Discovery of a Large-scale, Cell-state-responsive Allosteric Switch in the 7SK RNA Using DANCE-MaP

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2022 Mar 23

PMID 35320755

Authors

Samuel W Olson

Anne-Marie W Turner

J Winston Arney

Irfana Saleem

Chase A Weidmann

David M Margolis

Kevin M Weeks

Anthony M Mustoe

Affiliations

Soon will be listed here.

Abstract

7SK is a conserved noncoding RNA that regulates transcription by sequestering the transcription factor P-TEFb. 7SK function entails complex changes in RNA structure, but characterizing RNA dynamics in cells remains an unsolved challenge. We developed a single-molecule chemical probing strategy, DANCE-MaP (deconvolution and annotation of ribonucleic conformational ensembles), that defines per-nucleotide reactivity, direct base pairing interactions, tertiary interactions, and thermodynamic populations for each state in RNA structural ensembles from a single experiment. DANCE-MaP reveals that 7SK RNA encodes a large-scale structural switch that couples dissolution of the P-TEFb binding site to structural remodeling at distal release factor binding sites. The 7SK structural equilibrium shifts in response to cell growth and stress and can be targeted to modulate expression of P-TEFbresponsive genes. Our study reveals that RNA structural dynamics underlie 7SK function as an integrator of diverse cellular signals to control transcription and establishes the power of DANCE-MaP to define RNA dynamics in cells.

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References

Tan J, Fogley R, Flynn R, Ablain J, Yang S, Saint-Andre V . Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Mol Cell. 2016; 62(1):34-46. PMC: 4836061. DOI: 10.1016/j.molcel.2016.03.013. View

Ji C, Bader J, Ramanathan P, Hennlein L, Meissner F, Jablonka S . Interaction of 7SK with the Smn complex modulates snRNP production. Nat Commun. 2021; 12(1):1278. PMC: 7904863. DOI: 10.1038/s41467-021-21529-1. View

Krokhotin A, Mustoe A, Weeks K, Dokholyan N . Direct identification of base-paired RNA nucleotides by correlated chemical probing. RNA. 2016; 23(1):6-13. PMC: 5159650. DOI: 10.1261/rna.058586.116. View

Czudnochowski N, Vollmuth F, Baumann S, Vogel-Bachmayr K, Geyer M . Specificity of Hexim1 and Hexim2 complex formation with cyclin T1/T2, importin alpha and 7SK snRNA. J Mol Biol. 2009; 395(1):28-41. DOI: 10.1016/j.jmb.2009.10.055. View

Roth A, Breaker R . The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem. 2009; 78:305-34. PMC: 5325118. DOI: 10.1146/annurev.biochem.78.070507.135656. View

Calo E, Flynn R, Martin L, Spitale R, Chang H, Wysocka J . RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature. 2014; 518(7538):249-53. PMC: 4827702. DOI: 10.1038/nature13923. View

Homan P, Favorov O, Lavender C, Kursun O, Ge X, Busan S . Single-molecule correlated chemical probing of RNA. Proc Natl Acad Sci U S A. 2014; 111(38):13858-63. PMC: 4183288. DOI: 10.1073/pnas.1407306111. View

Rodnina M, Fischer N, Maracci C, Stark H . Ribosome dynamics during decoding. Philos Trans R Soc Lond B Biol Sci. 2017; 372(1716). PMC: 5311926. DOI: 10.1098/rstb.2016.0182. View

Margolis D, Garcia J, Hazuda D, Haynes B . Latency reversal and viral clearance to cure HIV-1. Science. 2016; 353(6297):aaf6517. PMC: 5021637. DOI: 10.1126/science.aaf6517. View

10.

Dobrowolski C, Valadkhan S, Graham A, Shukla M, Ciuffi A, Telenti A . Entry of Polarized Effector Cells into Quiescence Forces HIV Latency. mBio. 2019; 10(2). PMC: 6437053. DOI: 10.1128/mBio.00337-19. View

11.

He N, Pezda A, Zhou Q . Modulation of a P-TEFb functional equilibrium for the global control of cell growth and differentiation. Mol Cell Biol. 2006; 26(19):7068-76. PMC: 1592901. DOI: 10.1128/MCB.00778-06. View

12.

Gurney Jr T, Eliceiri G . Intracellular distribution of low molecular weight RNA species in HeLa cells. J Cell Biol. 1980; 87(2 Pt 1):398-403. PMC: 2110751. DOI: 10.1083/jcb.87.2.398. View

13.

Leontieva O, Demidenko Z, Blagosklonny M . Contact inhibition and high cell density deactivate the mammalian target of rapamycin pathway, thus suppressing the senescence program. Proc Natl Acad Sci U S A. 2014; 111(24):8832-7. PMC: 4066505. DOI: 10.1073/pnas.1405723111. View

14.

Quaresma A, Bugai A, Barboric M . Cracking the control of RNA polymerase II elongation by 7SK snRNP and P-TEFb. Nucleic Acids Res. 2016; 44(16):7527-39. PMC: 5027500. DOI: 10.1093/nar/gkw585. View

15.

Krueger B, Jeronimo C, Roy B, Bouchard A, Barrandon C, Byers S . LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res. 2008; 36(7):2219-29. PMC: 2367717. DOI: 10.1093/nar/gkn061. View

16.

Wilkinson M, Charenton C, Nagai K . RNA Splicing by the Spliceosome. Annu Rev Biochem. 2019; 89:359-388. DOI: 10.1146/annurev-biochem-091719-064225. View

17.

Van Herreweghe E, Egloff S, Goiffon I, Jady B, Froment C, Monsarrat B . Dynamic remodelling of human 7SK snRNP controls the nuclear level of active P-TEFb. EMBO J. 2007; 26(15):3570-80. PMC: 1949012. DOI: 10.1038/sj.emboj.7601783. View

18.

Peterlin B, Brogie J, Price D . 7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription. Wiley Interdiscip Rev RNA. 2011; 3(1):92-103. PMC: 3223291. DOI: 10.1002/wrna.106. View

19.

Smola M, Rice G, Busan S, Siegfried N, Weeks K . Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat Protoc. 2015; 10(11):1643-69. PMC: 4900152. DOI: 10.1038/nprot.2015.103. View

20.

Core L, Adelman K . Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation. Genes Dev. 2019; 33(15-16):960-982. PMC: 6672056. DOI: 10.1101/gad.325142.119. View