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Local euchromatin enrichment in lamina-associated domains anticipates their re-positioning in the adipogenic lineage

ABSTRACT: Local euchromatin enrichment in lamina-associated domains anticipates their re-positioning in the adipogenic lineage

PROVIDER: PRJNA767578 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16127000.fastq.gz	Fastqsanger.gz
	SRR16127001.fastq.gz	Fastqsanger.gz
	SRR16127002.fastq.gz	Fastqsanger.gz
	SRR16127003.fastq.gz	Fastqsanger.gz
	SRR16127004.fastq.gz	Fastqsanger.gz

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Local euchromatin enrichment in lamina-associated domains anticipates their re-positioning in the adipogenic lineage

Project description:Interactions of chromatin with the nuclear lamina via lamina-associated domains (LADs) confers structural stability to the genome. The dynamics of positioning of LADs during differentiation, and how LADs impinge on developmental gene expression, remains elusive, however. We examined changes in the association of lamin B1 with the genome in the first 72 hours of differentiation of adipose stem cells into adipocytes. We demonstrate a repositioning of entire stand-alone LADs and of LAD edges as a prominent nuclear structural feature of early adipogenesis. Whereas adipogenic genes are released from LADs, LADs sequester downregulated or repressed genes irrelevant for the adipose lineage. However, LAD repositioning only partly concurs with gene expression changes. Differentially expressed genes in LADs, including LADs conserved throughout differentiation, reside in local euchromatic and lamin-depleted sub-domains. In these sub-domains, pre-differentiation histone modification profiles correlate with the LAD versus inter-LAD outcome of these genes during adipogenic commitment. In addition, differentially expressed genes in LADs are linked to short-range enhancers which overall co-partition with these genes in LADs versus inter-LADs during differentiation. We conclude that LADs are predictable structural features of adipose nuclear architecture that restrain non-adipogenic genes in a repressive environment.

2022-03-21 | GSE185066 | GEO

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha [gene expression]

Project description:Lamins are components of the peripheral nuclear lamina and interact with heterochromatic genomic regions, termed lamina-associated domains (LADs). In contrast to lamin B1, lamin A/C also localizes throughout the nucleus, where it associates with the chromatin-binding protein lamina-associated polypeptide (LAP) 2alpha. Here we show lamin A/C also interacts with euchromatin, as determined by chromatin immunoprecipitation analyses of eu- and heterochromatin-enriched samples. By way of contrast, lamin B1 was only found associated with heterochromatin. Euchromatic regions occupied by lamin A/C overlap with those bound by LAP2alpha, the depletion of which shifts binding of lamin A/C towards more heterochromatic regions. These alterations in lamin A/C chromatin interaction affect epigenetic histone marks in euchromatin without significantly affecting gene expression, while loss of lamin A/C in heterochromatic regions increased gene expression. Our data show a novel role of nucleoplasmic lamin A/C and LAP2alpha in regulating euchromatin. Examination of LaminA, LaminB and Lap2a DNA binding in Lap2alpha +/+ and Lap2a -/- cells and according changes in Histone modifications and gene expression

2016-01-19 | E-GEOD-70148 | biostudies-arrayexpress

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha [ChIP-Seq]

Project description:Lamins are components of the peripheral nuclear lamina and interact with heterochromatic genomic regions, termed lamina-associated domains (LADs). In contrast to Lamin B11, lamin A/C also localizes throughout the nucleus, where it associates with the chromatin-binding protein lamina-associated polypeptide (LAP) 2alpha. Here we show lamin A/C also interacts with euchromatin, as determined by chromatin immunoprecipitation analyses of eu- and heterochromatin-enriched samples. By way of contrast, Lamin B11 was only found associated with heterochromatin. Euchromatic regions occupied by lamin A/C overlap with those bound by LAP2alpha, the depletion of which shifts binding of lamin A/C towards more heterochromatic regions. These alterations in lamin A/C chromatin interaction affect epigenetic histone marks in euchromatin without significantly affecting gene expression, while loss of lamin A/C in heterochromatic regions increased gene expression. Our data show a novel role of nucleoplasmic lamin A/C and LAP2alpha in regulating euchromatin. Examination of Lamin A/C, Lamin B1 and Lap2a DNA binding in Lap2alpha +/+ and Lap2a -/- cells and according changes in Histone modifications and gene expression

2016-01-19 | E-GEOD-70147 | biostudies-arrayexpress

lamina joint positioning and differentiation

Project description:Oryza sativa LIGULELESS 2s determine lamina joint positioning and differentiation by inhibiting auxin signaling

| PRJEB40447 | ENA

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha [gene expression]

2016-01-19 | GSE70148 | GEO

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha [ChIP-Seq]

Project description:Lamins are components of the peripheral nuclear lamina and interact with heterochromatic genomic regions, termed lamina-associated domains (LADs). In contrast to Lamin B11, lamin A/C also localizes throughout the nucleus, where it associates with the chromatin-binding protein lamina-associated polypeptide (LAP) 2alpha. Here we show lamin A/C also interacts with euchromatin, as determined by chromatin immunoprecipitation analyses of eu- and heterochromatin-enriched samples. By way of contrast, Lamin B11 was only found associated with heterochromatin. Euchromatic regions occupied by lamin A/C overlap with those bound by LAP2alpha, the depletion of which shifts binding of lamin A/C towards more heterochromatic regions. These alterations in lamin A/C chromatin interaction affect epigenetic histone marks in euchromatin without significantly affecting gene expression, while loss of lamin A/C in heterochromatic regions increased gene expression. Our data show a novel role of nucleoplasmic lamin A/C and LAP2alpha in regulating euchromatin.

2016-01-19 | GSE70147 | GEO

Role of Prdm16 in fibro-adipogenic progenitors

Project description:Here, we identified Prdm16 as a FAPs-enriched factor that mediates their developmental capacities by modulating H3K9me2-marked heterochromatin organization at the nuclear lamina. We show that deletion of Prdm16 prevents FAPs adipogenic differentiation and unlocks a myogenic capacity. We found that Prdm16 localizes at the nuclear lamina where it cooperates with the H3K9 methyltransferases (KMTs), G9a and GLP, to mediate H3K9me2 deposition.

2021-06-02 | GSE148432 | GEO

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha

Project description:A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha

| PRJNA287718 | ENA

lamina joint initiation in rice

Project description:Oryza sativa LIGULELESS 2s determine lamina joint positioning and differentiation by inhibiting auxin signaling

| PRJEB40431 | ENA

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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