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

ABSTRACT: The chromatin structure in eukaryotic nucleus is highly ordered and organized in hierarchical frameworks. We performed Hi-C assay in WT and MATR3-degradated mouse ES cells to reveal the MATR3's role in ES cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE225500 | GEO | 2023/06/28

REPOSITORIES: GEO

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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

The transcriptome profile before and after knocking-down of nuclear matrix protein MATR3 [ssRNA-Seq]

Project description:We performed RNA-seq assay in WT and MATR3-depleted AML12 cells to reveal the trscriptiome associated with MATR3 protein. The libraries were constructed by poly-A enriched and strand-specific kits.

2023-06-28 | GSE200245 | GEO

MATR3-antisense LINE1 RNA meshwork scaffolds higher-order chromatin organization

Project description: Not available

| S-SCDT-10_15252-EMBR_202357550 | biostudies-other

DNA methylation maintains integrity of higher order genome architecture (Hi-C)

Project description:DNA replication timing and 3D chromatin organisation are associated with epigenomic changes across large domains during human differentiation and cancer progression. However, it is unclear if epigenome changes, in particular cancer-associated DNA hypomethylation, is a consequence or cause of changes observed in higher order genome architecture. Here, we compare replication timing profiles and three dimensional (3D) genome organisation, using Hi-C and single cell Repli-Seq in the DNMT1 and DNMT3B DNA methyltransferases double knockout hypomethylated DKO1 colorectal cancer cell line and its parental HCT116 cell line. We find that the hypomethylated cells show a profound loss of replication timing precision, gain of single cell replication timing heterogeneity and loss of chromatin conformation integrity. Discrete regions, that undergo a large change in replication timing in the hypomethylated cells, are associated with a loss of allelic replication timing and shrinking of late replicating Partially Methylated Domain (PMD) boundaries. In contrast, conservation of replication timing after DNA methylation depletion at PMDs is associated with the formation of new H3K9me3/H3K4me3 bivalent domains which may serve to prevent ectopic transcription and maintain cell viability. Together our results show that a loss of global methylation, a common hallmark of cancer, directly impacts on the precision of replication timing and contribute to deregulation of the 3D chromatin architecture.

2021-09-21 | GSE158007 | GEO

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

Project description:We performed RNA binding protein immunoprecipitation (RIP) assay with anti-IgG/anti-MATR3 antibody. The RNA libraries were constructed using rib-off and strand-specific kits. Next-generation sequencing (NGS) were performed to analyze MATR3-binding RNAs.

2023-06-28 | GSE225501 | GEO

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

2023-06-28 | GSE200244 | GEO

MATR3 is an endogenous inhibitor of DUX4 in FSHD muscular dystrophy

Project description:We identified MATR3 as the first direct endogenous inhibitor of DUX4. We found that MATR3 directly binds to DUX4 DNA-binding domain and blocks DUX4-mediated gene expression. As a result, MATR3 administration rescues cell viability and myogenic differentiation of FSHD muscle cells, while it does not affect healthy muscle cells. Notably, we characterized a short MATR3 fragment that is necessary and sufficient to directly block DUX4-induced toxicity to the same extent of the full-length protein.

2023-08-21 | GSE210008 | GEO

MATR3 pathogenic variants differentially impair its cryptic splicing repression function

Project description:To investigate the role of MATR3 in splicing regulation, we performed RNA sequencing on HeLa cells treated with either control siRNA or MATR3 siRNA and then conducted alternative and cryptic splicing analysis

2024-01-10 | GSE205343 | GEO

4SU-iCLIP of PTBP1 from HEK293 cells with or without MATR3 depletion

Project description:The aim of the experiment was to compare binding of PTBP1 in presence and absence of MATR3. HEK293T cells were transfected with siRNA targeting MATR3 or control sequences and labelled with 4thio-uridine for 8 hours (100µM, crosslinking 2x400mJ/cm2 365nm UV light).

2018-05-01 | E-MTAB-6286 | biostudies-arrayexpress

iCLIP of MATR3 from C57BL/6J wildtype mice

Project description:The aim of the experiment was to find binding sites MATR3 in mouse brain tissue. Whole brain was prepped from mice at P0 and replicates are from separate animals.

2018-05-01 | E-MTAB-6283 | biostudies-arrayexpress

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