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Genome-nuclear lamina interactions regulate progenitor cell behavior during cardiac development

ABSTRACT: Genome-nuclear lamina interactions regulate progenitor cell behavior during cardiac development

PROVIDER: PRJNA270253 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1709270.fastq.gz	Fastqsanger.gz
	SRR1709271.fastq.gz	Fastqsanger.gz
	SRR1709272_1.fastq.gz	Fastqsanger.gz
	SRR1709272_2.fastq.gz	Fastqsanger.gz
	SRR1709263.fastq.gz	Fastqsanger.gz

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Genome-nuclear lamina interactions regulate progenitor cell behavior during cardiac development

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

2018-10-10 | GSE64149 | GEO

Genome-nuclear lamina interactions in the heart at embryonic days E9.5 and E12.5

Project description:Lamin B1 ChIP-seq analysis of microdissected whole hearts from E9.5 and E12.5 CD1 embryos. Results provide insight into in vivo genome-nuclear lamina interactions over the course of embryonic development. Progenitor cells require coordinated expression of lineage-specific genes to regulate differentiation into daughter cell types. Epigenetic regulators are ideally positioned to synchronize transcription of disparate genomic loci. Using cardiac development to model progenitor cell behavior, we map genome- lamina interactions in vivo to reveal dynamic changes during cardiac development and propose that Hdac3 mediates chromatin organization and gene positioning in cardiac progenitors to regulate fate decisions.

2018-12-01 | GSE64148 | GEO

Genome-Nuclear Lamina Interactions Regulate Cardiac Stem Cell Lineage Restriction.

Project description:Progenitor cells differentiate into specialized cell types through coordinated expression of lineage-specific genes and modification of complex chromatin configurations. We demonstrate that a histone deacetylase (Hdac3) organizes heterochromatin at the nuclear lamina during cardiac progenitor lineage restriction. Specification of cardiomyocytes is associated with reorganization of peripheral heterochromatin, and independent of deacetylase activity, Hdac3 tethers peripheral heterochromatin containing lineage-relevant genes to the nuclear lamina. Deletion of Hdac3 in cardiac progenitor cells releases genomic regions from the nuclear periphery, leading to precocious cardiac gene expression and differentiation into cardiomyocytes; in contrast, restricting Hdac3 to the nuclear periphery rescues myogenesis in progenitors otherwise lacking Hdac3. Our results suggest that availability of genomic regions for activation by lineage-specific factors is regulated in part through dynamic chromatin-nuclear lamina interactions and that competence of a progenitor cell to respond to differentiation signals may depend upon coordinated movement of responding gene loci away from the nuclear periphery.

| S-EPMC5683101 | biostudies-literature

Genome-nuclear lamina interactions regulate progenitor cell lineage restriction during cardiogenesis

Project description:Genome-nuclear lamina interactions regulate progenitor cell lineage restriction during cardiogenesis

| PRJNA383129 | ENA

Evolutionary conservation of nuclear lamina-genome interactions

Project description:Regulation of gene expression is highly conserved between vertebrates, yet the genomic binding patterns of transcription factors are poorly conserved, suggesting that other mechanisms may contribute. The spatial organization of chromosomes in the nucleus is known to affect gene activity, but it is unclear to what extent this organization is conserved in evolution. Genome-wide maps of nuclear lamina (NL) interactions show that human and mouse chromosomes have highly similar folding patterns inside the nucleus. Breaks in synteny are often located at transition points between NL interacting and intra-nuclear regions. Data were compared against data from Peric-Hupkes, Meuleman et al. (Molecular Cell, 2010). LaminB1-chromatin interactions were assayed in human ESCs and human HT1080 cells. LaminA-chromatin interactions were assayed in human HT1080 cells. For the all samples there were 2 biological replicates, that were hybridized in a dye-swap design.

2012-10-10 | E-GEOD-22428 | biostudies-arrayexpress

Reorganization of nuclear lamina – genome interactions upon differentiation of embryonic stem cells.

Project description:The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. We present a genome-wide analysis of the interactions between chromatin and the nuclear lamina during differentiation of mouse embryonic stem cells (ESCs) into lineage-committed neural precursor cells (NPCs) and terminally differentiated astrocytes. Chromatin in each of these cell types shows a similar organization into large lamina associated domains (LADs), which represent a transcriptionally repressive environment. During sequential differentiation steps, lamina interactions are progressively modified at hundreds of genomic locations. This remodeling is typically confined to individual transcription units and involves many genes that determine cellular identity. From ESCs to NPCs, the majority of genes that move away from the lamina are concomitantly activated. Strikingly, a significant amount remain inactive yet become primed for activation by further differentiation. These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation. laminB1-chromatin interactions were assayed in 4 different mouse cell-types. For each cell-type there were 2 biological replicates, that were hybridized in a dye-swap design.

2010-05-27 | E-GEOD-17051 | biostudies-arrayexpress

Genome-nuclear lamina interactions regulate progenitor cell lineage restriction during cardiogenesis

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

2017-10-12 | GSE97878 | GEO

Effects of transcription on genome - nuclear lamina interactions: RNA-seq data

Project description:In mammalian nuclei, transcriptionally active genomic regions tend to localize to the interior of the nucleus while inactive regions are often located at at the nuclear lamina. In this study we activated specific genes in lamina-associated domains by TALE-VP64 or CRISPRa-mediated activation. We also reduced transcription of individual genes by knockout of promoter/enhancer regions, or by insertion of a transcription termination sequence. In each case we generated genome-wide DamID maps to determine changes in nuclear lamina interactions, and in selected cases we also generated Repli-seq maps and/or RNAseq data.

2019-06-28 | GSE133273 | GEO