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MATRIN3 deficiency leads to cGAS-STING activation (PAR-CLIP)

ABSTRACT: To explore the role of MATR3 as an RNA-binding protein, we performed Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of MATR3 in HAP1 cells, together with a MATR3 KO negative control.

ORGANISM(S): Homo sapiens

PROVIDER: GSE216828 | GEO | 2025/10/28

REPOSITORIES: GEO

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MATRIN3 deficiency leads to cGAS-STING activation

Project description:To determine the direct targets of MATR3 in human HAP1 cells, we performed PAR-CLIP.

2024-05-15 | GSE262647 | GEO

MATRIN3 deficiency leads to cGAS-STING activation (NanoString)

Project description:To investigate the role of Matrin 3 (MATR3) in innate immune response, we analyzed and compared MATR3 KO clones versus wildtype HAP1 cells.

2024-05-15 | GSE216829 | GEO

MATRIN3 deficiency leads to cGAS-STING activation (MinION RNA-Seq)

Project description:To investigate the role of Matrin 3 (MATR3) in innate immune response we analyzed and compared MATR3 KO Clones versus wildtype HAP1 cells.

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MATRIN3 deficiency leads to cGAS-STING activation (Illumina RNA-Seq)

Project description:To investigate the role of Matrin 3 (MATR3) in the innate immune response we analyzed and compared MATR3 KO Clones versus wildtype HAP1 cells.

2024-05-15 | GSE216825 | GEO

Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of the RNA-binding protein (RBP) RBM4 in KBM-7 derived near-haploid human cell line, HAP1.

Project description:We hypothesized that RBM4 regulates HERVs by directly binding to their transcripts. To test this possibility, we performed photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP). We performed four independent PAR-CLIP replicates of our own using HAP1 cells stably expressing a FLAG-tagged RBM4 (FLAG-RBM4) transgene under control of a doxycycline-inducible promoter. Following metabolic labeling with 4-thiouridine (4SU) and crosslinking with ultraviolet light (UV) of 312 nm wavelength, we isolated RNA covalently linked to FLAG-RBM4. The RNA recovered from four biological replicates was converted into cDNA libraries and deep sequenced.

2020-09-03 | GSE147895 | GEO

Identification of Nucleolin-binding targets and sequences in LPS-stimulated RAW 264.7 cells by PAR-CLIP

Project description:To investigate the consensus RNA-binding motifs of Nucleoli, we performed photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) analysis in nucleolar fractions from unstimulated or 12 h LPS-stimulated RAW 264.7 cells

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Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B [PAR-CLIP]

Project description:Purpose: Matrin3 (MATR3) is a DNA and RNA-binding protein and one of the major components of the nuclear matrix. Matrin3 is upregulated in colorectal cancer (CRC) compared to normal tissues, indicating potential oncogenic function in CRC. We found that depletion of Matrin3 results in decreased proliferation and colony formation in two CRC cell lines. To understand the molecular mechanism(s) by which Matrin3 mediates these effects, we aimed to find Matrin3 direct RNA targets and the effects of Matrin3 on them. Methods: We performed PAR-CLIP for endogenous Matrin3 and RNA-seq after Matrin3 silencing in HCT116 cells, a colorectal cancer cell line. Results: We uncovered Matrin3-mediated regulation of spindle dynamics in colorectal cancer (CRC) cells. We identified bound and regulated Matrin3 target RNAs transcriptome-wide in CRC cells, and found that Matrin3 broadly regulates alternative splicing. Among the top Matrin3 targets, we focused on CDC14B and found that Matrin3 loss resulted in misprocessing of the CDC14B transcript that has a premature termination codon and simultaneous down-regulation of the standard CDC14B transcript in our model. Selective knockdown of the CDC14B standard variant phenocopied the loss of Matrin3 and resulted in reduced CRC cell proliferation, stabilized microtubules, and defects in mitotic spindle formation with tumbled mitotic spindles, suggesting that CDC14B is a key downstream effector of Matrin3. Conclusions: Our data show that by regulating the abundance of CDC14B standard variant, Matrin3 contributes to maintenance of microtubules dynamics, spindle morphology and proper mitotic spindle orientation and suggest that defects in this pathway may contribute to the reduced proliferation of cells after depletion of Matrin3.

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PAR-CLIP-seq of HA-METTL14 in HepG2 cells

Project description:The METTL3-METTL14 heterodimer is the core component of the N6-methyltransferase complex (MTC) that catalyzes methylation of adenosine residues at the N(6) position of RNA. As the non-catalytic subunit of MTC, METTL14 functions as the RNA-binding scaffold that recognizes the RNA substrate. To identify METTL14 binding sites in the transcriptome, we overexpressed HA-tagged METTL14 in HepG2 cells and performed PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) using HA antibody. Subsequent deep sequencing identified 5,961 METTL14 binding sites, in which the GGAC motif was enriched.

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CLIP-Seq of H. sapiens HeLa cells to investigate transcriptome-wide mapping of Matrin3

Project description:Matr3 iCLIP with 4thio-uridine labelling in HeLa cells

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PAR-CLIP Semliki Forest virus capsid protein

Project description:Using photoactivatable ribonucleoside crosslinking and biotinylated Cp retrieval, multiple binding sites on viral gRNA where identified.

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