Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ChIP-Seq]
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE119691 | GEO | 2019/08/01
REPOSITORIES: GEO
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Project description:Dynamic control of the accessibility of the genomic regulatory information is at the heart of stimulus-induced gene expression changes. Whereas chromatin accessibility assays describe dynamic changes in open chromatin over time, they provide only indirect and limited information on the nucleosome remodeling events that underlie such changes. Here, we combined accessibility assays and ChIP-seq on nucleosomes generated by micrococcal nuclease digestion in resting and LPS-activated macrophages. We devised a novel quantitative framework to discriminate different types of nucleosome remodeling events and used it to analyze nucleosome organization at genomic cis-regulatory elements modulated by stimulation on a genomic scale. At typical stimulus-activated enhancers, remodeling events were commonly asymmetric, with only one of the two nucleosomes flanking the central accessible region being remodeled. A systematic analysis of nucleosome organization revealed distinct associations of individual TFs with remodeling and showed that most remodeling events tended to occur early in the response and to be maintained over time, with progressively fewer novel events occurring at later times.
2019-08-01 | GSE119690 | GEO
Project description:Dynamic control of the accessibility of the genomic regulatory information is at the heart of stimulus-induced gene expression changes. Whereas chromatin accessibility assays describe dynamic changes in open chromatin over time, they provide only indirect and limited information on the nucleosome remodeling events that underlie such changes. Here, we combined accessibility assays and ChIP-seq on nucleosomes generated by micrococcal nuclease digestion in resting and LPS-activated macrophages. We devised a novel quantitative framework to discriminate different types of nucleosome remodeling events and used it to analyze nucleosome organization at genomic cis-regulatory elements modulated by stimulation on a genomic scale. At typical stimulus-activated enhancers, remodeling events were commonly asymmetric, with only one of the two nucleosomes flanking the central accessible region being remodeled. A systematic analysis of nucleosome organization revealed distinct associations of individual TFs with remodeling and showed that most remodeling events tended to occur early in the response and to be maintained over time, with progressively fewer novel events occurring at later times.
2019-08-01 | GSE119692 | GEO
Project description:The position of nucleosomes influences DNA accessibility to DNA-binding proteins. Genome-wide nucleosome profiles often report the observation of a canonical nucleosome organization at gene promoters where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. It is unclear how this canonical promoter nucleosome organization forms and how it is related to transcription activation and the establishment of histone marks during development. Here we report the genome-wide organization of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear in thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization cannot be explained by DNA sequence preference, and is independent of transcription and the presence of RNA polymerase II, but strongly correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3). Our study further suggests that promoter nucleosome structure primes genes to future transcription activation. Together, this study reveals that genome activation but not transcription underlies the organization of nucleosome arrays during early embryogenesis. MNase-seq to generate nucleosome organization in two stages of zebrafish development; two biological replicates for each stage. 7 ChIP-seq experiments in three stages.
2013-10-18 | E-GEOD-44269 | biostudies-arrayexpress
Project description:The position of nucleosomes influences DNA accessibility to DNA-binding proteins. Genome-wide nucleosome profiles often report the observation of a canonical nucleosome organization at gene promoters where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. It is unclear how this canonical promoter nucleosome organization forms and how it is related to transcription activation and the establishment of histone marks during development. Here we report the genome-wide organization of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear in thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization cannot be explained by DNA sequence preference, and is independent of transcription and the presence of RNA polymerase II, but strongly correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3). Our study further suggests that promoter nucleosome structure primes genes to future transcription activation. To determine whether the occlusions are consistent in mammalian pluripotent cells, we performed the same analyses in mouse embryonic stem cells and found similar relationships. MNase-seq to generate nucleosome organization in mouse embryonic stem cell (J1)
2013-10-29 | E-GEOD-51766 | biostudies-arrayexpress
Project description:Nucleosomes arrange into extended arrays, much like beads on a string. They are often phased at genomic landmarks and are thought to be evenly spaced. Here we tested to what extent this stereotypic organization describes the nucleosome landscape in Saccharomyces cerevisiae using a long-read nucleosome-sequencing technique called Fiber-Seq. Fiber-Seq maps the nucleosome pattern on individual chromatin fibers. As such, it is ideally suited to measure the density of nucleosomes per read and quantitate the nucleosome occupancy throughout the genome. We document substantial deviations from the stereotypical nucleosome organization, with unexpectedly long linker DNAs between individual nucleosomes, genomic regions lacking entire nucleosomes, heterogeneous phasing of arrays, truly irregular spacing of arrays and read-to-read variation in nucleosome densities. We exploited the technology to test mechanistic models for the biogenesis of nucleosome arrays. We can rule out transcription elongation playing a decisive role in array formation and detect signatures for a clamping activity of remodelers of the ISWI and CHD1 families after acute nucleosome depletion in vivo. Given that nucleosomes are cis-regulatory elements, the cell-to-cell heterogeneity that Fiber-Seq uncovers provides much needed information to understand chromatin structure and function.
2024-01-17 | GSE224713 | GEO
Project description:The yeast Ssn6-Tup1 complex regulates gene expression through a variety of mechanisms, including positioning of nucleosomes over promoters of some target genes to limit accessibility to the transcription machinery. To further define the functions of Ssn6-Tup1 in gene regulation and chromatin remodeling, we performed genome-wide profiling of changes in nucleosome organization and gene expression that occur upon loss of SSN6 or TUP1, and observed extensive nucleosome alterations in both promoters and gene bodies of derepressed genes. Our improved nucleosome profiling and analysis approaches revealed low-occupancy promoter nucleosomes (P nucleosomes) at locations previously defined as nucleosome-free regions. In the absence of SSN6 or TUP1, this P nucleosome is frequently lost, whereas nucleosomes are gained at -1 and +1 positions, accompanying up-regulation of downstream genes. Our analysis of public ChIP-seq data revealed that Ssn6 and Tup1 preferentially bind TATA-containing promoters, which are also enriched in genes derepressed upon loss of SSN6 or TUP1. These results suggest that stabilization of the P nucleosome on TATA-containing promoters may be a central feature of the repressive chromatin architecture created by the Ssn6-Tup1 corepressor, and that releasing the P nucleosome contributes to gene activation. Genome-wide expression profiling Yeast gene expression in three cell type, Each cell type is tested in duplicate.
2012-10-10 | E-GEOD-37466 | biostudies-arrayexpress
Project description:The yeast Ssn6-Tup1 complex regulates gene expression through a variety of mechanisms, including positioning of nucleosomes over promoters of some target genes to limit accessibility to the transcription machinery. To further define the functions of Ssn6-Tup1 in gene regulation and chromatin remodeling, we performed genome-wide profiling of changes in nucleosome organization and gene expression that occur upon loss of SSN6 or TUP1, and observed extensive nucleosome alterations in both promoters and gene bodies of derepressed genes. Our improved nucleosome profiling and analysis approaches revealed low-occupancy promoter nucleosomes (P nucleosomes) at locations previously defined as nucleosome-free regions. In the absence of SSN6 or TUP1, this P nucleosome is frequently lost, whereas nucleosomes are gained at -1 and +1 positions, accompanying up-regulation of downstream genes. Our analysis of public ChIP-seq data revealed that Ssn6 and Tup1 preferentially bind TATA-containing promoters, which are also enriched in genes derepressed upon loss of SSN6 or TUP1. These results suggest that stabilization of the P nucleosome on TATA-containing promoters may be a central feature of the repressive chromatin architecture created by the Ssn6-Tup1 corepressor, and that releasing the P nucleosome contributes to gene activation. nucleosomes were prepared from isogenic wild type (BY4742), ssn6 KO and tup1 KO cells after varying degrees of micrococcal nuclease (MNase) digestion, followed by isolation of mononucleosomal DNA and sequencing. Three replicates of each strain (9 samples) were subjected to Illumina sequencing.
2012-10-10 | E-GEOD-37465 | biostudies-arrayexpress
Project description:Chromatin accessibility plays a fundamental role in gene regulation. One mechanism to regulate accessibility is nucleosome placement, which is often measured by quantifying protection of DNA from enzymatic digestion. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC, quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both location of nucleosomes and accessibility to MNase in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares behavior of nucleosomes to that of non-histone proteins. We find that enhancers, promoters and other regulatory regions have changes in accessibility that do not correlate with changes in nucleosome occupancy. Moreover, we show that high nucleosome occupancy does not necessarily preclude high accessibility, revealing novel principles of chromatin regulation.
2016-04-18 | GSE78984 | GEO
Project description:Javasky E, Shamir I, Gandhi S, Egri S, Sandler O, Rothbart SB, Kaplan N, Jaffe JD, Goren A, and Simon I. Genome Research 2018. Mitosis encompasses key molecular changes including chromatin condensation, nuclear envelope breakdown and reduced transcription levels. Immediately after mitosis, the interphase chromatin structure is reestablished and transcription resumes. The reestablishment of the interphase chromatin requires bookmarking, i.e., the retention of at least partial information during mitosis. Yet, while recent studies demonstrate that chromatin accessibility is generally preserved during mitosis and is only locally modulated, the exact details of the bookmarking process and its components are still unclear. To gain a deeper understanding of the mitotic bookmarking process, we merged proteomics, immunofluorescence, and ChIP-seq approaches to study the mitotic and interphase organization in human cells. We focused on key histone modifications, and employed the HeLa-S3 cells as a model system. Generally, we observed a global concordance between the genomic organization of histone modifications in interphase and mitosis, yet the abundance of the two types of modifications we investigated was different. Whereas histone methylation patterns remain highly similar, histone acetylation patterns show a general reduction while maintaining their genomic organization. In line with a recent study demonstrating that minimal transcription is retained during mitosis, we show that RNA polymerase II does not fully disassociate from the genome, but rather maintains its genomic localization at reduced levels. Next, we followed up on previous studies demonstrating that nucleosome depleted regions (NDRs) become occupied by a nucleosome during mitosis. Surprisingly, we observed that the nucleosome introduced into the NDR during mitosis encompasses a distinctive set of histone modifications, differentiating it from the surrounding nucleosomes. We show that the nucleosomes in the vicinity of the NDR appear to both shift into the NDR during mitosis and undergo deacetylation. HDAC inhibition by the small molecule TSA reverts the deacetylation pattern of the shifted nucleosome. Taken together, our results demonstrate that the epigenomic landscape can serve as a major component of the mitotic bookmarking process, and provide evidence for a mitotic deposition and deacetylation of the nucleosomes surrounding the NDR.
2018-08-14 | MSV000082818 | MassIVE
Project description:ATP-dependent chromatin remodeling enzymes re-position and evict nucleosomes at specific genomic loci and therefore are essential regulators of all DNA dependent processes. They act in the context of large multiprotein complexes. The malaria-causing parasite Plasmodium falciparum (Pf) possesses a reduced set of chromatin remodeling enzymes, which are highly divergent, and no associated complex subunits are known. Within a detailed characterization of the ISWI-type remodeler PfSnf2L (PF3D7_1104200), potential interactors were identified. The protein was tagged endogenously in the parasite and co-immunoprecipitated. Subsequent LC-MS/MS analysis provided a list of specific protein interactors with a strong link to chromatin organization including nucleosome assembly factors, transcription factors as well as Plasmodium-specific uncharacterized proteins. The results suggest a functional role of PfSnf2L in nucleosome assembly and transcription regulation and point towards novel Plasmodium-specific chromatin remodeling complexes.
2024-10-17 | PXD041155 | Pride