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Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors

Chen, Yung-Chia Ariel and Stuwe, Evelyn and Luo, Yicheng and Ninova, Maria and Le Thomas, Adrien and Rozhavskaya, Ekaterina and Li, Sisi and Vempati, Sivani and Laver, John D. and Patel, Dinshaw J. and Smibert, Craig A. and Lipshitz, Howard D. and Fejes Toth, Katalin and Aravin, Alexei A. (2016) Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors. Molecular Cell, 63 (1). pp. 97-109. ISSN 1097-2765. PMCID PMC4980073. https://resolver.caltech.edu/CaltechAUTHORS:20160614-103714874

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Abstract

Small non-coding RNAs called piRNAs serve as guides for an adaptable immune system that represses transposable elements in germ cells of Metazoa. In Drosophila the RDC complex, composed of Rhino, Deadlock and Cutoff (Cuff) bind chromatin of dual-strand piRNA clusters, special genomic regions, which encode piRNA precursors. The RDC complex is required for transcription of piRNA precursors, though the mechanism by which it licenses transcription remained unknown. Here, we show that Cuff prevents premature termination of RNA polymerase II. Cuff prevents cleavage of nascent RNA at poly(A) sites by interfering with recruitment of the cleavage and polyadenylation specificity factor (CPSF) complex. Cuff also protects processed transcripts from degradation by the exonuclease Rat1. Our work reveals a conceptually different mechanism of transcriptional enhancement. In contrast to other factors that regulate termination by binding to specific signals on nascent RNA, the RDC complex inhibits termination in a chromatin-dependent and sequence-independent manner.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1016/j.molcel.2016.05.010DOIArticle
http://www.sciencedirect.com/science/article/pii/S1097276516301472PublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980073/PubMed CentralArticle
ORCID:
AuthorORCID
Ninova, Maria0000-0001-5051-5502
Additional Information:© 2016 Elsevier Inc. Received: December 28, 2015; Revised: April 4, 2016; Accepted: May 6, 2016; Published: June 9, 2016. We thank members of the A.A.A. lab for discussion. We thank Igor Antoshechkin (Caltech) for help with sequencing and Sergei Manakov for processing the RNA-seq data. E.S. was supported by a PhD fellowship of the Boehringer Ingelheim Fonds. This work was supported by grants from the NIH (R01 GM097363 and DP2 OD007371A), by the Searle Scholar and the Packard Fellowship Awards to A.A.A., by a Ellison Medical Foundation award to K.F.T., grants from the Canadian Institutes of Health Research (MOP-14409) and the Natural Sciences and Engineering Research Council of Canada (RGPIN-201) to H.D.L., a grant from the Natural Sciences and Engineering Research Council of Canada (RGPIN-435985) to C.A.S., and by funds from the Abby Rockefeller Mauze Trust and Maloris and STARR Foundations to D.J.P. Author Contributions: Experiments were designed and performed by Y.-C.A.C. piRNA-seq, total RNA-seq, and polyA RNA-seq in Figures 1 and 2A, and Figures 2C, 2D, 4B, 4C, 4E, 4F, 4H, 6A, 6B, 6E, 7A–7C, and 7E–7G, E.S. GRO-seq and chromRNA-seq in Figures 1, 2A, 2B, and 3, Y.L. Figures 2D, 4D, 4G, 5, 6C, 6D, and 7D, A.L.T. Pld promoter deletion and piRNA analysis, Figure 2A, with help from E.R. and S.V. All bioinformatic analysis was performed by M.N., and S.L. and D.J.P. modeled the Cuff structure. J.D.L., C.A.S., and H.D.L. generated the CBP80 antibody. A.A.A. and K.F.T. aided in study design and data interpretation. Y.-C.A.C. and A.A.A. wrote the paper with input from E.S., M.N., Y.L., and K.F.T.
Funders:
Funding AgencyGrant Number
Boehringer Ingelheim FondsUNSPECIFIED
NIHR01 GM097363
NIHDP2 OD007371A
Searle Scholars ProgramUNSPECIFIED
David and Lucile Packard FoundationUNSPECIFIED
Ellison Medical FoundationUNSPECIFIED
Canadian Institutes of Health ResearchMOP-14409
Natural Sciences and Engineering Research Council of Canada (NSERC)RGPIN-201
Natural Sciences and Engineering Research Council of Canada (NSERC)RGPIN-435985
Abby Rockefeller Mauze TrustUNSPECIFIED
Maloris FoundationUNSPECIFIED
STARR FoundationUNSPECIFIED
Issue or Number:1
PubMed Central ID:PMC4980073
Record Number:CaltechAUTHORS:20160614-103714874
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160614-103714874
Official Citation:Yung-Chia Ariel Chen, Evelyn Stuwe, Yicheng Luo, Maria Ninova, Adrien Le Thomas, Ekaterina Rozhavskaya, Sisi Li, Sivani Vempati, John D. Laver, Dinshaw J. Patel, Craig A. Smibert, Howard D. Lipshitz, Katalin Fejes Toth, Alexei A. Aravin, Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors, Molecular Cell, Volume 63, Issue 1, 7 July 2016, Pages 97-109, ISSN 1097-2765, http://dx.doi.org/10.1016/j.molcel.2016.05.010. (http://www.sciencedirect.com/science/article/pii/S1097276516301472)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:67909
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:14 Jun 2016 18:46
Last Modified:03 Oct 2019 10:09

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