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

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

PROVIDER: PRJNA531657 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8870030_1.fastq.gz	Fastqsanger.gz
	SRR8870030_2.fastq.gz	Fastqsanger.gz
	SRR8870040_1.fastq.gz	Fastqsanger.gz
	SRR8870040_2.fastq.gz	Fastqsanger.gz
	SRR8870031_1.fastq.gz	Fastqsanger.gz

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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

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

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R-loop dependent promoter-proximal termination ensures genome stability

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Dynamics and consequences of widespread transcript isoform changes during neuronal differentiation

Project description:Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform change upon cell-state transitions during cell differentiation, and the determinants and functional consequences have largely remained unclear. Here, we used an improved model for human neurogenesis in vitro that we show is amenable for systems-wide analyses of gene expression. Our multi-omics analysis reveals that the pronounced alterations in cell morphology correlate strongly with widespread changes in RNA isoform expression. Our approach identifies thousands of new RNA isoforms that are expressed at distinct stages during neurogenesis. RNA isoforms mainly arise from the alternative usage of transcription start sites and poly-adenylation sites as well as the skipping of individual exons during human neurogenesis. The transcript isoform changes can remodel the abundance and functions of protein isoforms. Finally, our study identifies a set of RNA-binding proteins as a likely determinant of differentiation stage-specific global isoform changes.

2024-04-11 | PXD046084 | Pride

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.

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

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

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