Journal
NATURE COMMUNICATIONS
Volume 11, Issue 1, Pages -Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/s41467-020-16390-7
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Funding
- Novo Nordisk Foundation [NNF15OC0014202]
- Copenhagen Plant Science Centre Young Investigator Starting Grant
- European Research Council
- Marie Curie Actions under the European Union's Horizon 2020 research and innovation programme [StG2017-757411]
- European Molecular Biology Organization Long-Term Fellowship [ALTF 463-2016]
- SciLifeLab Fellowship (Karolinska Institutet SFO-PRIO)
- Swedish Research Council [VR 2016-01842]
- Wallenberg Academy Fellowship [KAW 2016.0123]
- Ragnar Soderberg Foundation
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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 similar to 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.
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