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Mus musculus

ABSTRACT: Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies [ChIP-seq]

PROVIDER: PRJNA295206 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2320440.fastq.gz	Fastqsanger.gz
	SRR2320450.fastq.gz	Fastqsanger.gz
	SRR2320460.fastq.gz	Fastqsanger.gz
	SRR2320441.fastq.gz	Fastqsanger.gz
	SRR2320451.fastq.gz	Fastqsanger.gz

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PWWP2A variant NuRD complex represses intragenic spurious transcription initiation

Project description:H3 trimethylation at K36 deposited over the body of actively transcribed gene, is recognized by readers to modulate the epigenetic states, such as DNA methylation and histone deacetylation, to ensure the proper gene transcription. PWWP2A was identified as the reading component of variant NuRD complex to deacetylate gene bodies in mammalian cells. However, whether this deacetylation affects intragenic transcription is not investigated. Here, we performed CAGE-seq to profile transcription initiation in PWWP2A/B double knockout and fount that intragenic spurious transcription initiations at pre-existing low-level initiation from highly expressed genes were enhanced, accompanying with elevated acetylation level at H3K9 and H3K27, as well as nascent transcription. Additionally, the intragenic spurious transcriptions in PWWP2A/B loss are distinct with those in DNMT3B loss which is prone to produce de novo initiation and lack of PWWP2A/B-related chromatin changes. Collectively, PWWP2A/B-NuRD complex deacetylates active gene bodies to suppress intragenic spurious transcription in mammals.

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Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies [DECAP-seq]

Project description:In mammals, DNA methylation occurs mainly at 5mC of CpG dinucleotides. The methylation on the promoter leads to the suppression of gene expression, while the functional role of gene body DNA methylation in highly expressed genes has yet to be clarified. Here, we show that the Dnmt3b-dependent intragenic DNA methylation protects the gene body from RNA Polymerase II (RNA Pol II) spurious entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that loss of Dnmt3b leads to an increase of the RNA Pol II engagement within gene bodies and spurious intragenic transcription initiation events. Furthermore, inhibition of RNA Pol II spurious entry depends on the enzymatic activity of the Dnmt3b recruited by H3K36me3. Thus, elongating RNA Pol II triggers an epigenetic crosstalk that involves SetD2, H3K36me3, Dnmt3b, and DNA methylation to ensure gene transcription initiation fidelity with implications for intragenic hypomethylation in cancer.

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Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies [ChIP-seq]

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