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YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RIP-seq)

ABSTRACT: YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RIP-seq)

PROVIDER: PRJNA1092092 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28464812_1.fastq.gz	Fastqsanger.gz
	SRR28464812_2.fastq.gz	Fastqsanger.gz
	SRR28464813_1.fastq.gz	Fastqsanger.gz
	SRR28464813_2.fastq.gz	Fastqsanger.gz

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YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RIP-seq)

Project description:Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding of its impact on a fully efficient DNA damage response remains limited. Here, through a targeted CRISPR-knockout screen, we identified RNA binding proteins and modifiers that participate in mediating the p53 response. Among the top hits, m6A reader YTHDC1 was identified as a master regulator of p53 expression. YTHDC1 binds to the transcription start sites ofTP53and other genes involved in DNA damage response, promoting their transcriptional elongation. YTHDC1 deficiency leads to reducedTP53expression, and also retention of introns leading to aberrant protein production of key DNA damage factors. While intron retention is dependent on m6A, YTHDC1 favoursTP53transcriptionalpause-release independently of m6A. Depletion of YTHDC1 causes genomic instability and aberrant cancer cell proliferation mediated by genes regulated by YTHDC1. Our results uncover YTHDC1 as an orchestrator of the DNA damage response through distinct mechanisms of co-transcriptional mRNA regulation.

2024-05-07 | GSE262504 | GEO

YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (Ythdc1 ChIP-Seq)

2024-05-07 | GSE239331 | GEO

YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (Ythdc1 ChIP-Seq)

Project description:YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (Ythdc1 ChIP-Seq)

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YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RNA-Seq)

2024-05-07 | GSE239330 | GEO

YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response

Project description:YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response

| PRJNA998818 | ENA

YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RNAP II ChIP-Seq)

2024-05-07 | GSE239332 | GEO

YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RNA-Seq)

Project description:YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RNA-Seq)

| PRJNA998828 | ENA

YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RNAP II ChIP-Seq)

Project description:YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RNAP II ChIP-Seq)

| PRJNA998830 | ENA

YTHDC1 m6A-dependent and m6A-independent functions converge to preserve the DNA damage response

Project description:Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding of its impact on a fully efficient DNA damage response remains limited. Here, through a targeted CRISPR-knockout screen, we identify RNA binding proteins and modifiers that participate in the p53 response. Among the top hits, we find the m6A reader YTHDC1 as a master regulator of p53 expression. YTHDC1 binds to the transcription start sites of TP53 and other genes involved in the DNA damage response, promoting their transcriptional elongation. YTHDC1 deficiency also causes the retention of introns and therefore aberrant protein production of key DNA damage factors. While YTHDC1-mediated intron retention requires m6A, TP53 transcriptional pause-release is promoted by YTHDC1 independently of m6A. Depletion of YTHDC1 causes genomic instability and aberrant cancer cell proliferation mediated by genes regulated by YTHDC1. Our results uncover YTHDC1 as an orchestrator of the DNA damage response through distinct mechanisms of co-transcriptional mRNA regulation.

| S-SCDT-10_1038-S44318-024-00153-X | biostudies-other

Structural basis of YTH domain as m6A reader

Project description:The N6-methyladenosine (m6A) is the most abundant internal modification in almost all eukaryotic messenger RNAs, and is dynamically regulated. Therefore, identification of m6A readers is especially important in determining the cellular function of m6A. YTHDF2 has recently been characterized as the first m6A reader that regulates the cytoplasmic stability of methylated RNA. Here we show that YTHDC1 is a nuclear m6A reader and report the crystal structure of the YTH domain of YTHDC1 bound to m6A-containing RNA. We further determined the structure of another YTH domain, YTHDF1, and found that the YTH domain utilizes a conserved aromatic cage to specifically recognize the methyl group of m6A. Our structural characterizations of the YTHDC1-m6A RNA complex also shed light on the molecular basis for the preferential binding of the GG(m6A)C sequence by YTHDC1 and confirm the YTH domain as a specific m6A RNA reader. PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) was applied to human YTHDC1 protein to identify its binding sites.

2014-09-18 | E-GEOD-58352 | biostudies-arrayexpress

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