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

Arabidopsis / genetics Arabidopsis Proteins / genetics Chromatin / genetics Cleavage Stimulation Factor / genetics Gene Expression Regulation, Plant Mutation Plants, Genetically Modified Polyadenylation Promoter Regions, Genetic Protein Isoforms / genetics RNA, Plant Nicotiana / genetics Transcription Initiation Site Transcription Termination, Genetic

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
22 05 2020
Historique:
received: 24 06 2019
accepted: 29 04 2020
entrez: 24 5 2020
pubmed: 24 5 2020
medline: 25 8 2020
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41467-020-16390-7 PMID: 32444691 PMC: PMC7244574
pubmed: 32444691
doi: 10.1038/s41467-020-16390-7
pii: 10.1038/s41467-020-16390-7
pmc: PMC7244574
doi:

Substances chimiques

Arabidopsis Proteins 0
Chromatin 0
Cleavage Stimulation Factor 0
CstF77 protein, Arabidopsis 0
Protein Isoforms 0
RNA, Plant 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

2589

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Auteurs

Quentin Angelo Thomas (QA)

Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
ORCID: 0000-0002-3522-5125

Ryan Ard (R)

Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
ORCID: 0000-0002-9070-9747

Jinghan Liu (J)

Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
ORCID: 0000-0001-7816-4791

Bingnan Li (B)

SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.

Jingwen Wang (J)

SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
ORCID: 0000-0001-9688-8793

Vicent Pelechano (V)

SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
ORCID: 0000-0002-9415-788X

Sebastian Marquardt (S)

Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark. sebastian.marquardt@plen.ku.dk.
ORCID: 0000-0003-1709-2717

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Brassicaceae › Arabidopsis › Transcript isoform sequencing reveals...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines végétales › Protéines d'Arabidopsis › Transcript isoform sequencing reveals...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Transcript isoform sequencing reveals...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Nucléoprotéines › Protéines de liaison à l'ARN › Facteurs de clivage et de polyadénylation de l'ARN messager › Facteur de stimulation du clivage › Transcript isoform sequencing reveals...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Régulation de l'expression des gènes végétaux › Transcript isoform sequencing reveals...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Mutation › Transcript isoform sequencing reveals...
questionsmedicales.fr › Stades d'organismes › Organismes génétiquement modifiés › Végétaux génétiquement modifiés › Transcript isoform sequencing reveals...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Maturation post-transcriptionnelle des ARN › Maturation de l'extrémité 3' des ARN › Polyadénylation › Transcript isoform sequencing reveals...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Composants de gène › Éléments de régulation transcriptionnelle › Régions promotrices (génétique) › Transcript isoform sequencing reveals...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Isoformes de protéines › Transcript isoform sequencing reveals...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN des plantes › Transcript isoform sequencing reveals...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Composants de gène › Éléments de régulation transcriptionnelle › Site d'initiation de la transcription › Transcript isoform sequencing reveals...
questionsmedicales.fr › Phénomènes génétiques › Expression des gènes › Transcription génétique › Terminaison de la transcription › Transcript isoform sequencing reveals...