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ABSTRACT: Identification of Chromatin proteins involved in gene repression in lamina-associated domains

PROVIDER: PRJNA1089502 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28385513.fastq.gz	Fastqsanger.gz
	SRR28385514.fastq.gz	Fastqsanger.gz
	SRR28385515.fastq.gz	Fastqsanger.gz
	SRR28385516.fastq.gz	Fastqsanger.gz
	SRR28385517.fastq.gz	Fastqsanger.gz

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Identification of Chromatin proteins involved in gene repression in lamina-associated domains

Project description:Identification of Chromatin proteins involved in gene repression in lamina-associated domains

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Identification of Chromatin proteins involved in gene repression in lamina-associated domains (pA-DamID)

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Identification of Chromatin proteins involved in gene repression in lamina-associated domains (RNA-Seq)

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Project description:Chromatin protein complexes involved in gene repression in lamina-associated domains

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A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq]

Project description:A large fraction of the mammalian genome is organized into inactive chromosomal domains associated with the nuclear lamina. Using genomic repositioning assays we show that Lamina associated domains (LADs), spanning the developmentally regulated IgH and Cyp3a loci, contain transportable DNA regions that associate chromatin with the nuclear lamina and repress gene activity in fibroblasts. We characterized DNA regions within LADs that are functionally capable of positioning chromatin domains at the inner nuclear membrane (INM) lamina. We mapped and characterized the IgH and other LADs in murine fibroblasts. We show that these murine LADs have a unique chromatin structure with discrete boundaries. We demonstrate DNA regions within LADs that are capable of directing the association of chromatin domains with the INM-lamina as well as the silencing of a co-integrated reporter gene.

2012-02-24 | E-GEOD-36048 | biostudies-arrayexpress

Project description:Promoter-intrinsic and local chromatin features determine gene repression in lamina-associated domains

| PRJNA504533 | ENA

A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq]

2012-02-24 | GSE36048 | GEO

Identification of Chromatin proteins involved in gene repression in lamina-associated domains (RNA-Seq)

Project description:Lamina-associated domains (LADs) are large chromatin regions that are associated with the nuclear lamina and form a repressive environment for transcription. The molecular players that mediate gene repression in LADs are currently unknown. Here we performed a full-genome genetic screen in human cells using LAD-integrated fluorescent reporters to identify such regulators. Surprisingly, the screen identified very few lamina proteins, but revealed roles for dozens of known chromatin regulators. Among these are the negative elongation factor (NELF) complex and interacting factors, suggesting that regulation of RNA polymerase pausing can be a mechanism to repress transcription in LADs. Furthermore, the chromatin remodeler complex BAF and the activation complex Mediator can work both as activators and repressors in LADs, depending on the local context and possibly rewiring of heterochromatin. Our data suggest that fundamental regulatory steps of the transcription process and chromatin remodeling, rather than interaction with NL proteins, have a major role in the regulation of transcription in LADs.

2024-07-10 | GSE261953 | GEO

Identification of Chromatin proteins involved in gene repression in lamina-associated domains (pA-DamID)

2024-07-10 | GSE261868 | GEO

Spatially restricted position-dependent implications of lamin A promoter occupancy on gene activity (expression)

Project description:Interactions between the nuclear lamina (NL) and chromatin are thought to occur through large lamin association domains (LADs) and correlate with gene repression in these domains. We show that binding of lamin A/C (LMNA) to promoters occurs on discrete domains that are associated with distinct transcriptional outputs. Chromatin immunoprecipitation identifies thousands of LMNA-bound promoters, primarily linked to signaling functions. LMNA often occupies narrow domains on promoters, yet LMNA-bound promoters are often contiguous. LMNA-bound genes are overall repressed, but repression correlates with co-enrichment in repressive histone marks rather than LMNA occupancy per se. Genes marked by LMNA and H3K4me3 escape LMNA-associated repression in the absence of repressive histone marks. Positioning of LMNA on promoters relative to the TSS correlates with distinct transcriptional outputs: whereas upstream-distal binding can be transcriptionally permissive, TSS occupancy is associated with promoter inactivity. Perturbation in NL organization causes reorganization of lamin promoter occupancy and uncouples LMNA binding from promoter inactivity. Our results show the existence of many spatially restricted LMNA binding events on promoter regions, with distinct position-dependent transcriptional outputs. Total RNA obtained from ASCs and ASCs depleted of LMNA (LMNA-KD) and processed for microarray hybridization.

2013-07-14 | E-GEOD-42523 | biostudies-arrayexpress

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