Transcript Isoform Sequencing Reveals Widespread Promoter-proximal Transcriptional Termination in Arabidopsis

Overview

Journal Nat Commun

Specialty Biology

Date 2020 May 24

PMID 32444691

Citations 30

Authors

Quentin Angelo Thomas

Ryan Ard

Jinghan Liu

Bingnan Li

Jingwen Wang

Vicent Pelechano

Sebastian Marquardt

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

The nuclear exosome subunit HEN2 acts independently of the core exosome to assist transcription in Arabidopsis.

Bhat S, Asgari M, Mermet S, Mishra P, Kindgren P Plant Physiol. 2024; 196(4):2625-2637.

PMID: 39321187 PMC: 11638103. DOI: 10.1093/plphys/kiae503.

Enhancers associated with unstable RNAs are rare in plants.

McDonald B, Picard C, Brabb I, Savenkova M, Schmitz R, Jacobsen S Nat Plants. 2024; 10(8):1246-1257.

PMID: 39080503 PMC: 11335568. DOI: 10.1038/s41477-024-01741-9.

Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function.

Lin M, Jensen M, Elrod N, Chu H, Haseley M, Beam A Mol Cell. 2024; 84(15):2900-2917.e10.

PMID: 39032490 PMC: 11316654. DOI: 10.1016/j.molcel.2024.06.017.

LncRNAs exert indispensable roles in orchestrating the interaction among diverse noncoding RNAs and enrich the regulatory network of plant growth and its adaptive environmental stress response.

Zhang L, Lin T, Zhu G, Wu B, Zhang C, Zhu H Hortic Res. 2023; 10(12):uhad234.

PMID: 38156284 PMC: 10753412. DOI: 10.1093/hr/uhad234.

Comparative analysis of nascent RNA sequencing methods and their applications in studies of cotranscriptional splicing dynamics.

Liu M, Zhu J, Huang H, Chen Y, Dong Z Plant Cell. 2023; 35(12):4304-4324.

PMID: 37708036 PMC: 10689179. DOI: 10.1093/plcell/koad237.

References

Jonkers I, Lis J . Getting up to speed with transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol. 2015; 16(3):167-77. PMC: 4782187. DOI: 10.1038/nrm3953. View

Portin P, Wilkins A . The Evolving Definition of the Term "Gene". Genetics. 2017; 205(4):1353-1364. PMC: 5378099. DOI: 10.1534/genetics.116.196956. View

Pumplin N, Sarazin A, Jullien P, Bologna N, Oberlin S, Voinnet O . DNA Methylation Influences the Expression of DICER-LIKE4 Isoforms, Which Encode Proteins of Alternative Localization and Function. Plant Cell. 2016; 28(11):2786-2804. PMC: 5155348. DOI: 10.1105/tpc.16.00554. View

Kadonaga J . Perspectives on the RNA polymerase II core promoter. Wiley Interdiscip Rev Dev Biol. 2013; 1(1):40-51. PMC: 3695423. DOI: 10.1002/wdev.21. View

Trcek T, Larson D, Moldon A, Query C, Singer R . Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast. Cell. 2011; 147(7):1484-97. PMC: 3286490. DOI: 10.1016/j.cell.2011.11.051. View

Leppek K, Das R, Barna M . Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat Rev Mol Cell Biol. 2017; 19(3):158-174. PMC: 5820134. DOI: 10.1038/nrm.2017.103. View

Jensen T, Jacquier A, Libri D . Dealing with pervasive transcription. Mol Cell. 2013; 52(4):473-84. DOI: 10.1016/j.molcel.2013.10.032. View

Kindgren P, Ard R, Ivanov M, Marquardt S . Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation. Nat Commun. 2018; 9(1):4561. PMC: 6212407. DOI: 10.1038/s41467-018-07010-6. View

Wiesner T, Lee W, Obenauf A, Ran L, Murali R, Zhang Q . Alternative transcription initiation leads to expression of a novel ALK isoform in cancer. Nature. 2015; 526(7573):453-7. PMC: 4807020. DOI: 10.1038/nature15258. View

10.

Venkatesh S, Workman J . Histone exchange, chromatin structure and the regulation of transcription. Nat Rev Mol Cell Biol. 2015; 16(3):178-89. DOI: 10.1038/nrm3941. View

11.

Proudfoot N . Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut. Science. 2016; 352(6291):aad9926. PMC: 5144996. DOI: 10.1126/science.aad9926. View

12.

Kamieniarz-Gdula K, Proudfoot N . Transcriptional Control by Premature Termination: A Forgotten Mechanism. Trends Genet. 2019; 35(8):553-564. PMC: 7471841. DOI: 10.1016/j.tig.2019.05.005. View

13.

Schmid M, Jensen T . Controlling nuclear RNA levels. Nat Rev Genet. 2018; 19(8):518-529. DOI: 10.1038/s41576-018-0013-2. View

14.

Marquardt S, Escalante-Chong R, Pho N, Wang J, Churchman L, Springer M . A chromatin-based mechanism for limiting divergent noncoding transcription. Cell. 2014; 157(7):1712-23. PMC: 4090027. DOI: 10.1016/j.cell.2014.04.036. View

15.

Ibrahim M, Karabacak A, Glahs A, Kolundzic E, Hirsekorn A, Carda A . Determinants of promoter and enhancer transcription directionality in metazoans. Nat Commun. 2018; 9(1):4472. PMC: 6203779. DOI: 10.1038/s41467-018-06962-z. View

16.

Wu A, van Werven F . Transcribe this way: Rap1 confers promoter directionality by repressing divergent transcription. Transcription. 2019; 10(3):164-170. PMC: 6602560. DOI: 10.1080/21541264.2019.1608716. View

17.

Almada A, Wu X, Kriz A, Burge C, Sharp P . Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature. 2013; 499(7458):360-3. PMC: 3720719. DOI: 10.1038/nature12349. View

18.

Oh J, Di C, Venters C, Guo J, Arai C, So B . U1 snRNP telescripting regulates a size-function-stratified human genome. Nat Struct Mol Biol. 2017; 24(11):993-999. PMC: 5685549. DOI: 10.1038/nsmb.3473. View

19.

Ule J, Blencowe B . Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. Mol Cell. 2019; 76(2):329-345. DOI: 10.1016/j.molcel.2019.09.017. View

20.

Shi Y, Manley J . The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes Dev. 2015; 29(9):889-97. PMC: 4421977. DOI: 10.1101/gad.261974.115. View