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DNA topoisomerase 2-associated proteins PATL1 and PATL2 regulate the biogenesis of hERG K + channels. Proc Natl Acad Sci U S A 2023; 120:e2206146120. [PMID: 36608291 PMCID: PMC9926248 DOI: 10.1073/pnas.2206146120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The human ether-a-go-go-related gene (hERG) K+ channel conducts a rapidly activating delayed rectifier K+ current (IKr), which is essential for normal electrical activity of the heart. Precise regulation of hERG channel biogenesis is critical for serving its physiological functions, and deviations from the regulation result in human diseases. However, the mechanism underlying the precise regulation of hERG channel biogenesis remains elusive. Here, by using forward genetic screen, we found that PATR-1, the Caenorhabditis elegans homolog of the yeast DNA topoisomerase 2-associated protein PAT1, is a critical regulator for the biogenesis of UNC-103, the ERG K+ channel in C. elegans. A loss-of-function mutation in patr-1 down-regulates the expression level of UNC-103 proteins and suppresses the phenotypic defects resulted from a gain-of-function mutation in the unc-103 gene. Furthermore, downregulation of PATL1 and PATL2, the human homologs of PAT1, decreases protein levels and the current density of native hERG channels in SH-SY5Y cells and human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Knockdown of PATL1 and PATL2 elongates the duration of action potentials in hiPSC-CMs, suggesting that PATL1 and PATL2 affect the function of hERG channels and hence electrophysiological characteristics in the human heart. Further studies found that PATL1 and PATL2 interact with TFIIE, a general transcription factor required for forming the RNA polymerase II preinitiation complex, and dual-luciferase reporter assays indicated that PATL1 and PATL2 facilitate the transcription of hERG mRNAs. Together, our study discovers that evolutionarily conserved DNA topoisomerase 2-associated proteins regulate the biogenesis of hERG channels via a transcriptional mechanism.
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Vindry C, Weil D, Standart N. Pat1 RNA-binding proteins: Multitasking shuttling proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1557. [PMID: 31231973 DOI: 10.1002/wrna.1557] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/02/2019] [Accepted: 05/07/2019] [Indexed: 12/11/2022]
Abstract
Post-transcriptional regulation of gene expression is largely achieved at the level of splicing in the nucleus, and translation and mRNA decay in the cytosol. While the regulation may be global, through the direct inhibition of central factors, such as the spliceosome, translation initiation factors and mRNA decay enzymes, in many instances transcripts bearing specific sequences or particular features are regulated by RNA-binding factors which mobilize or impede recruitment of these machineries. This review focuses on the Pat1 family of RNA-binding proteins, conserved from yeast to man, that enhance the removal of the 5' cap by the decapping enzyme Dcp1/2, leading to mRNA decay and also have roles in translational repression. Like Dcp1/2, other decapping coactivators, including DDX6 and Edc3, and translational repressor proteins, Pat1 proteins are enriched in cytoplasmic P-bodies, which have a principal role in mRNA storage. They also concentrate in nuclear Cajal-bodies and splicing speckles and in man, impact splice site choice in some pre-mRNAs. Pivotal to these functions is the association of Pat1 proteins with distinct heptameric Lsm complexes: the cytosolic Pat1/Lsm1-7 complex mediates mRNA decay and the nuclear Pat1/Lsm2-8 complex alternative splicing. This dual role of human Pat1b illustrates the power of paralogous complexes to impact distinct processes in separate compartments. The review highlights our recent findings that Pat1b mediates the decay of AU-rich mRNAs, which are particularly enriched in P-bodies, unlike the decapping activator DDX6, which acts on GC-rich mRNAs, that tend to be excluded from P-bodies, and discuss the implications for mRNA decay pathways. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNRNA Processing > Splicing Regulation/Alternative Splicing Translation > Translation Regulation.
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Affiliation(s)
- Caroline Vindry
- Centre International de Recherche en Infectiologie, CIRI, Lyon, France
| | - Dominique Weil
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie du Développement, Paris, France
| | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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Vindry C, Marnef A, Broomhead H, Twyffels L, Ozgur S, Stoecklin G, Llorian M, Smith CW, Mata J, Weil D, Standart N. Dual RNA Processing Roles of Pat1b via Cytoplasmic Lsm1-7 and Nuclear Lsm2-8 Complexes. Cell Rep 2018; 20:1187-1200. [PMID: 28768202 PMCID: PMC5554784 DOI: 10.1016/j.celrep.2017.06.091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/12/2017] [Accepted: 06/28/2017] [Indexed: 12/16/2022] Open
Abstract
Pat1 RNA-binding proteins, enriched in processing bodies (P bodies), are key players in cytoplasmic 5' to 3' mRNA decay, activating decapping of mRNA in complex with the Lsm1-7 heptamer. Using co-immunoprecipitation and immunofluorescence approaches coupled with RNAi, we provide evidence for a nuclear complex of Pat1b with the Lsm2-8 heptamer, which binds to the spliceosomal U6 small nuclear RNA (snRNA). Furthermore, we establish the set of interactions connecting Pat1b/Lsm2-8/U6 snRNA/SART3 and additional U4/U6.U5 tri-small nuclear ribonucleoprotein particle (tri-snRNP) components in Cajal bodies, the site of snRNP biogenesis. RNA sequencing following Pat1b depletion revealed the preferential upregulation of mRNAs normally found in P bodies and enriched in 3' UTR AU-rich elements. Changes in >180 alternative splicing events were also observed, characterized by skipping of regulated exons with weak donor sites. Our data demonstrate the dual role of a decapping enhancer in pre-mRNA processing as well as in mRNA decay via distinct nuclear and cytoplasmic Lsm complexes.
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Affiliation(s)
- Caroline Vindry
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse UT3, 31062 Toulouse, France
| | - Helen Broomhead
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Laure Twyffels
- Center for Microscopy and Molecular Imaging (CMMI), Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Sevim Ozgur
- Max Planck Institute of Biochemistry, Am Klopferspitz, 82152 Martinsried, Germany
| | - Georg Stoecklin
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, Heidelberg University, 69047 Heidelberg, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69047 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 68167 Mannheim, Germany
| | - Miriam Llorian
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Christopher W Smith
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Dominique Weil
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie du développement Paris Seine - Institut de Biologie Paris Seine (LBD - IBPS), 75005 Paris, France
| | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
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Reimer KA, Stark MR, Aguilar LC, Stark SR, Burke RD, Moore J, Fahlman RP, Yip CK, Kuroiwa H, Oeffinger M, Rader SD. The sole LSm complex in Cyanidioschyzon merolae associates with pre-mRNA splicing and mRNA degradation factors. RNA (NEW YORK, N.Y.) 2017; 23:952-967. [PMID: 28325844 PMCID: PMC5435867 DOI: 10.1261/rna.058487.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 03/15/2017] [Indexed: 05/22/2023]
Abstract
Proteins of the Sm and Sm-like (LSm) families, referred to collectively as (L)Sm proteins, are found in all three domains of life and are known to promote a variety of RNA processes such as base-pair formation, unwinding, RNA degradation, and RNA stabilization. In eukaryotes, (L)Sm proteins have been studied, inter alia, for their role in pre-mRNA splicing. In many organisms, the LSm proteins form two distinct complexes, one consisting of LSm1-7 that is involved in mRNA degradation in the cytoplasm, and the other consisting of LSm2-8 that binds spliceosomal U6 snRNA in the nucleus. We recently characterized the splicing proteins from the red alga Cyanidioschyzon merolae and found that it has only seven LSm proteins. The identities of CmLSm2-CmLSm7 were unambiguous, but the seventh protein was similar to LSm1 and LSm8. Here, we use in vitro binding measurements, microscopy, and affinity purification-mass spectrometry to demonstrate a canonical splicing function for the C. merolae LSm complex and experimentally validate our bioinformatic predictions of a reduced spliceosome in this organism. Copurification of Pat1 and its associated mRNA degradation proteins with the LSm proteins, along with evidence of a cytoplasmic fraction of CmLSm complexes, argues that this complex is involved in both splicing and cytoplasmic mRNA degradation. Intriguingly, the Pat1 complex also copurifies with all four snRNAs, suggesting the possibility of a spliceosome-associated pre-mRNA degradation complex in the nucleus.
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Affiliation(s)
- Kirsten A Reimer
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Martha R Stark
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Lisbeth-Carolina Aguilar
- Laboratory of RNP Biochemistry, Institut de Recherches Cliniques de Montréal (IRCM), Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Sierra R Stark
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Robert D Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Jack Moore
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Haruko Kuroiwa
- Kuroiwa Initiative Research Unit, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Marlene Oeffinger
- Laboratory of RNP Biochemistry, Institut de Recherches Cliniques de Montréal (IRCM), Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC H2W 1R7, Canada
| | - Stephen D Rader
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
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