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

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

PROVIDER: PRJNA551545 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9600780.fastq.gz	Fastqsanger.gz
	SRR9600790.fastq.gz	Fastqsanger.gz
	SRR9600781.fastq.gz	Fastqsanger.gz
	SRR9600791.fastq.gz	Fastqsanger.gz
	SRR9600772.fastq.gz	Fastqsanger.gz

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Effects of transcription on genome - nuclear lamina interactions

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Effects of transcription on genome - nuclear lamina interactions: DamID-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.

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

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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

A lamina-associated domain border governs nuclear lamina interactions, transcription and recombination of the Tcrb locus.

Project description:A lamina-associated domain border governs nuclear lamina interactions, transcription and recombination of the Tcrb locus.

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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.

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A lamina-associated domain border governs nuclear lamina interactions, transcription and recombination of the Tcrb locus [DamID]

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| PRJNA480692 | ENA

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