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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages

ABSTRACT: Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages

PROVIDER: PRJNA490018 | ENA |

REPOSITORIES: ENA

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ChIP-Seq]

Project description:Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ChIP-Seq]

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ATAC-Seq]

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ChIP-Seq]

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 | GSE119691 | GEO

Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ATAC-Seq]

2019-08-01 | GSE119690 | GEO

Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [chromatin-associated RNA-Seq]

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [chromatin-associated RNA-Seq]

Project description:Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [chromatin-associated RNA-Seq]

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages

Project description:This SuperSeries is composed of the SubSeries listed below.

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Msn2-mediated nucleosome remodeling dynamics

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S.cerevisiae INO80 is required for promoter proximal nucleosome remodeling.

Project description:During transcription, nucleosomes are evicted from regulatory and coding regions yet chromatin structure is stable. Restoration of chromatin structure involves concerted action of chromatin modifying activities. Our analysis demonstrates a genome wide function of the INO80 remodeling complex for stable repositioning of the nucleosome immediately proximal to the transcription initiation site. INO80 dependent remodeling of the promoter proximal nucleosomes has a global repressive role. Recruitment of INO80 to proximal nucleosomes overlaps with the elongating Polymerase II complex assembly. The amount of associated Polymerase II at start sites correlates with INO80 recruitment for inducible and constantly transcribed genes. Furthermore, at highly inducible promoters INO80 is required for repression of bidirectional transcription. Therefore, we suggest a function for INO80 after transcription initiation to achieve Polymerase II dependent reassembly of promoter proximal nucleosomes.

2016-12-24 | E-MTAB-1810 | biostudies-arrayexpress

Replication-coupled nucleosome assembly and positioning by ATP-dependent chromatin remodeling enzymes

Project description:We have previously shown that Okazaki fragments in Saccharomyces cerevisiae are sized according to the chromatin repeat. Here we demonstrate that nucleosome positioning is rapidly established on newly synthesized DNA. Using deep sequencing, we demonstrate that ATP-dependent chromatin remodeling enzymes, Isw1 and Chd1, collaborate with histone chaperones, such as CAF-1 and Rtt106, to remodel nucleosomes, as they are loaded. Importantly, we find that nucleosome positioning is ultimately specified by select sequence-specific DNA-binding factors, which serve as physical cues for chromatin remodeling. Our results provide a mechanistic understanding of how chromatin structures are replicated in vivo, and show that chromatin structure at gene promoters is rapidly established after DNA replication. Altogether, our data provide evidence for coordinated âloading and remodelingâ of nucleosomes behind the replication fork, in collaboration with packing of nucleosomes against a barrier. 7 samples, including a wild type, are included. All are single-end sequenced via Ion Torrent PGM methodology.

2016-04-14 | E-GEOD-63583 | biostudies-arrayexpress

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