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

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

PROVIDER: PRJNA551544 | ENA |

REPOSITORIES: ENA

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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.

2019-06-28 | GSE133272 | GEO

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

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

2019-06-28 | GSE133273 | GEO

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

Project description:Tcrb locus V(D)J recombination is regulated by positioning at the nuclear periphery. Here we used DamID to profile Tcrb locus interactions with the nuclear lamina at high-resolution. We identified a lamina-associated domain (LAD) border composed of several CTCF binding elements that segregates active non-LAD from inactive LAD regions of the locus. Deletion of the LAD border caused an enhancer-dependent spread of H3K27ac from the active recombination center into recombination center-proximal LAD chromatin. This was associated with a disruption to LAD organization, increased chromatin looping to the recombination center, and increased transcription and recombination of recombination center-proximal gene segments. Our results show that a Tcrb locus LAD and LAD border are critical components of Tcrb locus gene regulation and suggest that LAD borders may generally function to constrain the activity of nearby enhancers.

2018-10-22 | GSE116953 | GEO

Effects of transcription on genome - nuclear lamina interactions

Project description:Effects of transcription on genome - nuclear lamina interactions

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DamID LaminB1 data in mouse MEFs, wild-type and POU2F1-/-. DamID LaminA data in mouse Neural Precursor Cells and Astrocytes.

Project description:DamID LaminB1 data were generated in POU2F1-/- MEFs to study the potential role of POU2F1/Oct1 in genome - nuclear lamina interactions. DamID LaminA data were generated in NPCs and Astrocytes to study similarities/differences between LaminA and LaminB1 binding. Comparison of MEF wt versus MEF POU2F1-/-. Comparison of LaminA (NPC & AC) with LaminB1 (NPC & AC data in GSE17051)

2012-10-10 | E-GEOD-36132 | biostudies-arrayexpress

The insulator protein SU(HW) modulates nuclear lamina interactions of the Drosophila genome: DamID

Project description:Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that of these five proteins, only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens LAD – NL interactions by a local antagonistic effect. Our results provide insights into the evolution of LAD organization and reveal a role for SU(HW) in the regulation of genome – NL interactions. DamID experiments for Lamin, CTCF, SU(HW), GAF, DWG, and BEAF-32, and for Lamin after overexpression and after knockdown of SU(HW), were performed in Drosophila cell cultures. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Every experiment was done in duplicate in the reverse dye orientation. The supplementary file 'GSE20311_DamID_norm_mean.txt' contains the mean log2(Dam-fusion/Dam-only) values of two replicates.

2011-01-24 | E-GEOD-20311 | biostudies-arrayexpress

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

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

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Stochastic genome-nuclear lamina interactions: Modulating roles of Lamin A and BAF

Project description:The nuclear lamina (NL) is a filamentous layer lining the inner-nuclear-membrane (INM) that aids in the organization of the genome in large domains of low transcriptional activity. Recently, it was shown that the single-cell genome-NL interactions are much more dynamic than previously anticipated, which challenges the concept of the NL as a safe guard for transcriptional repressed genes. Here we discuss the role of the NL in light of these new findings and introduce Lamin A and BAF as potential modulators of LAD positioning BAF-chromatin and Lamin B2-chromatin interactions were assayed in human HT1080 by DamID on Nimblegen microarrays, with two biological replicates each, that were hybridized in a dye-swap design.

2014-02-15 | E-GEOD-55066 | biostudies-arrayexpress

Genome-wide maps of nuclear lamina interactions in AML12 cells upon Safb KD [DamID]

Project description:Genome-wide maps of nuclear lamina interactions in AML12 cells upon Safb KD [DamID]

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