4429111.fastq.gz | Fastqsanger.gz | |||
| SRR4429121.fastq.gz | Fastqsanger.gz | |||
| SRR4429112.fastq.gz | Fastqsanger.gz |
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Project description:Histone tail modifications can greatly influence chromatin-associated processes. Asymmetrically modified nucleosomes exist in multiple cell types, but whether modifications on both sister histones contribute equally to chromatin dynamics remains elusive. Here, we devised a bivalent nucleosome system that allowed for the constitutive assembly of asymmetrically modified sister histone H3s in nucleosomes in Saccharomyces cerevisiae. The sister H3K36 methylations independently affected cryptic transcription in gene coding regions, whereas sister H3K79 methylation had cooperative effects on gene silencing near telomeres. H3K4 methylation on sister histones played an independent role in suppressing the recruitment of Gal4 activator to the GAL1 promoter and in inhibiting GAL1 transcription. Under starvation stress, sister H3K4 methylations acted cooperatively, independently or redundantly to regulate transcription. Thus, we provide a unique tool for comparing symmetrical and asymmetrical modifications of sister histone H3s in vivo.
| S-EPMC5677365 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2017-10-15 | GSE104313 | GEO
Project description:Modifications on histone tails largely affect chromatin associated processes. Previous studies have shown the existence of asymmetrically modified nucleosomes in promoters in multiple cell types. However, whether modifications on both sister histones contribute equally to chromatin dynamics remains elusive. Here we devised a bivalent nucleosome system which allows for the constitutive assembly of asymmetrically modified sister histone H3 in nucleosomes in vivo. We found that the H3K36 methylation on either of sister histones sensitize chromatin structure in gene coding region, while the H3K79 methylation on both sister histone H3s are indispensable for maintaining silent chromatin near telomeres. Additionally, the H3K4 methylation on sister histones plays an equivalent role in suppressing the recruitment of Gal4 activator at GAL1 promoter and GAL1 transcription. Moreover, under starvation stress the expression of a significant proportion of genes in the whole genome is affected by the lack of the H3K4 methylation on one tail of the sister histones, indicating that both sister histones function in fine-tuning transcription through their modifications. We conclude that modifications on sister histones either cooperatively or independently respond to the change of an environmental cue to regulate chromatin structure and function. This work provides a unique experimental strategy to investigate the cross talk between sister histones, and for the first time elaborate their contributions to chromatin in vivo.
2017-10-16 | GSE104312 | GEO
Project description:During genome replication, parental histones are recycled to newly replicated DNA with their post-translational modifications (PTMs). It remains unknown whether sister chromatids inherit modified histones evenly. Here, we measured histone PTM partition to sister chromatids in embryonic stem cells. We found that parental histones H3-H4 segregate to both daughter DNA strands with a weak leading strand bias, skewing partition at topologically associating domain (TAD) borders and enhancers proximal to replication initiation zones. Segregation of parental histones to the leading strand increased markedly in cells with histone-binding mutations in MCM2, part of the replicative helicase, exacerbating histone PTM sister chromatid asymmetry. This work reveals how histones are inherited to sister chromatids and identifies a mechanism for how symmetric cell division is ensured by the replication machinery.
2018-08-16 | GSE117274 | GEO
Project description:Histone tail modificationscan greatly influencechromatin-associated processes. Asymmetrically modified nucleosomes exist inmultiple cell types; however,whether modifications on both sister histones contribute equally to chromatin dynamicsremainselusive. Here, we devised a bivalent nucleosome system thatallowedfor the constitutive assembly of asymmetrically modified sister histone H3s in nucleosomes inSaccharomyces cerevisiae. The sister H3K36 methylationsaffectedcryptic transcription in gene coding regions, whereassister H3K79 methylation had cooperative effectsongene silencing near telomeres.H3K4 methylation on sister histonesplayed an independent role in suppressing the recruitmentof the Gal4 activator and inhibitingGAL1transcription. Under starvation stress, the expression of glycometabolism pathway geneswasfinetuned by sisterH3K4 methylation.Thus,different modifications on sister histones act either cooperatively or independentlyto regulate transcription in response to external stimuli.
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Project description:The doublet histones of Marseillevirus are distantly related to the four eukaryotic core histones and wrap DNA to form remarkably similar nucleosomes. By releasing Marseillevirus chromatin from virions into solution and performing genome-wide nuclease digestion and chemical cleavage assays, we find that the higher-order organization of Marseillevirus chromatin differs greatly from that of eukaryotes. Marseillevirus nucleosomes fully protect DNA within virions, without linker DNA or phasing along genes. Likewise, we observe that most nucleosomes reconstituted onto 3-copy tandem repeats of a nucleosome positioning sequence are tightly packed and fully wrapped. We also document repeat generation and instability during viral passage in amoeboid culture. Dense promiscuous packing of fully wrapped nucleosomes rather than “beads-on-a-string” with genic punctuation suggests a viral genome protection function for doublet histones.
2022-09-27 | GSE193224 | GEO
Project description:Chromatin transactions are typically studied in vivo, or in vitro using artificial chromatin lacking the epigenetic complexity of the natural material. Attempting to bridge the gap between these approaches, we established a system for isolating the yeast genome as a library of mono-nucleosomes harbouring the natural epigenetic signature, suitable for biochemical manipulation. Combined with deep sequencing, this library was used to investigate the stability of individual nucleosomes, and – as proof of principle - the nucleosome preference of the chromatin remodeling complex, RSC. In order to generate a library of native yeast nucleosomes, we developed a three-step purification protocol: first, purified yeast nuclei were incubated with micrococcal nuclease (MNase), which preferentially digests naked DNA to generate short chromatin fragments. The resulting fragments were extracted from the nuclei, then bound to and eluted from DEAE sepharose. This was followed by ultracentrifugation through a sucrose gradient to separate the fragments by length to further remove contaminating proteins and free DNA. We chose a simple disassembly assay, which involves incubating the nucleosome library with ATP and the histone chaperone Nap1, with or without RSC. In this assay, RSC binds to nucleosomes and transfers the histones to Nap1, thereby releasing ‘naked’ DNA. Under certain conditions, reaction intermediates can be observed (tetramers or hexasomes), but for simplicity we chose to compare the input nucleosomes with the final naked DNA product. To separate the RSC-dependent released DNA from the non-remodeled nucleosomes, the reactions were subjected to native agarose gel electrophoresis, and DNA of the four bands isolated by gel-extraction. The upper bands, harboring nucleosomes, were named NUC (no RSC) and NUCR (with RSC), whereas the lower, ‘naked’ DNA bands were named DNA (no RSC) and DNAR (with RSC).
2019-05-08 | E-MTAB-7926 | biostudies-arrayexpress
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
Project description:Here we examined whether histones H3 and H4 produced using native chemical ligation reaction affect protein binding to di-nucleosomes. To test this we performed a set of affinity purification pull-downs using di-nucleosomes containing the following histones H3 and H4: 1. unmodified ligated histone H3 and recombinant wild type histone H4 (unmod. H3), 2. recombinant wild type histone H3 and ligated unmodified histone H4 (unmod. H4) 3. ligated unmodified histones H3 and H4 (unmod. H3&H4). 4. recombinant wild type histones H3 and H4 (WT) Each pull-down was performed in three replicates. Co-purified proteins were quantified using label-free MS. Note that ligated histones H3 and H4 contain T32C or I29C single amino acid substitutions, respectively, that are introduced by the native chemical ligation procedure. In addition, ligated histone H4 is N-terminally acetylated to mimic its naturally blocked N-terminus.
2023-12-12 | PXD042390 | Pride
Project description:Nucleosomes are the principal packaging units of chromatin and critical for gene regulation and genome stability. In mammals, a subset of nucleosomes fail to be replaced by protamines during spermatogenesis and are retained in mature spermatozoa providing opportunities for paternal epigenetic transmission. In humans, the remaining 10% localize at regulatory elements of genes. To assess evolutionary conservation and to dissect the molecular logic underlying nucleosome retention, we determined the genome wide nucleosome occupancy in mouse spermatozoa that only contain 1% residual histones. In striking contrast to mammalian somatic cells and haploid round spermatids, we observe high enrichment of nucleosomes at CpG-rich sequences throughout the genome, at conserved regulatory sequences as well as at intra- and intergenic regions and repetitive DNA. This preferred occupancy occurs mutually exclusive with DNA methylation both in mouse and human sperm. At unmethylated CpG-rich sequences, residing nucleosomes are largely composed of the H3.3 histone variant, and trimethylated at lysine 4 (H3K4me3). Both canonical H3.1/H3.2 and H3.3 variant histones are present at promoters marked by Polycomb-mediated H3K27me3, which is strongly predictive for gene repression in pre-implantation embryos. Our data indicate important roles of DNA sequence composition, DNA methylation, variant H3.3 and canonical H3.1/H3.2 histones and associated modifications in nucleosome retention versus eviction during the histone-to-protamine remodeling process in elongating spermatids and potentially in epigenetic inheritance by nucleosomes between generations. Identification of histone, histone variant and histone modification states in round spermatids and sperm
2013-06-15 | E-GEOD-42629 | biostudies-arrayexpress