Global Analysis of Short RNAs Reveals Widespread Promoter-proximal Stalling and Arrest of Pol II in Drosophila

Overview

Journal Science

Specialty Science

Date 2009 Dec 17

PMID 20007866

Citations 281

Authors

Sergei Nechaev

David C Fargo

Gilberto Dos Santos

Liwen Liu

Yuan Gao

Karen Adelman

Affiliations

Soon will be listed here.

Abstract

Emerging evidence indicates that gene expression in higher organisms is regulated by RNA polymerase II stalling during early transcription elongation. To probe the mechanisms responsible for this regulation, we developed methods to isolate and characterize short RNAs derived from stalled RNA polymerase II in Drosophila cells. Significant levels of these short RNAs were generated from more than one-third of all genes, indicating that promoter-proximal stalling is a general feature of early polymerase elongation. Nucleotide composition of the initially transcribed sequence played an important role in promoting transcriptional stalling by rendering polymerase elongation complexes highly susceptible to backtracking and arrest. These results indicate that the intrinsic efficiency of early elongation can greatly affect gene expression.

Citing Articles

Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome.

Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M Sci Adv. 2025; 11(10):eadu0577.

PMID: 40043114 PMC: 11881899. DOI: 10.1126/sciadv.adu0577.

New insights into the structure domain and function of NLR family CARD domain containing 5.

Zhu H, Xiao C, Chen J, Guo B, Wang W, Tang Z Cell Commun Signal. 2025; 23(1):42.

PMID: 39849460 PMC: 11755879. DOI: 10.1186/s12964-024-02012-y.

Cell cycle-regulated transcriptional pausing of replication-dependent histone genes.

Kemp Jr J, Kemp J, Geisler M, Hoover M, Cho C, OFarrell P bioRxiv. 2025; .

PMID: 39763942 PMC: 11702538. DOI: 10.1101/2024.12.16.628706.

RNA 3'end tailing safeguards cells against products of pervasive transcription termination.

Wu G, Rouviere J, Schmid M, Jensen T Nat Commun. 2024; 15(1):10446.

PMID: 39617768 PMC: 11609308. DOI: 10.1038/s41467-024-54834-6.

The chromatin landscape of the histone-possessing bacteria.

Marinov G, Doughty B, Kundaje A, Greenleaf W Genome Res. 2024; 35(1):109-123.

PMID: 39572228 PMC: 11789641. DOI: 10.1101/gr.279418.124.

References

Kephart D, Marshall N, Price D . Stability of Drosophila RNA polymerase II elongation complexes in vitro. Mol Cell Biol. 1992; 12(5):2067-77. PMC: 364378. DOI: 10.1128/mcb.12.5.2067-2077.1992. View

Jove R, Manley J . In vitro transcription from the adenovirus 2 major late promoter utilizing templates truncated at promoter-proximal sites. J Biol Chem. 1984; 259(13):8513-21. View

Lee C, Li X, Hechmer A, Eisen M, Biggin M, Venters B . NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol Cell Biol. 2008; 28(10):3290-300. PMC: 2423147. DOI: 10.1128/MCB.02224-07. View

Ahsan B, Saito T, Hashimoto S, Muramatsu K, Tsuda M, Sasaki A . MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. Nucleic Acids Res. 2008; 37(Database issue):D49-53. PMC: 2686457. DOI: 10.1093/nar/gkn694. View

Core L, Waterfall J, Lis J . Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008; 322(5909):1845-8. PMC: 2833333. DOI: 10.1126/science.1162228. View

Coppola J, Field A, Luse D . Promoter-proximal pausing by RNA polymerase II in vitro: transcripts shorter than 20 nucleotides are not capped. Proc Natl Acad Sci U S A. 1983; 80(5):1251-5. PMC: 393573. DOI: 10.1073/pnas.80.5.1251. View

Tadigotla V, O Maoileidigh D, Sengupta A, Epshtein V, Ebright R, Nudler E . Thermodynamic and kinetic modeling of transcriptional pausing. Proc Natl Acad Sci U S A. 2006; 103(12):4439-44. PMC: 1450190. DOI: 10.1073/pnas.0600508103. View

Rougvie A, Lis J . Postinitiation transcriptional control in Drosophila melanogaster. Mol Cell Biol. 1990; 10(11):6041-5. PMC: 361402. DOI: 10.1128/mcb.10.11.6041-6045.1990. View

Renner D, Yamaguchi Y, Wada T, Handa H, Price D . A highly purified RNA polymerase II elongation control system. J Biol Chem. 2001; 276(45):42601-9. DOI: 10.1074/jbc.M104967200. View

10.

Palangat M, Landick R . Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II. J Mol Biol. 2001; 311(2):265-82. DOI: 10.1006/jmbi.2001.4842. View

11.

Aida M, Chen Y, Nakajima K, Yamaguchi Y, Wada T, Handa H . Transcriptional pausing caused by NELF plays a dual role in regulating immediate-early expression of the junB gene. Mol Cell Biol. 2006; 26(16):6094-104. PMC: 1592793. DOI: 10.1128/MCB.02366-05. View

12.

Krumm A, Hickey L, Groudine M . Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. Genes Dev. 1995; 9(5):559-72. DOI: 10.1101/gad.9.5.559. View

13.

Kireeva M, Hancock B, Cremona G, Walter W, Studitsky V, Kashlev M . Nature of the nucleosomal barrier to RNA polymerase II. Mol Cell. 2005; 18(1):97-108. DOI: 10.1016/j.molcel.2005.02.027. View

14.

Komissarova N, Kashlev M . RNA polymerase switches between inactivated and activated states By translocating back and forth along the DNA and the RNA. J Biol Chem. 1997; 272(24):15329-38. DOI: 10.1074/jbc.272.24.15329. View

15.

Palangat M, Renner D, Price D, Landick R . A negative elongation factor for human RNA polymerase II inhibits the anti-arrest transcript-cleavage factor TFIIS. Proc Natl Acad Sci U S A. 2005; 102(42):15036-41. PMC: 1257689. DOI: 10.1073/pnas.0409405102. View

16.

. Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature. 2009; 457(7232):1028-32. PMC: 2719882. DOI: 10.1038/nature07759. View

17.

Reeder T, HAWLEY D . Promoter proximal sequences modulate RNA polymerase II elongation by a novel mechanism. Cell. 1996; 87(4):767-77. DOI: 10.1016/s0092-8674(00)81395-1. View

18.

Rasmussen E, Lis J . In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc Natl Acad Sci U S A. 1993; 90(17):7923-7. PMC: 47259. DOI: 10.1073/pnas.90.17.7923. View

19.

Pal M, McKean D, Luse D . Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence. Mol Cell Biol. 2001; 21(17):5815-25. PMC: 87301. DOI: 10.1128/MCB.21.17.5815-5825.2001. View

20.

Juven-Gershon T, Hsu J, Theisen J, Kadonaga J . The RNA polymerase II core promoter - the gateway to transcription. Curr Opin Cell Biol. 2008; 20(3):253-9. PMC: 2586601. DOI: 10.1016/j.ceb.2008.03.003. View