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Genome-wide maps of nuclear lamina interactions in AML12 cells upon MATR3 KD [DamID-Seq]

ABSTRACT: We performed DamID-seq assay in WT and MATR3-depleted AML12 cells to investigate the Lamina-associated-domains (LADs) affected by loss of MATR3.

ORGANISM(S): Mus musculus

PROVIDER: GSE200242 | GEO | 2025/03/14

REPOSITORIES: GEO

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Genome-wide maps of nuclear lamina interactions in AML12 cells upon MATR3 KD [DamID-Seq]

Project description:Genome-wide maps of nuclear lamina interactions in AML12 cells upon MATR3 KD [DamID-Seq]

| PRJNA823728 | ENA

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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Genome-wide maps of nuclear lamina interactions in AML12 cells.

Project description:We have used microarrays to identify LaminB1 occupancy signal in AML12 cell using the DamID protocol.

2015-11-30 | GSE73703 | GEO

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

Project description:Eukaryotic chromosomes fold into topologically associating domains (TADs), which further gather in active (A) or inactive (B) genomic compartments. Here we show that Scaffold Attachment Factor B (SAFB), a nuclear matrix-associated protein with RNA binding functions, modulates global chromatin condensation in a dosage-dependent manner. Upon the depletion of SAFB, the genome coverage of Lamina-associated-domains (LADs) decreases from 53.33% to 45.93%, and both inter- and intra-TAD chromatin-chromatin interactions in compartment B decrease significantly. In the nucleus, SAFB favorably co-localizes with H3K9me3, a marker of heterochromatin, and the disruption of SAFB leads to a collapse of H3K9me3 foci. Furthermore, we show that SAFB proteins can form liquid-liquid phase separation in the cell and in vitro. Intriguingly, SAFB interacts with RNAs from repetitive elements enriched in heterochromatin (e.g., Major Satellites and LINE1), which can promote SAFB-mediated phase separation, depending on the density of SAFB recognizing motifs in the RNAs.

2019-12-01 | GSE141109 | GEO

MATR3-binding RNAs in AML12 cells [RIP-Seq]

Project description:MATR3-binding RNAs in AML12 cells [RIP-Seq]

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The nuclear matrix protein MATR3 maintains higher-order chromatin architecture [Hi-C]

Project description:The chromatin structure in eukaryotic nucleus is highly ordered and organized in hierarchical frameworks. We performed Hi-C assay in WT and MATR3-depleted AML12 cells to reveal the MATR3's role in AML12 cells.

2023-06-28 | GSE200243 | GEO

LaminB1 DamID analysis in RIF1 depleted preimplantation mouse embryos

Project description:We investigated how RIF1 depletion affects the nuclear organization in mouse preimplantation embryos by performing DamID-seq to map lamina-associated domains (LADs).

2025-03-18 | GSE262788 | GEO

Genome-wide maps of nuclear lamina interactions in AML12 cells upon G9a/GLP inhibition [DamID]

Project description:Genome-wide maps of nuclear lamina interactions in AML12 cells upon G9a/GLP inhibition [DamID]

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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

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

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