Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE72690 | GEO | 2016/08/01
SECONDARY ACCESSION(S): PRJNA294665
REPOSITORIES: GEO
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Project description:By analysis of ChIP-exo of FOXA1 in LNCaP, we find that an astonishing genome-wide "well-positioned" configuration prevalently occurs between FOXA1 motif and the dyad of nucleosome. Here we performed ChIP-seq data of eight chromatin remodelers and found a higher occupancy of these remodelers on these well-positioned FOXA1 motif sites. Together, our results support a positional-nucleosome-oriented accessing model, in which FOXA1 can examine each underlying DNA nucleotide and be able to sense all potential motifs regardless if they face inward or outward to histone octamers along the DNA helix axis. We have performed ChIP-seq of eight chromatin remodeler factors.
2016-08-01 | E-GEOD-72690 | biostudies-arrayexpress
Project description:Nucleosome arrays begin at nucleosome-free promoter regions (NFRs) and regulate gene expression. Reconstituting such organization throughout a genome with purified proteins is a critical challenge in establishing biochemical mechanisms for chromosome assembly. Here we establish a four-step hierarchical building plan for yeast genomic nucleosome organization using only purified components: genomic DNA, histones, site-specific organizing factors Abf1 and Reb1, and the chromatin remodelers RSC, ISW2, INO80, and ISW1a. First, RSC makes NFRs by translating promoter poly(dA:dT) tracts into directional nucleosome removal. Second, +1 nucleosomes are positioned by INO80 at most genes potentially involving DNA shape, or by ISW2 using gene-specific Abf1 and Reb1. Third, INO80 or ISW2 create arrays with wide spacing. Fourth, ISW1a tightens the spacing and creates properly positioned arrays. We conclude that entire genomes use a simple set of rules and proteins, without transcription, to build a common chromatin architecture. In this study, nucleosomes were assembled using Salt Gradient Dialysis (SGD) on yeast genomic DNA library. Assembled nucleosomes were either left untreated (labelled as "SGD", control), treated with whole cell extract (WCE), mutant extracts (rsc3ts WCE, isw1 isw2 chd1 WCE), purified remodelers; singly or in combinations (RSC, ISW1a, ISW1b, ISW2, INO80, CHD1, SWI/SNF), combinations of mutant extracts and chromatin remodelers or combination of General Regulatory Factors (Abf1, Reb1) and chromatin remodelers. The resulting nucleosome positions were mapped genome-wide using MNase-(anti-H3-ChIP)-Seq.
2016-08-14 | E-GEOD-72106 | biostudies-arrayexpress
Project description:Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. The Chd1 remodeler specializes in shifting nucleosomes into evenly spaced arrays, a defining characteristic of chromatin in gene bodies that blocks spurious transcription initiation. Linked to some forms of autism and commonly mutated in prostate cancer, Chd1 is essential for maintaining pluripotency in stem cells. Here we report a complex of yeast Chd1 bound to a nucleosome in a nucleotide-free state, determined by cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. The structure shows a bulge of the DNA tracking strand where the ATPase motor engages the nucleosome, consistent with an initial stage in DNA translocation. Unlike other remodeler-nucleosome complexes, nucleosomal DNA compensates for the remodeler-induced bulge with a bulge of the complementary DNA strand one helical turn downstream from the ATPase motor. Unexpectedly, the structure also reveals an N-terminal binding motif, called ChEx, which binds on the exit-side acidic patch of the nucleosome. The ChEx motif can displace a LANA-based peptide from the acidic patch, which suggests a means by which Chd1 remodelers may block competing chromatin remodelers from acting on the opposite side of the nucleosome.
2022-02-23 | PXD025287 | Pride
Project description:We assessed the interplay between DNA sequences and ATP-dependent chromatin remodelers in defining the nucleosomal organization of the eukaryotic genome. We compared the genome-wide distribution and impact on chromatin of NURD, (P)BAP, INO80 and ISWI representing four major families of Drosophila remodelers. Each remodeler has a unique set of genomic targets, and generates distinct chromatin signatures. Remodeler loci have characteristic DNA sequence features, predicted to influence nucleosome formation. Strikingly, remodelers counteract DNA sequence-driven nucleosome distribution in two ways: NURD, (P)BAP and INO80 increase histone density at their target sequences, which disfavor positioned nucleosome formation. In contrast, ISWI promotes open chromatin at sites that are propitious for precise nucleosome placement. Thus, both selective targeting and distinct mechanisms of remodeling underlie the functional differentiation of remodelers. We conclude that chromatin organization involves a class-specific antagonism between remodeler activity and DNA sequence-driven nucleosome placement. The supplementary bed files (P)BAP_sites.bed, NURD_sites.bed, INO80_sites.bed, ISWI_sites.bed contain high quality binding sites for each remodeler obtained by intersecting the sets of significant ChIP-chip peaks for each antibody.
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Project description:Eukaryotic DNA is wrapped around histone octamers to form nucleosomes, which are separated by linker DNA bound by histone H1. In many species, the DNA exhibits methylation of CG dinucleotides, which is epigenetically inherited via a semiconservative mechanism. How methyltransferases access DNA within nucleosomes remains mysterious. Here we show that methylation of nucleosomes requires DDM1/Lsh nucleosome remodelers in Arabidopsis thaliana and mouse. We also show that removal of histone H1, which partially restores methylation in ddm1 mutants, does so primarily in the linker DNA between nucleosomes. In h1ddm1 compound mutants, substantial portions of the genome exhibit dramatically periodic methylation that approaches wild-type levels in linker DNA but is virtually absent in nucleosomes. We also present evidence that de novo methylation supplements semiconservative maintenance of CG methylation across generations. Overall, our results demonstrate that nucleosomes and H1 are barriers to DNA methylation, which are overcome by DDM1/Lsh nucleosome remodelers.
2017-11-15 | GSE96994 | GEO
Project description:Histone octamers are thought to be a rigid part of nucleosomes that shape chromatin and block cellular machinery from accessing DNA. ATP-dependent chromatin remodelers like ISW2 mobilize nucleosomes to provide DNA access. We find evidence for histone octamer distortion preceding DNA being moved into nucleosomes and processive movement of the ATPase motor of ISW2 on nucleosomal DNA. DNA entering nucleosome is uncoupled from the ATPase activity of ISW2 and alterations of the histone octamer structure mediated by ISW2 by deletion of the SANT domain from the C-terminus of the Isw2 catalytic subunit. We also find that restricting histone movement by chemical crosslinking traps remodeling intermediates resembling those seen by loss of the SANT domain, further supporting the importance of changes in histone octamer structure early in ISW2 remodeling. Transient octamer distortions are stabilized by H3-H4 tetramer disulfide crosslinking, thereby linking intrinsic histone octamer flexibility to chromatin remodeling.
2020-05-27 | PXD013967 | Pride
Project description:The positioning of the nucleosome by ATP-dependent nucleosome remodelers provides the fundamental chromatin environment for the regulation of diverse cellular processes acting on the underlying DNA. Here, we report that the fission yeast CHD remodeler, Hrp3, is a global regulator that drives higher-order chromatin structure and genomic stability. The loss of Hrp3 resulted in the production of antisense transcripts and perturbation of the nucleosome in an ATPase mutant of Hrp3 was also associated with destabilization of the DNA-histone interaction. Furthermore, the effect of Hrp3 in the pericentric region was found to be accomplished via a physical interaction with Swi6, and appeared to cooperate with other heterochromatin factors for gene silencing. Taken together, our data indicate that a well-positioned nucleosome is important for the spatial-temporal control of transcription-associated processes, and show that this is accomplished by the chromatin remodeler, Hrp3, in fission yeast. Two-condition experiment, Mutant vs Wild-type (control)
2012-05-07 | E-GEOD-37697 | biostudies-arrayexpress
Project description:Knowing the exact positions of nucleosomes not only advances our understanding of their role in gene regulation, but also the mechanisms that underlie between-species variation in chromatin structure. We have generated a chemical map of nucleosomes in vivo in Schizosaccharomyces pombe at base pair resolution. This new map reveals that S.pombe genome shares a similar periodic linker length distribution with Saccharomyces cerevisiae, but with major distinctions in nucleosomal/linker DNA sequence features. In S.pombe, A/T rich sequences are enriched in the nucleosome core region, particularly +/-20 bp of dyad, while they are disfavored in S.cerevisiae nucleosomes. The poly (dA-dT) tracts only slightly affect the nucleosome occupancy in S.pombe; and they possess preferential rotational positions within the nucleosome core with significant enrichment in the 10-30 bp region from the dyad for longer tracts. S.pombe does not have well-defined nucleosome free region immediately upstream of most transcription start sites (TSS), instead the -1 nucleosome is positioned with regular distance to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. The nucleosomes around TSS show more pronounced bidirectional phasing when the intergenic distance is relatively short, and the downstream nucleosome positioning is strongly correlated with DNA sequence features. We discovered that heterochromatin regions tend to have sparse nucleosome positioning, mixed with both well-positioned and fuzzy nucleosomes. The S.pombe map suggests that some of nucleosome positioning codes, formerly thought to be intrinsic, may largely depend on species-specific extrinsic factors including linker histone, chromatin remodelers and other DNA-binding proteins. 2 samples were analyzed with high throughput paired-end parallel sequencing. Both samples were created using the same chemical mapping protocol
2013-11-12 | E-GEOD-46975 | biostudies-arrayexpress
Project description:Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. Remodelers are also enriched in the bodies of genes displaying high nucleosome turnover. We hypothesize that remodelers bind but do not act at 5' NDRs, remaining in physical proximity to gene bodies, where they act on regions of transient nucleosome depletion following transcriptional elongation. We have analyzed the dynamics of yeast ISWI and CHD chromatin remodeler genomic association at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).
2013-03-01 | E-GEOD-39430 | biostudies-arrayexpress
Project description:Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. Remodelers are also enriched in the bodies of genes displaying high nucleosome turnover. We hypothesize that remodelers bind but do not act at 5' NDRs, remaining in physical proximity to gene bodies, where they act on regions of transient nucleosome depletion following transcriptional elongation. We have analyzed the dynamics of yeast ISWI and CHD chromatin remodeler genomic association at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).
2013-03-01 | E-GEOD-39431 | biostudies-arrayexpress