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Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition

ABSTRACT: Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition

PROVIDER: PRJNA984722 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24953410_1.fastq.gz	Fastqsanger.gz
	SRR24953410_2.fastq.gz	Fastqsanger.gz
	SRR24953411_1.fastq.gz	Fastqsanger.gz
	SRR24953411_2.fastq.gz	Fastqsanger.gz
	SRR24953412_1.fastq.gz	Fastqsanger.gz

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Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition

Project description:Metazoan gene transcription by RNA polymerase (Pol) II is regulated in the promoter-proximal region. Pol II can undergo termination in the promoter-proximal region, but whether this can contribute to transcription regulation in cells remains unclear. Here, we extend our previous multi-omics analysis to quantify changes in transcription kinetics during a human cell type transition event. We observe that upregulation of transcription involves an increase in initiation frequency and, at a set of genes, a decrease in promoter-proximal termination. In turn, downregulation of transcription involves a decrease in initiation frequency and an increase in promoter-proximal termination. Thus, promoter-proximal termination of Pol II contributes to the regulation of human gene transcription.

2025-02-10 | GSE235181 | GEO

STL-seq reveals distinct pause release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts

Project description:Despite the critical regulatory function of promoter-proximal pausing, the influence of pausing kinetics on transcriptional control remains an active area of investigation. Here, we present Start-TimeLapse-seq (STL-seq), a method that captures the genome-wide kinetics of short, capped RNA turnover and reveals principles of regulation at the pause site. By measuring the rates of release into elongation and premature termination through inhibition of pause release, we determine that pause-release rates are highly variable and most promoter-proximal paused RNA Polymerase II molecules prematurely terminate (~80%). The preferred regulatory mechanism upon a hormonal stimulus (20-hydroxyecdysone) is to influence pause-release rather than termination rates. Transcriptional shutdown occurs concurrently with induction of promoter-proximal termination under hyperosmotic stress but paused transcripts from TATA box-containing promoters remain stable, demonstrating an important role for cis-acting DNA elements in pausing. STL-seq dissects the kinetics of pause release and termination, providing an opportunity to identify mechanisms of transcriptional regulation.

2021-09-13 | GSE166202 | GEO

Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis

Project description:RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that ~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.

2019-10-29 | GSE129523 | GEO

R-loop dependent promoter-proximal termination ensures genome stability

Project description:R-loop dependent promoter-proximal termination ensures genome stability

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TFIID enables RNA polymerase II promoter-proximal pausing

Project description:TFIID enables RNA polymerase II promoter-proximal pausing

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STL-seq reveals distinct pause release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts

Project description:STL-seq reveals distinct pause release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts

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Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis

Project description:Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis

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R-loop dependent promoter-proximal termination ensures genome stability [ChIP-seq]

Project description:R-loop dependent promoter-proximal termination ensures genome stability [ChIP-seq]

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Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci

Project description:Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci

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R-loop dependent promoter-proximal termination ensures genome stability [CUT&Tag]

Project description:R-loop dependent promoter-proximal termination ensures genome stability [CUT&Tag]

| PRJNA929275 | ENA

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