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

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

PROVIDER: PRJNA1089636 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28389703.fastq.gz	Fastqsanger.gz
	SRR28389704.fastq.gz	Fastqsanger.gz
	SRR28389705.fastq.gz	Fastqsanger.gz
	SRR28389706.fastq.gz	Fastqsanger.gz
	SRR28389707.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)

Project description: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)

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

Mapping the micro-proteome of the nuclear lamina and lamin associated domains

Project description:The nuclear lamina is a proteinaceous network of filaments that provide both structural and gene regulatory functions by tethering proteins and large domains of DNA, so-called lamin associated domains (LADs), to the periphery of the nucleus. LADs are a large fraction of the mammalian genome that are repressed, in part, by their association to the nuclear periphery. The genesis and maintenance of LADs is poorly understood as are the proteins that participate in these functions. In an effort to identify proteins that reside at the nuclear periphery and potentially interact with LADs, we have taken a two-pronged approach. First, we have undertaken an interactome analysis of the inner nuclear membrane bound LAP2β to further characterize the nuclear lamina proteome. To accomplish this, we have leveraged the BioID system, which previously has been successfully used to characterize the nuclear lamina proteome. Second, we have established a system to identify proteins that bind to LADs by developing a chromatin directed BioID system. We combined the BioID system with the m6A-tracer system which binds to LADs in live cells to identify LAD proximal and nuclear lamina proteins. In combining these datasets, we have further characterized the protein network at the nuclear lamina as well as identified putative LAD proximal proteins. Our analysis identifies many heterochromatin related proteins related to H3K9 methylation processes as well as many proteins related to cell cycle regulation identifying important proteins essential for LAD function.

2021-03-09 | PXD012943 | Pride

Gene regulatory loops at lamina-associated domains

Project description:Gene regulatory loops at lamina-associated domains

| PRJNA913836 | ENA

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

| PRJNA1089502 | ENA

Chromatin protein complexes involved in gene repression in lamina-associated domains.

Project description:Lamina-associated domains (LADs) are large chromatin regions that are associated with the nuclear lamina (NL) and form a repressive environment for transcription. The molecular players that mediate gene repression in LADs are currently unknown. Here, we performed FACS-based whole-genome genetic screens in human cells using LAD-integrated fluorescent reporters to identify such regulators. Surprisingly, the screen identified very few NL proteins, but revealed roles for dozens of known chromatin regulators. Among these are the negative elongation factor (NELF) complex and interacting factors involved in RNA polymerase pausing, suggesting that regulation of transcription elongation is 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 by rewiring heterochromatin. Our data indicate that the fundamental regulators of transcription and chromatin remodeling, rather than interaction with NL proteins, play a major role in transcription regulation within LADs.

| S-EPMC11535540 | biostudies-literature

DNA Adenine Methyltransferase Identification (DamID) Coupled to Next Generation Sequencing For Profiling Lamina Associated Domains

Project description:Purpose: To compare the interaction of various proteins (in particular Lap2b and Lamin A) at the nuclear periphery with the Lamina Associated Domains (LADs) Results: Using an optimized data analysis workflow (LADetector, available at https://github.com/thereddylab/LADetector), We found near identical sequences within the genome-wide maps indicating that LAP2β and Lamin A, and hence LaminB1, are in close proximity to all LADs, suggesting that these proteins are not involved in discriminating subsets of LADs.

2019-11-01 | GSE128239 | GEO

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

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