1
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Jang S, Bedwell GJ, Singh SP, Yu HJ, Arnarson B, Singh PK, Radhakrishnan R, Douglas AW, Ingram ZM, Freniere C, Akkermans O, Sarafianos SG, Ambrose Z, Xiong Y, Anekal PV, Montero Llopis P, KewalRamani VN, Francis AC, Engelman AN. HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration. Nucleic Acids Res 2024:gkae769. [PMID: 39258548 DOI: 10.1093/nar/gkae769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/13/2024] [Accepted: 08/25/2024] [Indexed: 09/12/2024] Open
Abstract
HIV-1 integration favors nuclear speckle (NS)-proximal chromatin and viral infection induces the formation of capsid-dependent CPSF6 condensates that colocalize with nuclear speckles (NSs). Although CPSF6 displays liquid-liquid phase separation (LLPS) activity in vitro, the contributions of its different intrinsically disordered regions, which includes a central prion-like domain (PrLD) with capsid binding FG motif and C-terminal mixed-charge domain (MCD), to LLPS activity and to HIV-1 infection remain unclear. Herein, we determined that the PrLD and MCD both contribute to CPSF6 LLPS activity in vitro. Akin to FG mutant CPSF6, infection of cells expressing MCD-deleted CPSF6 uncharacteristically arrested at the nuclear rim. While heterologous MCDs effectively substituted for CPSF6 MCD function during HIV-1 infection, Arg-Ser domains from related SR proteins were largely ineffective. While MCD-deleted and wildtype CPSF6 proteins displayed similar capsid binding affinities, the MCD imparted LLPS-dependent higher-order binding and co-aggregation with capsids in vitro and in cellulo. NS depletion reduced CPSF6 puncta formation without significantly affecting integration into NS-proximal chromatin, and appending the MCD onto a heterologous capsid binding protein partially restored virus nuclear penetration and integration targeting in CPSF6 knockout cells. We conclude that MCD-dependent CPSF6 condensation with capsids underlies post-nuclear incursion for viral DNA integration and HIV-1 pathogenesis.
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Affiliation(s)
- Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Satya P Singh
- Institute of Molecular Biophysics, Department of Biological Sciences, Florida State University, Tallahassee, FL 32304, USA
| | - Hyun Jae Yu
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Bjarki Arnarson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Rajalingam Radhakrishnan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - AidanDarian W Douglas
- Institute of Molecular Biophysics, Department of Biological Sciences, Florida State University, Tallahassee, FL 32304, USA
| | - Zachary M Ingram
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Christian Freniere
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Onno Akkermans
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Zandrea Ambrose
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Praju V Anekal
- MicRoN Core, Harvard Medical School, Boston, MA 02215, USA
| | | | - Vineet N KewalRamani
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Ashwanth C Francis
- Institute of Molecular Biophysics, Department of Biological Sciences, Florida State University, Tallahassee, FL 32304, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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2
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Liu X, Xie H, Liu W, Zuo J, Li S, Tian Y, Zhao J, Bai M, Li J, Bao L, Han J, Zhang ZC. Dynamic regulation of alternative polyadenylation by PQBP1 during neurogenesis. Cell Rep 2024; 43:114525. [PMID: 39037895 DOI: 10.1016/j.celrep.2024.114525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/07/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
Alternative polyadenylation (APA) is a critical post-transcriptional process that generates mRNA isoforms with distinct 3' untranslated regions (3' UTRs), thereby regulating mRNA localization, stability, and translational efficiency. Cell-type-specific APA extensively shapes the diversity of the cellular transcriptome, particularly during cell fate transition. Despite its recognized significance, the precise regulatory mechanisms governing cell-type-specific APA remain unclear. In this study, we uncover PQBP1 as an emerging APA regulator that actively maintains cell-specific APA profiles in neural progenitor cells (NPCs) and delicately manages the equilibrium between NPC proliferation and differentiation. Multi-omics analysis shows that PQBP1 directly interacts with the upstream UGUA elements, impeding the recruitment of the CFIm complex and influencing polyadenylation site selection within genes associated with the cell cycle. Our findings elucidate the molecular mechanism by which PQBP1 orchestrates dynamic APA changes during neurogenesis, providing valuable insights into the precise regulation of cell-type-specific APA and the underlying pathogenic mechanisms in neurodevelopmental disorders.
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Affiliation(s)
- Xian Liu
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Hao Xie
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Wenhua Liu
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Jian Zuo
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Song Li
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Yao Tian
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | | | - Meizhu Bai
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lan Bao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junhai Han
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226019, China.
| | - Zi Chao Zhang
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China.
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3
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Mironov A, Franchitti L, Ghosh S, Ritz MF, Hutter G, De Bortoli M, Zavolan M. Leveraging multi-omics data to infer regulators of mRNA 3' end processing in glioblastoma. Front Mol Biosci 2024; 11:1363933. [PMID: 39188787 PMCID: PMC11345230 DOI: 10.3389/fmolb.2024.1363933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 07/24/2024] [Indexed: 08/28/2024] Open
Abstract
Alterations in mRNA 3' end processing and polyadenylation are widely implicated in the biology of many cancer types, including glioblastoma (GBM), one the most aggressive tumor types. Although several RNA-binding proteins (RBPs) responsible for alternative polyadenylation (APA) were identified from functional studies in cell lines, their contribution to the APA landscape in tumors in vivo was not thoroughly addressed. In this study we analyzed a large RNA-seq data set of glioblastoma (GBM) samples from The Cancer Genome Atlas (TCGA) to identify APA patterns differentiating the main molecular subtypes of GBM. We superimposed these to RBP footprinting data and to APA events occurring upon depletion of individual RBPs from a large panel tested by the ENCODE Consortium. Our analysis revealed 22 highly concordant and statistically significant RBP-APA associations, whereby changes in RBP expression were accompanied by APA in both TCGA and ENCODE datasets. Among these, we found a previously unknown PTBP1-regulated APA event in the PRRC2B gene and an HNRNPU-regulated event in the SC5D gene. Both of these were further supported by RNA-sequencing data of paired tumor center-periphery GBM samples obtained at the University Hospital of Basel. In addition, we validated the regulation of APA in PRRC2B by PTBP1 in siRNA-knockdown and overexpression experiments followed by RNA-sequencing in two glioblastoma cell lines. The transcriptome analysis workflow that we present here enables the identification of concordant RBP-APA associations in cancers.
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Affiliation(s)
| | - Lorenzo Franchitti
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | | | | | - Gregor Hutter
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Michele De Bortoli
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
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4
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Bialas K, Diaz-Griffero F. HIV-1-induced translocation of CPSF6 to biomolecular condensates. Trends Microbiol 2024; 32:781-790. [PMID: 38267295 PMCID: PMC11263504 DOI: 10.1016/j.tim.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Cleavage and polyadenylation specificity factor subunit 6 (CPSF6, also known as CFIm68) is a 68 kDa component of the mammalian cleavage factor I (CFIm) complex that modulates mRNA alternative polyadenylation (APA) and determines 3' untranslated region (UTR) length, an important gene expression control mechanism. CPSF6 directly interacts with the HIV-1 core during infection, suggesting involvement in HIV-1 replication. Here, we review the contributions of CPSF6 to every stage of the HIV-1 replication cycle. Recently, several groups described the ability of HIV-1 infection to induce CPSF6 translocation to nuclear speckles, which are biomolecular condensates. We discuss the implications for CPSF6 localization in condensates and the potential role of condensate-localized CPSF6 in the ability of HIV-1 to control the protein expression pattern of the cell.
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Affiliation(s)
- Katarzyna Bialas
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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5
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Fanara S, Schloesser M, Joris M, De Franco S, Vandevenne M, Kerff F, Hanikenne M, Motte P. The Arabidopsis SR45 splicing factor bridges the splicing machinery and the exon-exon junction complex. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2280-2298. [PMID: 38180875 DOI: 10.1093/jxb/erae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/04/2024] [Indexed: 01/07/2024]
Abstract
The Arabidopsis splicing factor serine/arginine-rich 45 (SR45) contributes to several biological processes. The sr45-1 loss-of-function mutant exhibits delayed root development, late flowering, unusual numbers of floral organs, shorter siliques with decreased seed sets, narrower leaves and petals, and altered metal distribution. SR45 bears a unique RNA recognition motif (RRM) flanked by one serine/arginine-rich (RS) domain on both sides. Here, we studied the function of each SR45 domains by examining their involvement in: (i) the spatial distribution of SR45; (ii) the establishment of a protein-protein interaction network including spliceosomal and exon-exon junction complex (EJC) components; and (iii) the RNA binding specificity. We report that the endogenous SR45 promoter is active during vegetative and reproductive growth, and that the SR45 protein localizes in the nucleus. We demonstrate that the C-terminal arginine/serine-rich domain is a determinant of nuclear localization. We show that the SR45 RRM domain specifically binds purine-rich RNA motifs via three residues (H101, H141, and Y143), and is also involved in protein-protein interactions. We further show that SR45 bridges both mRNA splicing and surveillance machineries as a partner of EJC core components and peripheral factors, which requires phosphoresidues probably phosphorylated by kinases from both the CLK and SRPK families. Our findings provide insights into the contribution of each SR45 domain to both spliceosome and EJC assemblies.
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Affiliation(s)
- Steven Fanara
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Marie Schloesser
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Marine Joris
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Simona De Franco
- InBioS-Center for Protein Engineering, Laboratory of Biological Macromolecules, University of Liège, 4000, Liège, Belgium
| | - Marylène Vandevenne
- InBioS-Center for Protein Engineering, Laboratory of Biological Macromolecules, University of Liège, 4000, Liège, Belgium
| | - Frédéric Kerff
- InBioS-Center for Protein Engineering, Laboratory of Crystallography, University of Liège, 4000, Liège, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, 4000, Liège, Belgium
| | - Patrick Motte
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
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6
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Zhou Y, Yang J, Huang L, Liu C, Yu M, Chen R, Zhou Q. Nudt21-mediated alternative polyadenylation of MZT1 3'UTR contributes to pancreatic cancer progression. iScience 2024; 27:108822. [PMID: 38303721 PMCID: PMC10831950 DOI: 10.1016/j.isci.2024.108822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/26/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism and is involved in many diseases, but its function and mechanism in regulating pancreatic cancer (PC) pathogenesis remain unclear. In this study, we found that the 3' UTR shortening of MZT1 was the most prominent APA event in PC liver metastases. The short-3'UTR isoform exerted a stronger effect in promoting cell proliferation and migration both in vitro and in vivo. NUDT21, a core cleavage factor involved in APA, promoted the usage of proximal polyadenylation sites (PASs) on MZT1 mRNA by binding to the UGUA element located upstream of the proximal PAS. High percentage of distal polyA site usage index of MZT1 was significantly associated with a better prognosis. These findings demonstrate a crucial mechanism that NUDT21-mediated APA of MZT1 could promote the progression of PC. Our findings provided a better understanding of the connection between PC progression and APA machinery.
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Affiliation(s)
- Yu Zhou
- Department of Pancreatic Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jiabin Yang
- Department of Pancreatic Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong Province, China
| | - Leyi Huang
- Department of Pancreatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Chao Liu
- Department of Pathology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Min Yu
- Department of Pancreatic Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
| | - Rufu Chen
- Department of Pancreatic Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
| | - Quanbo Zhou
- Department of Pancreatic Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
- Department of Pancreatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
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7
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Gao G, Sumrall ES, Pitchiaya S, Bitzer M, Alberti S, Walter NG. Biomolecular condensates in kidney physiology and disease. Nat Rev Nephrol 2023; 19:756-770. [PMID: 37752323 DOI: 10.1038/s41581-023-00767-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2023] [Indexed: 09/28/2023]
Abstract
The regulation and preservation of distinct intracellular and extracellular solute microenvironments is crucial for the maintenance of cellular homeostasis. In mammals, the kidneys control bodily salt and water homeostasis. Specifically, the urine-concentrating mechanism within the renal medulla causes fluctuations in extracellular osmolarity, which enables cells of the kidney to either conserve or eliminate water and electrolytes, depending on the balance between intake and loss. However, relatively little is known about the subcellular and molecular changes caused by such osmotic stresses. Advances have shown that many cells, including those of the kidney, rapidly (within seconds) and reversibly (within minutes) assemble membraneless, nano-to-microscale subcellular assemblies termed biomolecular condensates via the biophysical process of hyperosmotic phase separation (HOPS). Mechanistically, osmotic cell compression mediates changes in intracellular hydration, concentration and molecular crowding, rendering HOPS one of many related phase-separation phenomena. Osmotic stress causes numerous homo-multimeric proteins to condense, thereby affecting gene expression and cell survival. HOPS rapidly regulates specific cellular biochemical processes before appropriate protective or corrective action by broader stress response mechanisms can be initiated. Here, we broadly survey emerging evidence for, and the impact of, biomolecular condensates in nephrology, where initial concentration buffering by HOPS and its subsequent cellular escalation mechanisms are expected to have important implications for kidney physiology and disease.
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Affiliation(s)
- Guoming Gao
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | - Emily S Sumrall
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Markus Bitzer
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Simon Alberti
- Technische Universität Dresden, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Engineering (CMCB), Dresden, Germany
| | - Nils G Walter
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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8
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Hunter OV, Ruiz JC, Flaherty JN, Conrad NK. Functional analysis of 3'-UTR hairpins supports a two-tiered model for posttranscriptional regulation of MAT2A by METTL16. RNA (NEW YORK, N.Y.) 2023; 29:1725-1737. [PMID: 37567786 PMCID: PMC10578476 DOI: 10.1261/rna.079695.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023]
Abstract
S-adenosylmethionine (SAM) is the methyl donor for nearly all cellular methylation events, so cells need to carefully control SAM levels. MAT2A encodes the only SAM synthetase expressed in the majority of human cells, and its 3'-UTR has six conserved regulatory hairpins (hp1-6) that can be methylated by the N6-methyladenosine methyltransferase METTL16. Hp1 begins 8 nt from the stop codon, whereas hp2-6 are clustered further downstream (∼800 nt). These hairpins have been proposed to regulate MAT2A mRNA levels in response to intracellular SAM levels by regulating intron detention of the last intron of MAT2A and by modulating the stability of the fully spliced mRNA. However, a dissection of these two posttranscriptional mechanisms has not been previously reported. Using a modular reporter system, we show that hp1 functions primarily when the detained intron is included in the reporter and when that intron has a suboptimal polypyrimidine tract. In contrast, the hp2-6 cluster modulates mRNA stability independent of the detained intron, although hp1 may make a minor contribution to the regulation of decay as well. Taken with previously published reports, these data support a two-tiered model for MAT2A posttranscriptional regulation by METTL16 through its interactions with hp1 and hp2-6. In the upstream tier, hp1 and METTL16 control MAT2A intron detention, whereas the second tier involves METTL16-dependent methylation of hp2-6 to control MAT2A mRNA stability. Thus, cells use a similar set of molecular factors to achieve considerable complexity in the posttranscriptional regulation of SAM homeostasis.
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Affiliation(s)
- Olga V Hunter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Julio C Ruiz
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Juliana N Flaherty
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Nicholas K Conrad
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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9
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Liu S, Wu R, Chen L, Deng K, Ou X, Lu X, Li M, Liu C, Chen S, Fu Y, Xu A. CPSF6 regulates alternative polyadenylation and proliferation of cancer cells through phase separation. Cell Rep 2023; 42:113197. [PMID: 37777964 DOI: 10.1016/j.celrep.2023.113197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 06/20/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023] Open
Abstract
Cancer cells usually exhibit shortened 3' untranslated regions (UTRs) due to alternative polyadenylation (APA) to promote cell proliferation and migration. Upregulated CPSF6 leads to a systematic prolongation of 3' UTRs, but CPSF6 expression in tumors is typically higher than that in healthy tissues. This contradictory observation suggests that it is necessary to investigate the underlying mechanism by which CPSF6 regulates APA switching in cancer. Here, we find that CPSF6 can undergo liquid-liquid phase separation (LLPS), and elevated LLPS is associated with the preferential usage of the distal poly(A) sites. CLK2, a kinase upregulated in cancer cells, destructs CPSF6 LLPS by phosphorylating its arginine/serine-like domain. The reduction of CPSF6 LLPS can lead to a shortened 3' UTR of cell-cycle-related genes and accelerate cell proliferation. These results suggest that CPSF6 LLPS, rather than its expression level, may be responsible for APA regulation in cancer cells.
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Affiliation(s)
- Susu Liu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Runze Wu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Liutao Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Ke Deng
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Xin Ou
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Xin Lu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Mengxia Li
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Chao Liu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Shangwu Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Yonggui Fu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China.
| | - Anlong Xu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China; School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, P.R. China.
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10
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Herron RS, Kunisky AK, Madden JR, Anyaeche VI, Maung MZ, Hwang HW. A twin UGUA motif directs the balance between gene isoforms through CFIm and the mTORC1 signaling pathway. eLife 2023; 12:e85036. [PMID: 37665675 PMCID: PMC10476966 DOI: 10.7554/elife.85036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/16/2023] [Indexed: 09/06/2023] Open
Abstract
Alternative polyadenylation (APA) generates mRNA isoforms and diversifies gene expression. Here we report the discovery that the mTORC1 signaling pathway balances the expression of two Trim9/TRIM9 isoforms through APA regulation in human and mouse. We showed that CFIm components, CPSF6 and NUDT21, promote the short Trim9/TRIM9 isoform (Trim9-S/TRIM9-S) expression. In addition, we identified an evolutionarily conserved twin UGUA motif, UGUAYUGUA, in TRIM9-S polyadenylation site (PAS) that is critical for its regulation by CPSF6. We found additional CPSF6-regulated PASs with similar twin UGUA motifs in human and experimentally validated the twin UGUA motif functionality in BMPR1B, MOB4, and BRD4-L. Importantly, we showed that inserting a twin UGUA motif into a heterologous PAS was sufficient to confer regulation by CPSF6 and mTORC1. Our study reveals an evolutionarily conserved mechanism to regulate gene isoform expression by mTORC1 and implicates possible gene isoform imbalance in cancer and neurological disorders with mTORC1 pathway dysregulation.
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Affiliation(s)
- R Samuel Herron
- Department of Pathology, University of PittsburghPittsburghUnited States
| | | | - Jessica R Madden
- Department of Pathology, University of PittsburghPittsburghUnited States
| | - Vivian I Anyaeche
- Department of Pathology, University of PittsburghPittsburghUnited States
| | - May Z Maung
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Hun-Way Hwang
- Department of Pathology, University of PittsburghPittsburghUnited States
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11
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Swale C, Hakimi MA. 3'-end mRNA processing within apicomplexan parasites, a patchwork of classic, and unexpected players. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1783. [PMID: 36994829 DOI: 10.1002/wrna.1783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 03/31/2023]
Abstract
The 3'-end processing of mRNA is a co-transcriptional process that leads to the formation of a poly-adenosine tail on the mRNA and directly controls termination of the RNA polymerase II juggernaut. This process involves a megadalton complex composed of cleavage and polyadenylation specificity factors (CPSFs) that are able to recognize cis-sequence elements on nascent mRNA to then carry out cleavage and polyadenylation reactions. Recent structural and biochemical studies have defined the roles played by different subunits of the complex and provided a comprehensive mechanistic understanding of this machinery in yeast or metazoans. More recently, the discovery of small molecule inhibitors of CPSF function in Apicomplexa has stimulated interest in studying the specificities of this ancient eukaryotic machinery in these organisms. Although its function is conserved in Apicomplexa, the CPSF complex integrates a novel reader of the N6-methyladenosine (m6A). This feature, inherited from the plant kingdom, bridges m6A metabolism directly to 3'-end processing and by extension, to transcription termination. In this review, we will examine convergence and divergence of CPSF within the apicomplexan parasites and explore the potential of small molecule inhibition of this machinery within these organisms. This article is categorized under: RNA Processing > 3' End Processing RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Christopher Swale
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Grenoble Alpes University, Grenoble, France
| | - Mohamed-Ali Hakimi
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Grenoble Alpes University, Grenoble, France
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12
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Ay S, Di Nunzio F. HIV-Induced CPSF6 Condensates. J Mol Biol 2023; 435:168094. [PMID: 37061085 DOI: 10.1016/j.jmb.2023.168094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/17/2023]
Abstract
Viruses are obligate parasites that rely on their host's cellular machinery for replication. To facilitate their replication cycle, many viruses have been shown to remodel the cellular architecture by inducing the formation of membraneless organelles (MLOs). Eukaryotic cells have evolved MLOs that are highly dynamic, self-organizing microenvironments that segregate biological processes and increase the efficiency of reactions by concentrating enzymes and substrates. In the context of viral infections, MLOs can be utilized by viruses to complete their replication cycle. This review focuses on the pathway used by the HIV-1 virus to remodel the nuclear landscape of its host, creating viral/host niches that enable efficient viral replication. Specifically, we discuss how the interaction between the HIV-1 capsid and the cellular factor CPSF6 triggers the formation of nuclear MLOs that support nuclear reverse transcription and viral integration in favored regions of the host chromatin. This review compiles current knowledge on the origin of nuclear HIV-MLOs and their role in early post-nuclear entry steps of the HIV-1 replication cycle.
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Affiliation(s)
- Selen Ay
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Francesca Di Nunzio
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur, Université Paris Cité, 75015 Paris, France.
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13
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Masamha CP. The emerging roles of CFIm25 (NUDT21/CPSF5) in human biology and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1757. [PMID: 35965101 PMCID: PMC9925614 DOI: 10.1002/wrna.1757] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/11/2022]
Abstract
The mammalian cleavage factor I subunit CFIm25 (NUDT21) binds to the UGUA sequences of precursor RNAs. Traditionally, CFIm25 is known to facilitate 3' end formation of pre-mRNAs resulting in the formation of polyadenylated transcripts. Recent studies suggest that CFIm25 may be involved in the cyclization and hence generation of circular RNAs (circRNAs) that contain UGUA motifs. These circRNAs act as competing endogenous RNAs (ceRNAs) that disrupt the ceRNA-miRNA-mRNA axis. Other emerging roles of CFIm25 include regulating both alternative splicing and alternative polyadenylation (APA). APA generates different sized transcripts that may code for different proteins, or more commonly transcripts that code for the same protein but differ in the length and sequence content of their 3' UTRs (3' UTR-APA). CFIm25 mediated global changes in 3' UTR-APA affect human physiology including spermatogenesis and the determination of cell fate. Deregulation of CFIm25 and changes in 3' UTR-APA have been implicated in several human diseases including cancer. In many cancers, CFIm25 acts as a tumor suppressor. However, there are some cancers where CFIm25 has the opposite effect. Alterations in CFIm25-driven 3' UTR-APA may also play a role in neural dysfunction and fibrosis. CFIm25 mediated 3' UTR-APA changes can be used to generate specific signatures that can be used as potential biomarkers in development and disease. Due to the emerging role of CFIm25 as a regulator of the aforementioned RNA processing events, modulation of CFIm25 levels may be a novel viable therapeutic approach. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Chioniso Patience Masamha
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Butler University, Indianapolis, Indiana, USA
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14
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Comparative genomics and interactomics of polyadenylation factors for the prediction of new parasite targets: Entamoeba histolytica as a working model. Biosci Rep 2023; 43:232462. [PMID: 36651565 PMCID: PMC9912109 DOI: 10.1042/bsr20221911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Protein-protein interactions (PPI) play a key role in predicting the function of a target protein and drug ability to affect an entire biological system. Prediction of PPI networks greatly contributes to determine a target protein and signal pathways related to its function. Polyadenylation of mRNA 3'-end is essential for gene expression regulation and several polyadenylation factors have been shown as valuable targets for controlling protozoan parasites that affect human health. Here, by using a computational strategy based on sequence-based prediction approaches, phylogenetic analyses, and computational prediction of PPI networks, we compared interactomes of polyadenylation factors in relevant protozoan parasites and the human host, to identify key proteins and define potential targets for pathogen control. Then, we used Entamoeba histolytica as a working model to validate our computational results. RT-qPCR assays confirmed the coordinated modulation of connected proteins in the PPI network and evidenced that silencing of the bottleneck protein EhCFIm25 affects the expression of interacting proteins. In addition, molecular dynamics simulations and docking approaches allowed to characterize the relationships between EhCFIm25 and Ehnopp34, two connected bottleneck proteins. Interestingly, the experimental identification of EhCFIm25 interactome confirmed the close relationships among proteins involved in gene expression regulation and evidenced new links with moonlight proteins in E. histolytica, suggesting a connection between RNA biology and metabolism as described in other organisms. Altogether, our results strengthened the relevance of comparative genomics and interactomics of polyadenylation factors for the prediction of new targets for the control of these human pathogens.
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15
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Xiao S, Gu H, Deng L, Yang X, Qiao D, Zhang X, Zhang T, Yu T. Relationship between NUDT21 mediated alternative polyadenylation process and tumor. Front Oncol 2023; 13:1052012. [PMID: 36816917 PMCID: PMC9933127 DOI: 10.3389/fonc.2023.1052012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Alternative polyadenylation (APA) is a molecular process that generates diversity at the 3' end of RNA polymerase II transcripts from over 60% of human genes. APA and microRNA regulation are both mechanisms of post-transcriptional regulation of gene expression. As a key molecular mechanism, Alternative polyadenylation often results in mRNA isoforms with the same coding sequence but different lengths of 3' UTRs, while microRNAs regulate gene expression by binding to specific mRNA 3' UTRs. Nudix Hydrolase 21 (NUDT21) is a crucial mediator involved in alternative polyadenylation (APA). Different studies have reported a dual role of NUDT21 in cancer (both oncogenic and tumor suppressor). The present review focuses on the functions of APA, miRNA and their interaction and roles in development of different types of tumors.NUDT21 mediated 3' UTR-APA changes can be used to generate specific signatures that can be used as potential biomarkers in development and disease. Due to the emerging role of NUDT21 as a regulator of the aforementioned RNA processing events, modulation of NUDT21 levels may be a novel viable therapeutic approach.
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Affiliation(s)
- Shan Xiao
- Department of Oncology, Affiliated Hospital of Southwest Medical University of China, Luzhou, China
| | - Huan Gu
- Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Li Deng
- Department of Oncology, Affiliated Hospital of Southwest Medical University of China, Luzhou, China
| | - Xiongtao Yang
- Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Dan Qiao
- Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xudong Zhang
- Department of Anesthesia, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Tian Zhang
- Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,*Correspondence: Tao Yu, ; Tian Zhang,
| | - Tao Yu
- Department of Oncology, Affiliated Hospital of Southwest Medical University of China, Luzhou, China,Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,*Correspondence: Tao Yu, ; Tian Zhang,
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16
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Carrasco J, Mateos F, Hilgers V. A critical developmental window for ELAV/Hu-dependent mRNA signatures at the onset of neuronal differentiation. Cell Rep 2022; 41:111542. [PMID: 36288718 PMCID: PMC9631114 DOI: 10.1016/j.celrep.2022.111542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/16/2022] [Accepted: 09/30/2022] [Indexed: 12/01/2022] Open
Abstract
Cell-type-specific gene regulatory programs are essential for cell differentiation and function. In animal neurons, the highly conserved ELAV/Hu family of proteins promotes alternative splicing and polyadenylation of mRNA precursors to create unique neuronal transcript isoforms. Here, we assess transcriptome profiles and neurogenesis success in Drosophila models engineered to express differing levels of ELAV activity in the course of development. We show that the ELAV-mediated establishment of a subset of neuronal mRNA isoforms at the onset of neuron differentiation constitutes a developmental bottleneck that cannot be overcome later by the nuclear activation of the paralog found in neurons (FNE). Loss of ELAV function outside of that critical time window results in neurological defects. We find that FNE, when activated early enough, can restore ELAV-dependent neuronal mRNA isoforms and fully rescue development. Our findings demonstrate the essential role of robust cellular strategies to maintain ELAV activity and intact neuronal signatures in neurogenesis and neuronal function.
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Affiliation(s)
- Judit Carrasco
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, Albert Ludwig University, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), 79108 Freiburg, Germany
| | - Fernando Mateos
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Valérie Hilgers
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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17
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Tseng HW, Mota-Sydor A, Leventis R, Jovanovic P, Topisirovic I, Duchaine T. Distinct, opposing functions for CFIm59 and CFIm68 in mRNA alternative polyadenylation of Pten and in the PI3K/Akt signalling cascade. Nucleic Acids Res 2022; 50:9397-9412. [PMID: 35993810 PMCID: PMC9458458 DOI: 10.1093/nar/gkac704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 07/29/2022] [Accepted: 08/18/2022] [Indexed: 12/24/2022] Open
Abstract
Precise maintenance of PTEN dosage is crucial for tumor suppression across a wide variety of cancers. Post-transcriptional regulation of Pten heavily relies on regulatory elements encoded by its 3'UTR. We previously reported the important diversity of 3'UTR isoforms of Pten mRNAs produced through alternative polyadenylation (APA). Here, we reveal the direct regulation of Pten APA by the mammalian cleavage factor I (CFIm) complex, which in turn contributes to PTEN protein dosage. CFIm consists of the UGUA-binding CFIm25 and APA regulatory subunits CFIm59 or CFIm68. Deep sequencing analyses of perturbed (KO and KD) cell lines uncovered the differential regulation of Pten APA by CFIm59 and CFIm68 and further revealed that their divergent functions have widespread impact for APA in transcriptomes. Differentially regulated genes include numerous factors within the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signalling pathway that PTEN counter-regulates. We further reveal a stratification of APA dysregulation among a subset of PTEN-driven cancers, with recurrent alterations among PI3K/Akt pathway genes regulated by CFIm. Our results refine the transcriptome selectivity of the CFIm complex in APA regulation, and the breadth of its impact in PTEN-driven cancers.
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Affiliation(s)
- Hsin-Wei Tseng
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal H3G 1Y6, Canada,Department of Biochemistry, McGill University, Montréal,H3G 1Y6, Canada
| | - Anthony Mota-Sydor
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal H3G 1Y6, Canada,Department of Biochemistry, McGill University, Montréal,H3G 1Y6, Canada
| | - Rania Leventis
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal H3G 1Y6, Canada,Department of Biochemistry, McGill University, Montréal,H3G 1Y6, Canada
| | - Predrag Jovanovic
- Lady Davis Institute for Medical Research, Montréal H3T 1E2, Canada,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal H4A 3J1, Canada
| | - Ivan Topisirovic
- Department of Biochemistry, McGill University, Montréal,H3G 1Y6, Canada,Lady Davis Institute for Medical Research, Montréal H3T 1E2, Canada,Gerald Bronfman Department of Oncology, McGill University, Montréal H4A 3T2, Canada,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal H4A 3J1, Canada
| | - Thomas F Duchaine
- To whom correspondence should be addressed. Tel: +1 514 918 0639; Fax: +1 514 398 6769;
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18
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Song J, Nabeel-Shah S, Pu S, Lee H, Braunschweig U, Ni Z, Ahmed N, Marcon E, Zhong G, Ray D, Ha KCH, Guo X, Zhang Z, Hughes TR, Blencowe BJ, Greenblatt JF. Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1. Mol Cell 2022; 82:3135-3150.e9. [PMID: 35914531 DOI: 10.1016/j.molcel.2022.06.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/09/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022]
Abstract
Alternative polyadenylation (APA) enhances gene regulatory potential by increasing the diversity of mRNA transcripts. 3' UTR shortening through APA correlates with enhanced cellular proliferation and is a widespread phenomenon in tumor cells. Here, we show that the ubiquitously expressed transcription factor Sp1 binds RNA in vivo and is a common repressor of distal poly(A) site usage. RNA sequencing identified 2,344 genes (36% of the total mapped mRNA transcripts) with lengthened 3' UTRs upon Sp1 depletion. Sp1 preferentially binds the 3' UTRs of such lengthened transcripts and inhibits cleavage at distal sites by interacting with the subunits of the core cleavage and polyadenylation (CPA) machinery. The 3' UTR lengths of Sp1 target genes in breast cancer patient RNA-seq data correlate with Sp1 expression levels, implicating Sp1-mediated APA regulation in modulating tumorigenic properties. Taken together, our findings provide insights into the mechanism for dynamic APA regulation by unraveling a previously unknown function of the DNA-binding transcription factor Sp1.
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Affiliation(s)
- Jingwen Song
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Shuye Pu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Hyunmin Lee
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, 10 King's College Road, Toronto, ON M5S 3G4, Canada
| | - Ulrich Braunschweig
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Zuyao Ni
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Nujhat Ahmed
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Edyta Marcon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Guoqing Zhong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Debashish Ray
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Kevin C H Ha
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Xinghua Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada; Department of Computer Science, University of Toronto, 10 King's College Road, Toronto, ON M5S 3G4, Canada
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada.
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19
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Yu L, Majerciak V, Zheng ZM. HPV16 and HPV18 Genome Structure, Expression, and Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094943. [PMID: 35563334 PMCID: PMC9105396 DOI: 10.3390/ijms23094943] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/18/2022] Open
Abstract
Human papillomaviruses (HPV) are a group of small non-enveloped DNA viruses whose infection causes benign tumors or cancers. HPV16 and HPV18, the two most common high-risk HPVs, are responsible for ~70% of all HPV-related cervical cancers and head and neck cancers. The expression of the HPV genome is highly dependent on cell differentiation and is strictly regulated at the transcriptional and post-transcriptional levels. Both HPV early and late transcripts differentially expressed in the infected cells are intron-containing bicistronic or polycistronic RNAs bearing more than one open reading frame (ORF), because of usage of alternative viral promoters and two alternative viral RNA polyadenylation signals. Papillomaviruses proficiently engage alternative RNA splicing to express individual ORFs from the bicistronic or polycistronic RNA transcripts. In this review, we discuss the genome structures and the updated transcription maps of HPV16 and HPV18, and the latest research advances in understanding RNA cis-elements, intron branch point sequences, and RNA-binding proteins in the regulation of viral RNA processing. Moreover, we briefly discuss the epigenetic modifications, including DNA methylation and possible APOBEC-mediated genome editing in HPV infections and carcinogenesis.
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20
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Zhang X, Nomoto M, Garcia-León M, Takahashi N, Kato M, Yura K, Umeda M, Rubio V, Tada Y, Furumoto T, Aoyama T, Tsuge T. CFI 25 Subunit of Cleavage Factor I is Important for Maintaining the Diversity of 3' UTR Lengths in Arabidopsis thaliana (L.) Heynh. PLANT & CELL PHYSIOLOGY 2022; 63:369-383. [PMID: 35016226 DOI: 10.1093/pcp/pcac002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/28/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Cleavage and polyadenylation at the 3' end of the pre-mRNA is essential for mRNA function, by regulating its translatability, stability and translocation to the cytoplasm. Cleavage factor I (CFI) is a multi-subunit component of the pre-mRNA 3' end processing machinery in eukaryotes. Here, we report that plant CFI 25 subunit of CFI plays an important role in maintaining the diversity of the 3' ends of mRNA. The genome of Arabidopsis thaliana (L.) Heynh. contained four genes encoding three putative CFI subunits (AtCFI 25, AtCFI 59 and AtCFI 68), orthologous to the mammalian CFI subunits. There were two CFI 25 paralogs (AtCFI 25a and AtCFI 25b) that shared homology with human CFI 25. Two null alleles of AtCFI 25a displayed smaller rosette leaves, longer stigmatic papilla, smaller anther, earlier flowering and lower fertility compared to wild-type plants. Null alleles of AtCFI 25b, as well as, plants ectopically expressing full-length cDNA of AtCFI 25a, displayed no obvious morphological defects. AtCFI 25a was shown to interact with AtCFI 25b, AtCFI 68 and itself, suggesting various forms of CFI in plants. Furthermore, we show that AtCFI 25a function was essential for maintaining proper diversity of the 3' end lengths of transcripts coding for CFI subunits, suggesting a self-regulation of the CFI machinery in plants. AtCFI 25a was also important to maintain 3' ends for other genes to different extent. Collectively, AtCFI 25a, but not AtCFI 25b, seemed to play important roles during Arabidopsis development by maintaining proper diversity of the 3' UTR lengths.
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Affiliation(s)
- Xiaojuan Zhang
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Nagoya, Aichi, 464-8601 Japan
| | - Marta Garcia-León
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Naoki Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192 Japan
| | - Mariko Kato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Kei Yura
- School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, 162-0041 Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo, Tokyo, 112-8610 Japan
- Center for Interdisciplinary AI and Data Science, Ochanomizu University, Bunkyo, Tokyo, 112-8610 Japan
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192 Japan
| | - Vicente Rubio
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya, Aichi, 464-8601 Japan
| | - Tsuyoshi Furumoto
- Department of Plant Life Science, Graduate School of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194 Japan
| | - Takashi Aoyama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
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21
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Ghosh S, Ataman M, Bak M, Börsch A, Schmidt A, Buczak K, Martin G, Dimitriades B, Herrmann CJ, Kanitz A, Zavolan M. CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. Nucleic Acids Res 2022; 50:3096-3114. [PMID: 35234914 PMCID: PMC8989530 DOI: 10.1093/nar/gkac114] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
The mammalian cleavage factor I (CFIm) has been implicated in alternative polyadenylation (APA) in a broad range of contexts, from cancers to learning deficits and parasite infections. To determine how the CFIm expression levels are translated into these diverse phenotypes, we carried out a multi-omics analysis of cell lines in which the CFIm25 (NUDT21) or CFIm68 (CPSF6) subunits were either repressed by siRNA-mediated knockdown or over-expressed from stably integrated constructs. We established that >800 genes undergo coherent APA in response to changes in CFIm levels, and they cluster in distinct functional classes related to protein metabolism. The activity of the ERK pathway traces the CFIm concentration, and explains some of the fluctuations in cell growth and metabolism that are observed upon CFIm perturbations. Furthermore, multiple transcripts encoding proteins from the miRNA pathway are targets of CFIm-dependent APA. This leads to an increased biogenesis and repressive activity of miRNAs at the same time as some 3′ UTRs become shorter and presumably less sensitive to miRNA-mediated repression. Our study provides a first systematic assessment of a core set of APA targets that respond coherently to changes in CFIm protein subunit levels (CFIm25/CFIm68). We describe the elicited signaling pathways downstream of CFIm, which improve our understanding of the key role of CFIm in integrating RNA processing with other cellular activities.
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Affiliation(s)
- Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Meric Ataman
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Maciej Bak
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Anastasiya Börsch
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Beatrice Dimitriades
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Christina J Herrmann
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Alexander Kanitz
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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22
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Wei L, Lai EC. Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins. Front Genet 2022; 13:848626. [PMID: 35281806 PMCID: PMC8904962 DOI: 10.3389/fgene.2022.848626] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
The process of alternative polyadenylation (APA) generates multiple 3' UTR isoforms for a given locus, which can alter regulatory capacity and on occasion change coding potential. APA was initially characterized for a few genes, but in the past decade, has been found to be the rule for metazoan genes. While numerous differences in APA profiles have been catalogued across genetic conditions, perturbations, and diseases, our knowledge of APA mechanisms and biology is far from complete. In this review, we highlight recent findings regarding the role of the conserved ELAV/Hu family of RNA binding proteins (RBPs) in generating the broad landscape of lengthened 3' UTRs that is characteristic of neurons. We relate this to their established roles in alternative splicing, and summarize ongoing directions that will further elucidate the molecular strategies for neural APA, the in vivo functions of ELAV/Hu RBPs, and the phenotypic consequences of these regulatory paradigms in neurons.
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Affiliation(s)
- Lu Wei
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, United States
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23
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Schmidt M, Kluge F, Sandmeir F, Kühn U, Schäfer P, Tüting C, Ihling C, Conti E, Wahle E. Reconstitution of 3' end processing of mammalian pre-mRNA reveals a central role of RBBP6. Genes Dev 2022; 36:195-209. [PMID: 35177537 PMCID: PMC8887130 DOI: 10.1101/gad.349217.121] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/21/2022] [Indexed: 11/24/2022]
Abstract
The 3' ends of almost all eukaryotic mRNAs are generated in an essential two-step processing reaction: endonucleolytic cleavage of an extended precursor followed by the addition of a poly(A) tail. By reconstituting the reaction from overproduced and purified proteins, we provide a minimal list of 14 polypeptides that are essential and two that are stimulatory for RNA processing. In a reaction depending on the polyadenylation signal AAUAAA, the reconstituted system cleaves pre-mRNA at a single preferred site corresponding to the one used in vivo. Among the proteins, cleavage factor I stimulates cleavage but is not essential, consistent with its prominent role in alternative polyadenylation. RBBP6 is required, with structural data showing it to contact and presumably activate the endonuclease CPSF73 through its DWNN domain. The C-terminal domain of RNA polymerase II is dispensable. ATP, but not its hydrolysis, supports RNA cleavage by binding to the hClp1 subunit of cleavage factor II with submicromolar affinity.
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Affiliation(s)
- Moritz Schmidt
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Florian Kluge
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Felix Sandmeir
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Uwe Kühn
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Peter Schäfer
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christian Tüting
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christian Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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24
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Tian S, Zhang B, He Y, Sun Z, Li J, Li Y, Yi H, Zhao Y, Zou X, Li Y, Cui H, Fang L, Gao X, Hu Y, Chen W. OUP accepted manuscript. Nucleic Acids Res 2022; 50:e26. [PMID: 35191504 PMCID: PMC8934656 DOI: 10.1093/nar/gkac108] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/01/2022] [Accepted: 02/19/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Yuhao He
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhiyuan Sun
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jun Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yisheng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongyang Yi
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yan Zhao
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xudong Zou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yunfei Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Huanhuan Cui
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei Chen
- To whom correspondence should be addressed. Tel: +86 755 88018449;
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25
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Alternative polyadenylation: An untapped source for prostate cancer biomarkers and therapeutic targets? Asian J Urol 2021; 8:407-415. [PMID: 34765448 PMCID: PMC8566364 DOI: 10.1016/j.ajur.2021.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/20/2021] [Accepted: 05/05/2021] [Indexed: 11/25/2022] Open
Abstract
Objective To review alternative polyadenylation (APA) as a mechanism of gene regulation and consider potential roles for APA in prostate cancer (PCa) biology and treatment. Methods An extensive review of mRNA polyadenylation, APA, and PCa literature was performed. This review article introduces APA and its association with human disease, outlines the mechanisms and components of APA, reviews APA in cancer biology, and considers whether APA may contribute to PCa progression and/or produce novel biomarkers and therapeutic targets for PCa. Results Eukaryotic mRNA 3′-end cleavage and polyadenylation play a critical role in gene expression. Most human genes encode more than one polyadenylation signal, and produce more than one transcript isoform, through APA. Polyadenylation can occur throughout the gene body to generate transcripts with differing 3′-termini and coding sequence. Differences in 3′-untranslated regions length can modify post-transcriptional gene regulation by microRNAs and RNA binding proteins, and alter mRNA stability, translation efficiency, and subcellular localization. Distinctive APA patterns are associated with human diseases, tissue origins, and changes in cellular proliferation rate and differentiation state. APA events may therefore generate unique mRNA biomarkers or therapeutic targets in certain cancer types or phenotypic states. Conclusions The full extent of cancer-associated and tissue-specific APA events have yet to be defined, and the mechanisms and functional consequences of APA in cancer remain incompletely understood. There is evidence that APA is active in PCa, and that it may be an untapped resource for PCa biomarkers or therapeutic targets.
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26
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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27
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Salgado-Martínez AI, Avila-Bonilla RG, Ramírez-Moreno E, Castañón-Sánchez CA, López-Camarillo C, Marchat LA. Unraveling the relevance of the polyadenylation factor EhCFIm25 in Entamoeba histolytica through proteomic analysis. FEBS Open Bio 2021; 11:2819-2835. [PMID: 34486252 PMCID: PMC8487052 DOI: 10.1002/2211-5463.13287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/06/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
We recently reported that silencing of the polyadenylation factor EhCFIm25 in Entamoeba histolytica, the protozoan which causes human amoebiasis, affects trophozoite proliferation, death, and virulence, suggesting that EhCFIm25 may have potential as a new biochemical target. Here, we performed a shotgun proteomic analysis to identify modulated proteins that could explain this phenotype. Data are available via ProteomeXchange with identifier PXD027784. Our results revealed changes in the abundance of 75 proteins. Interestingly, STRING analysis, functional GO‐term annotations, KEGG analyses, and literature review showed that modulated proteins are mainly related to glycolysis and carbon metabolism, cytoskeleton dynamics, and parasite virulence, as well as gene expression and protein modifications. Further studies are needed to confirm the hypotheses emerging from this proteomic analysis, to thereby acquire a comprehensive view of the molecular mechanisms involved.
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Affiliation(s)
| | | | - Esther Ramírez-Moreno
- Laboratorio de Biomedicina Molecular II, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Mexico
| | - Laurence A Marchat
- Laboratorio de Biomedicina Molecular II, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico
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28
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Huang Y, Zhu Q. Mechanisms Regulating Abnormal Circular RNA Biogenesis in Cancer. Cancers (Basel) 2021; 13:4185. [PMID: 34439339 PMCID: PMC8391333 DOI: 10.3390/cancers13164185] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs), which are a class of endogenous RNA with covalently closed loops, play important roles in epigenetic regulation of gene expression at both the transcriptional and post-transcriptional level. Accumulating evidence demonstrated that numerous circRNAs were abnormally expressed in tumors and their dysregulation was involved in the tumorigenesis and metastasis of cancer. Although the functional mechanisms of many circRNAs have been revealed, how circRNAs are dysregulated in cancer remains elusive. CircRNAs are generated by a "back-splicing" process, which is regulated by different cis-regulatory elements and trans-acting proteins. Therefore, how these cis and trans elements change during tumorigenesis and how they regulate the biogenesis of circRNAs in cancer are two questions that interest us. In this review, we summarized the pathways for the biogenesis of circRNAs; and then illustrated how circRNAs dysregulated in cancer by discussing the changes of cis-regulatory elements and trans-acting proteins that related to circRNA splicing and maturation in cancer.
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Affiliation(s)
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China;
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29
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Cleavage and Polyadenylation Specificity Factor 6 Is Required for Efficient HIV-1 Latency Reversal. mBio 2021; 12:e0109821. [PMID: 34154414 PMCID: PMC8262898 DOI: 10.1128/mbio.01098-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 latent reservoir is the major barrier to an HIV cure. Due to low levels or lack of transcriptional activity, HIV-1 latent proviruses in vivo are not easily detectable and cannot be targeted by either natural immune mechanisms or molecular therapies based on protein expression. To target the latent reservoir, further understanding of HIV-1 proviral transcription is required. In this study, we demonstrate a novel role for cleavage and polyadenylation specificity factor 6 (CPSF6) in HIV-1 transcription. We show that knockout of CPSF6 hinders reactivation of latent HIV-1 proviruses by PMA in primary CD4+ cells. CPSF6 knockout reduced HIV-1 transcription, concomitant with a drastic reduction in the phosphorylation levels of Pol II and CDK9. Knockout of CPSF6 led to abnormal stabilization of protein phosphatase 2A (PP2A) subunit A, which then acted to dephosphorylate CDK9, downmodulating CDK9's ability to phosphorylate the Pol II carboxy-terminal domain. In agreement with this mechanism, incubation with the PP2A inhibitor, LB100, restored HIV-1 transcription in the CPSF6 knockout cells. Destabilization of PP2A subunit A occurs in the ubiquitin proteasome pathway, wherein CPSF6 acts as a substrate adaptor for the ITCH ubiquitin ligase. Our observations reveal a novel role of CPSF6 in HIV-1 transcription, which appears to be independent of its known roles in cleavage and polyadenylation and the targeting of preintegration complexes to the chromatin for viral DNA integration. IMPORTANCE CPSF6 is a cellular factor that regulates cleavage and polyadenylation of mRNAs and participates in HIV-1 infection by facilitating targeting of preintegration complexes to the chromatin. Our observations reveal a second role of CPSF6 in the HIV-1 life cycle that involves regulation of viral transcription through controlling the stability of protein phosphatase 2A, which in turn regulates the phosphorylation/dephosphorylation status of critical residues in CDK9 and Pol II.
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30
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Shao L, Shen W, Wang S, Qiu J. Recent Advances in Molecular Biology of Human Bocavirus 1 and Its Applications. Front Microbiol 2021; 12:696604. [PMID: 34220786 PMCID: PMC8242256 DOI: 10.3389/fmicb.2021.696604] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/12/2021] [Indexed: 11/25/2022] Open
Abstract
Human bocavirus 1 (HBoV1) was discovered in human nasopharyngeal specimens in 2005. It is an autonomous human parvovirus and causes acute respiratory tract infections in young children. HBoV1 infects well differentiated or polarized human airway epithelial cells in vitro. Unique among all parvoviruses, HBoV1 expresses 6 non-structural proteins, NS1, NS1-70, NS2, NS3, NS4, and NP1, and a viral non-coding RNA (BocaSR), and three structural proteins VP1, VP2, and VP3. The BocaSR is the first identified RNA polymerase III (Pol III) transcribed viral non-coding RNA in small DNA viruses. It plays an important role in regulation of viral gene expression and a direct role in viral DNA replication in the nucleus. HBoV1 genome replication in the polarized/non-dividing airway epithelial cells depends on the DNA damage and DNA repair pathways and involves error-free Y-family DNA repair DNA polymerase (Pol) η and Pol κ. Importantly, HBoV1 is a helper virus for the replication of dependoparvovirus, adeno-associated virus (AAV), in polarized human airway epithelial cells, and HBoV1 gene products support wild-type AAV replication and recombinant AAV (rAAV) production in human embryonic kidney (HEK) 293 cells. More importantly, the HBoV1 capsid is able to pseudopackage an rAAV2 or rHBoV1 genome, producing the rAAV2/HBoV1 or rHBoV1 vector. The HBoV1 capsid based rAAV vector has a high tropism for human airway epithelia. A deeper understanding in HBoV1 replication and gene expression will help find a better way to produce the rAAV vector and to increase the efficacy of gene delivery using the rAAV2/HBoV1 or rHBoV1 vector, in particular, to human airways. This review summarizes the recent advances in gene expression and replication of HBoV1, as well as the use of HBoV1 as a parvoviral vector for gene delivery.
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Affiliation(s)
- Liting Shao
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Weiran Shen
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States
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31
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Scarborough AM, Flaherty JN, Hunter OV, Liu K, Kumar A, Xing C, Tu BP, Conrad NK. SAM homeostasis is regulated by CFI m-mediated splicing of MAT2A. eLife 2021; 10:e64930. [PMID: 33949310 PMCID: PMC8139829 DOI: 10.7554/elife.64930] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/03/2021] [Indexed: 12/14/2022] Open
Abstract
S-adenosylmethionine (SAM) is the methyl donor for nearly all cellular methylation events. Cells regulate intracellular SAM levels through intron detention of MAT2A, the only SAM synthetase expressed in most cells. The N6-adenosine methyltransferase METTL16 promotes splicing of the MAT2A detained intron by an unknown mechanism. Using an unbiased CRISPR knock-out screen, we identified CFIm25 (NUDT21) as a regulator of MAT2A intron detention and intracellular SAM levels. CFIm25 is a component of the cleavage factor Im (CFIm) complex that regulates poly(A) site selection, but we show it promotes MAT2A splicing independent of poly(A) site selection. CFIm25-mediated MAT2A splicing induction requires the RS domains of its binding partners, CFIm68 and CFIm59 as well as binding sites in the detained intron and 3´ UTR. These studies uncover mechanisms that regulate MAT2A intron detention and reveal a previously undescribed role for CFIm in splicing and SAM metabolism.
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Affiliation(s)
- Anna M Scarborough
- Department of Microbiology, UT Southwestern Medical CenterDallasUnited States
| | - Juliana N Flaherty
- Department of Microbiology, UT Southwestern Medical CenterDallasUnited States
| | - Olga V Hunter
- Department of Microbiology, UT Southwestern Medical CenterDallasUnited States
| | - Kuanqing Liu
- Department of Biochemistry, UT Southwestern Medical CenterDallasUnited States
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical CenterDallasUnited States
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical CenterDallasUnited States
- Department of Bioinformatics, UT Southwestern Medical CenterDallasUnited States
- Department of Population and Data Sciences, UT Southwestern Medical CenterDallasUnited States
| | - Benjamin P Tu
- Department of Biochemistry, UT Southwestern Medical CenterDallasUnited States
| | - Nicholas K Conrad
- Department of Microbiology, UT Southwestern Medical CenterDallasUnited States
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32
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Schwich OD, Blümel N, Keller M, Wegener M, Setty ST, Brunstein ME, Poser I, Mozos IRDL, Suess B, Münch C, McNicoll F, Zarnack K, Müller-McNicoll M. SRSF3 and SRSF7 modulate 3'UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels. Genome Biol 2021; 22:82. [PMID: 33706811 PMCID: PMC7948361 DOI: 10.1186/s13059-021-02298-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/11/2021] [Indexed: 12/23/2022] Open
Abstract
Background Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3′ untranslated regions (3′UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained unknown. Results Here we combine iCLIP and 3′-end sequencing and find that SRSF3 and SRSF7 bind upstream of proximal PASs (pPASs), but they exert opposite effects on 3′UTR length. SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, generating short 3′UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3′UTRs directly by counteracting SRSF7, but also indirectly by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon SRSF3 depletion, CFIm levels decrease and 3′UTRs are shortened. The indirect SRSF3 targets are particularly sensitive to low CFIm levels, because here CFIm serves a dual function; it enhances dPAS and inhibits pPAS usage by binding immediately downstream and assembling unproductive cleavage complexes, which together promotes long 3′UTRs. Conclusions We demonstrate that SRSF3 and SRSF7 are direct modulators of pPAS usage and show how small differences in the domain architecture of SR proteins can confer opposite effects on pPAS regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02298-y.
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Affiliation(s)
- Oliver Daniel Schwich
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Nicole Blümel
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
| | - Mario Keller
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.,Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Marius Wegener
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Samarth Thonta Setty
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Melinda Elaine Brunstein
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | | | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany
| | - François McNicoll
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany. .,Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Michaela Müller-McNicoll
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.
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Bedwell GJ, Engelman AN. Factors that mold the nuclear landscape of HIV-1 integration. Nucleic Acids Res 2021; 49:621-635. [PMID: 33337475 PMCID: PMC7826272 DOI: 10.1093/nar/gkaa1207] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 11/26/2020] [Indexed: 12/17/2022] Open
Abstract
The integration of retroviral reverse transcripts into the chromatin of the cells that they infect is required for virus replication. Retroviral integration has far-reaching consequences, from perpetuating deadly human diseases to molding metazoan evolution. The lentivirus human immunodeficiency virus 1 (HIV-1), which is the causative agent of the AIDS pandemic, efficiently infects interphase cells due to the active nuclear import of its preintegration complex (PIC). To enable integration, the PIC must navigate the densely-packed nuclear environment where the genome is organized into different chromatin states of varying accessibility in accordance with cellular needs. The HIV-1 capsid protein interacts with specific host factors to facilitate PIC nuclear import, while additional interactions of viral integrase, the enzyme responsible for viral DNA integration, with cellular nuclear proteins and nucleobases guide integration to specific chromosomal sites. HIV-1 integration favors transcriptionally active chromatin such as speckle-associated domains and disfavors heterochromatin including lamina-associated domains. In this review, we describe virus-host interactions that facilitate HIV-1 PIC nuclear import and integration site targeting, highlighting commonalities among factors that participate in both of these steps. We moreover discuss how the nuclear landscape influences HIV-1 integration site selection as well as the establishment of active versus latent virus infection.
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Affiliation(s)
- Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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Engelman AN. HIV Capsid and Integration Targeting. Viruses 2021; 13:125. [PMID: 33477441 PMCID: PMC7830116 DOI: 10.3390/v13010125] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/20/2022] Open
Abstract
Integration of retroviral reverse transcripts into the chromosomes of the cells that they infect is required for efficient viral gene expression and the inheritance of viral genomes to daughter cells. Before integration can occur, retroviral reverse transcription complexes (RTCs) must access the nuclear environment where the chromosomes reside. Retroviral integration is non-random, with different types of virus-host interactions impacting where in the host chromatin integration takes place. Lentiviruses such as HIV efficiently infect interphase cells because their RTCs have evolved to usurp cellular nuclear import transport mechanisms, and research over the past decade has revealed specific interactions between the HIV capsid protein and nucleoporin (Nup) proteins such as Nup358 and Nup153. The interaction of HIV capsid with cleavage and polyadenylation specificity factor 6 (CPSF6), which is a component of the cellular cleavage and polyadenylation complex, helps to dictate nuclear import as well as post-nuclear RTC invasion. In the absence of the capsid-CPSF6 interaction, RTCs are precluded from reaching nuclear speckles and gene-rich regions of chromatin known as speckle-associated domains, and instead mis-target lamina-associated domains out at the nuclear periphery. Highlighting this area of research, small molecules that inhibit capsid-host interactions important for integration site targeting are highly potent antiviral compounds.
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Affiliation(s)
- Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; ; Tel.: +1-617-632-4361
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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Aoyama-Ishiwatari S, Okazaki T, Iemura SI, Natsume T, Okada Y, Gotoh Y. NUDT21 Links Mitochondrial IPS-1 to RLR-Containing Stress Granules and Activates Host Antiviral Defense. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 206:154-163. [PMID: 33219146 DOI: 10.4049/jimmunol.2000306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/23/2020] [Indexed: 11/19/2022]
Abstract
Viral RNA in the cytoplasm of mammalian host cells is recognized by retinoic acid-inducible protein-I-like receptors (RLRs), which localize to cytoplasmic stress granules (SGs). Activated RLRs associate with the mitochondrial adaptor protein IPS-1, which activates antiviral host defense mechanisms, including type I IFN induction. It has remained unclear, however, how RLRs in SGs and IPS-1 in the mitochondrial outer membrane associate physically and engage in information transfer. In this study, we show that NUDT21, an RNA-binding protein that regulates alternative transcript polyadenylation, physically associates with IPS-1 and mediates its localization to SGs in response to transfection with polyinosinic-polycytidylic acid [poly(I:C)], a mimic of viral dsRNA. We found that despite its well-established function in the nucleus, a fraction of NUDT21 localizes to mitochondria in resting cells and becomes localized to SGs in response to poly(I:C) transfection. NUDT21 was also found to be required for efficient type I IFN induction in response to viral infection in both human HeLa cells and mouse macrophage cell line RAW264.7 cells. Our results together indicate that NUDT21 links RLRs in SGs to mitochondrial IPS-1 and thereby activates host defense responses to viral infection.
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Affiliation(s)
| | - Tomohiko Okazaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Shun-Ichiro Iemura
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Yasushi Okada
- Laboratory for Cell Dynamics Observation, Center for Biosystems Dynamics Research, RIKEN, Osaka 565-0874, Japan
- Department of Physics, Universal Biology Institute, Tokyo 113-0033, Japan; and
- International Research Center for Neurointelligence, World Premier International Research Center Initiative, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- International Research Center for Neurointelligence, World Premier International Research Center Initiative, The University of Tokyo, Tokyo 113-0033, Japan
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Hamilton K, Tong L. Molecular mechanism for the interaction between human CPSF30 and hFip1. Genes Dev 2020; 34:1753-1761. [PMID: 33122294 PMCID: PMC7706699 DOI: 10.1101/gad.343814.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
In this study, Hamilton and Tong set out to elucidate the molecular basis for the CPSF30–hFip1 interaction. Using structural, biophysical, and biochemical experiments, the authors define how the mammalian polyadenylation specificity factor (mPSF) is organized and add to our understanding of the pre-mRNA 3′-end processing machinery. Most eukaryotic pre-mRNAs must undergo 3′-end cleavage and polyadenylation prior to their export from the nucleus. A large number of proteins in several complexes participate in this 3′-end processing, including cleavage and polyadenylation specificity factor (CPSF) in mammals. The CPSF30 subunit contains five CCCH zinc fingers (ZFs), with ZF2–ZF3 being required for the recognition of the AAUAAA poly(A) signal. ZF4–ZF5 recruits the hFip1 subunit of CPSF, although the details of this interaction have not been characterized. Here we report the crystal structure of human CPSF30 ZF4–ZF5 in complex with residues 161–200 of hFip1 at 1.9 Å resolution, illuminating the molecular basis for their interaction. Unexpectedly, the structure reveals one hFip1 molecule binding to each ZF4 and ZF5, with a conserved mode of interaction. Our mutagenesis studies confirm that the CPSF30–hFip1 complex has 1:2 stoichiometry in vitro. Mutation of each binding site in CPSF30 still allows one copy of hFip1 to bind, while mutation of both sites abrogates binding. Our fluorescence polarization binding assays show that ZF4 has higher affinity for hFip1, with a Kd of 1.8 nM. We also demonstrate that two copies of the catalytic module of poly(A) polymerase (PAP) are recruited by the CPSF30–hFip1 complex in vitro, and both hFip1 binding sites in CPSF30 can support polyadenylation.
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Affiliation(s)
- Keith Hamilton
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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Sun Y, Chen H, Ye H, Liang W, Lam KK, Cheng B, Lu Y, Jiang C. Nudt21-mediated alternative polyadenylation of HMGA2 3'-UTR impairs stemness of human tendon stem cell. Aging (Albany NY) 2020; 12:18436-18452. [PMID: 32979259 PMCID: PMC7585117 DOI: 10.18632/aging.103771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/06/2020] [Indexed: 01/24/2023]
Abstract
Tendon-derived stem cells (TSCs) play a primary role in tendon physiology, pathology, as well as tendon repair and regeneration after injury. TSCs are often exposed to mechanical loading-related cellular stresses such as oxidative stress, resulting in loss of stemness and multipotent differentiation potential. Cytoprotective autophagy has previously been identified as an important mechanism to protect human TSCs (hTSCs) from oxidative stress induced impairments. In this study, we found that high-mobility AT-hook 2 (HMGA2) overexpression protects hTSCs against H2O2-induced loss of stemness through autophagy activation. Evidentially, H2O2 treatment increases the expression of Nudt21, a protein critical to polyadenylation site selection in alternative polyadenylation (APA) of mRNA transcripts. This leads to increased cleavage and polyadenylation of HMGA2 3'-UTR at the distal site, resulting in increased HMGA2 silencing by the microRNA let-7 and reduced HMGA2 expression. In conclusion, Nudt21-regulated APA of HMGA2 3'-UTR and subsequent HMGA2 downregulation mediates oxidative stress induced hTSC impairments.
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Affiliation(s)
- Yangbai Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hua Chen
- Department of Orthopedic Surgery, Shanghai Jiaotong University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Hui Ye
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenqing Liang
- Department of Orthopaedics, Shaoxing People’s Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing 312000, Zhejiang, China
| | - Kun-kuan Lam
- Department of Orthopaedic Surgery and Sports Medicine, University Hospital of Macau University of Science and Technology, Macau 999078, China
| | - Biao Cheng
- Department of Orthopedics, Shanghai Tenth People’s Hospital, Tongji University, School of Medicine, Shanghai 200072, China
| | - Yong Lu
- Department of Radiology, Rui Jin Hospital, Lu Wan Branch, School of Medicine, Shanghai Jiaotong University, Shanghai 200020, China
| | - Chaoyin Jiang
- Department of Orthopedic Surgery, Shanghai Jiaotong University Affiliated Sixth People’s Hospital, Shanghai 200233, China,Department of Orthopedic Surgery, Haikou Orthopedic and Diabetes Hospital of Shanghai Sixth People's Hospital, Hainan 570300, China
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38
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Wang BJ, Liu DC, Guo QY, Han XW, Bi XM, Wang H, Wu ZS, Wu WY. NUDT21 Suppresses Breast Cancer Tumorigenesis Through Regulating CPSF6 Expression. Cancer Manag Res 2020; 12:3069-3078. [PMID: 32431549 PMCID: PMC7200255 DOI: 10.2147/cmar.s239664] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background NUDT21, an RNA binding protein, has been reported to play an important role in the regulation of multiple biological responses. Detection of NUDT21 expression may lead to the identification of a novel marker for breast cancer. Purpose The aim of this study was to investigate the clinical significance and functional role of NUDT21 in breast cancer. Methods The protein expression of NUDT21 was examined by immunohistochemistry (IHC) in 100 paraffin-embedded, archived breast cancer samples and 100 benign breast tissues. Then, the correlations between the NUDT21 expression and clinicopathologic characteristics and prognoses of the breast cancer patients were analyzed. In addition, the function of NUDT21 in breast cancer cell lines was detected by the methyl thiazolyl tetrazolium, colony formation and transwell assays. Finally, mass spectrometry analysis and Western blotting were used to identify the proteins that interact directly with NUDT21. Results IHC analysis revealed that the expression of NUDT21 was significantly lower in breast cancer tissues compared with benign breast disease tissues. The correlation analysis revealed that low expression of NUDT21 was positively correlated with tumor size, lymph node metastasis, and TNM stage. Also, Kaplan–Meier survival curves showed that patients with lower NUDT21 expression had shorter overall survival and relapse-free survival compared with higher NUDT21 expression. In addition, the knockdown of NUDT21 enhanced cell proliferation, migration, invasion and epithelial-mesenchymal transition (EMT). Consistently, the overexpression of NUDT21 inhibited cell proliferation, migration, invasion, and EMT. In addition, NUDT21 directly interacted with CPSF6 and negatively regulated its expression. Moreover, the knockdown of CPSF6 reversed NUDT21 expression-induced cancer cell migration and invasion. Conclusion NUDT21 might play a tumor-suppressive role by inhibiting cell proliferation and invasion via the NUDT21/CPSF6 signaling pathway in breast cancer cells.
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Affiliation(s)
- Bi-Jun Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Da-Chao Liu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Qian-Ying Guo
- Department of Pathology, Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Xiao-Wen Han
- Department of Pathology, Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Xiao-Min Bi
- Department of Pathology, Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Hao Wang
- Department of Pathology, Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Zheng-Sheng Wu
- Department of Pathology, Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Wen-Yong Wu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
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Alcott CE, Yalamanchili HK, Ji P, van der Heijden ME, Saltzman A, Elrod N, Lin A, Leng M, Bhatt B, Hao S, Wang Q, Saliba A, Tang J, Malovannaya A, Wagner EJ, Liu Z, Zoghbi HY. Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation. eLife 2020; 9:e50895. [PMID: 32319885 PMCID: PMC7176433 DOI: 10.7554/elife.50895] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 04/05/2020] [Indexed: 12/19/2022] Open
Abstract
We previously showed that NUDT21-spanning copy-number variations (CNVs) are associated with intellectual disability (Gennarino et al., 2015). However, the patients' CNVs also included other genes. To determine if reduced NUDT21 function alone can cause disease, we generated Nudt21+/- mice to mimic NUDT21-deletion patients. We found that although these mice have 50% reduced Nudt21 mRNA, they only have 30% less of its cognate protein, CFIm25. Despite this partial protein-level compensation, the Nudt21+/- mice have learning deficits, cortical hyperexcitability, and misregulated alternative polyadenylation (APA) in their hippocampi. Further, to determine the mediators driving neural dysfunction in humans, we partially inhibited NUDT21 in human stem cell-derived neurons to reduce CFIm25 by 30%. This induced APA and protein level misregulation in hundreds of genes, a number of which cause intellectual disability when mutated. Altogether, these results show that disruption of NUDT21-regulated APA events in the brain can cause intellectual disability.
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Affiliation(s)
- Callison E Alcott
- Program in Developmental Biology, Baylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Medical Scientist Training Program, Baylor College of MedicineHoustonUnited States
| | - Hari Krishna Yalamanchili
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Ping Ji
- Department of Biochemistry & Molecular Biology, University of Texas Medical BranchGalvestonUnited States
| | - Meike E van der Heijden
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - Alexander Saltzman
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of MedicineHoustonUnited States
| | - Nathan Elrod
- Department of Biochemistry & Molecular Biology, University of Texas Medical BranchGalvestonUnited States
| | - Ai Lin
- Department of Biochemistry & Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Mei Leng
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of MedicineHoustonUnited States
| | - Bhoomi Bhatt
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of MedicineHoustonUnited States
| | - Shuang Hao
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Section of Neurology, Department of Pediatrics, Baylor College of MedicineHoustonUnited States
| | - Qi Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Section of Neurology, Department of Pediatrics, Baylor College of MedicineHoustonUnited States
| | - Afaf Saliba
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Jianrong Tang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Section of Neurology, Department of Pediatrics, Baylor College of MedicineHoustonUnited States
| | - Anna Malovannaya
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Mass Spectrometry Proteomics Core, Baylor College of MedicineHoustonUnited States
- Dan L Duncan Comprehensive Cancer Center, Baylor College of MedicineHoustonUnited States
| | - Eric J Wagner
- Department of Biochemistry & Molecular Biology, University of Texas Medical BranchGalvestonUnited States
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Section of Neurology, Department of Pediatrics, Baylor College of MedicineHoustonUnited States
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of MedicineHoustonUnited States
| | - Huda Y Zoghbi
- Program in Developmental Biology, Baylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Department of Pediatrics, Baylor College of MedicineHoustonUnited States
- Howard Hughes Medical Institute, Baylor College of MedicineHoustonUnited States
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40
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CFIm25-regulated lncRNA acv3UTR promotes gastric tumorigenesis via miR-590-5p/YAP1 axis. Oncogene 2020; 39:3075-3088. [PMID: 32066878 PMCID: PMC7142022 DOI: 10.1038/s41388-020-1213-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
Accumulating evidences indicate that 3ʹUTR of the coding gene can act as crucial regulators in gastric cancer (GC). However, the detailed mechanisms and responsive targets are not well established. Here, we found that acvr1b gene 3ʹUTR (acv3UTR) was elevated in GC tissue, the expression of which was significantly correlated with advanced pTNM-stage and poor outcome in clinical patients. Forced expression of acv3UTR promoted GC cells growth in vitro and in vivo. Mechanistically, our results suggested that acv3UTR functioned as an oncogenic competing endogenous RNA via sponging miR-590-5p and enhancing YAP1 level. Tumor suppressor miR-590-5p was a molecular module in acv3UTR regulatory axis, the forced expression of which led to impairing of oncogenic potential of acv3UTR. The positive correlation of acv3UTR and YAP1 expression, and the negative correlation of acv3UTR and miR-590-5p expression, were verified in GC patients. Moreover, CFIm25 was identified as a key regulator contributing to acv3UTR aberrant expression in GC binding to UGUA-264 motif. Overall, our finding defines a mechanism for understanding the potential role of acv3UTR transcription in GC tumorigenesis, and indicates a correlation between 3ʹUTR trans-regulatory effect and GC development.
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41
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Ghanbari M, Ohler U. Deep neural networks for interpreting RNA-binding protein target preferences. Genome Res 2020; 30:214-226. [PMID: 31992613 PMCID: PMC7050519 DOI: 10.1101/gr.247494.118] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/07/2020] [Indexed: 11/29/2022]
Abstract
Deep learning has become a powerful paradigm to analyze the binding sites of regulatory factors including RNA-binding proteins (RBPs), owing to its strength to learn complex features from possibly multiple sources of raw data. However, the interpretability of these models, which is crucial to improve our understanding of RBP binding preferences and functions, has not yet been investigated in significant detail. We have designed a multitask and multimodal deep neural network for characterizing in vivo RBP targets. The model incorporates not only the sequence but also the region type of the binding sites as input, which helps the model to boost the prediction performance. To interpret the model, we quantified the contribution of the input features to the predictive score of each RBP. Learning across multiple RBPs at once, we are able to avoid experimental biases and to identify the RNA sequence motifs and transcript context patterns that are the most important for the predictions of each individual RBP. Our findings are consistent with known motifs and binding behaviors and can provide new insights about the regulatory functions of RBPs.
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Affiliation(s)
- Mahsa Ghanbari
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Uwe Ohler
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany.,Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany.,Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany
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Bernardes WS, Menossi M. Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1252. [PMID: 32922424 PMCID: PMC7457121 DOI: 10.3389/fpls.2020.01252] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.
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The C. elegans 3' UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3'-UTR biology, and miRNA targeting. Genome Res 2019; 29:2104-2116. [PMID: 31744903 PMCID: PMC6886508 DOI: 10.1101/gr.254839.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022]
Abstract
3′ Untranslated regions (3′ UTRs) of mRNAs emerged as central regulators of cellular function because they contain important but poorly characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode Caenorhabditis elegans is ideal to study these interactions because it possesses a well-defined 3′ UTRome. To improve its annotation, we have used a genome-wide bioinformatics approach to download raw transcriptome data for 1088 transcriptome data sets corresponding to the entire collection of C. elegans trancriptomes from 2015 to 2018 from the Sequence Read Archive at the NCBI. We then extracted and mapped high-quality 3′-UTR data at ultradeep coverage. Here, we describe and release to the community the updated version of the worm 3′ UTRome, which we named 3′ UTRome v2. This resource contains high-quality 3′-UTR data mapped at single-base ultraresolution for 23,084 3′-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this data set to study and probe principles of mRNA cleavage and polyadenylation in C. elegans. The worm 3′ UTRome v2 represents the most comprehensive and high-resolution 3′-UTR data set available in C. elegans and provides a novel resource to investigate the mRNA cleavage and polyadenylation reaction, 3′-UTR biology, and miRNA targeting in a living organism.
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Li X, Ding J, Wang X, Cheng Z, Zhu Q. NUDT21 regulates circRNA cyclization and ceRNA crosstalk in hepatocellular carcinoma. Oncogene 2019; 39:891-904. [DOI: 10.1038/s41388-019-1030-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/14/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022]
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45
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Qiu C, Dutcher RC, Porter DF, Arava Y, Wickens M, Hall TM. Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity. Nucleic Acids Res 2019; 47:8770-8784. [PMID: 31294800 PMCID: PMC7145691 DOI: 10.1093/nar/gkz583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 01/07/2023] Open
Abstract
PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct architecture and comprise a highly conserved subfamily among fungal species. Puf1/Puf2 proteins contain two types of RNA-binding domain: a divergent PUM-HD and an RNA recognition motif (RRM). They recognize RNAs containing UAAU motifs, often in clusters. Here, we report a crystal structure of the PUM-HD of a fungal Puf1 in complex with a dual UAAU motif RNA. Each of the two UAAU tetranucleotides are bound by a Puf1 PUM-HD forming a 2:1 protein-to-RNA complex. We also determined crystal structures of the Puf1 RRM domain that identified a dimerization interface. The PUM-HD and RRM domains act in concert to determine RNA-binding specificity: the PUM-HD dictates binding to UAAU, and dimerization of the RRM domain favors binding to dual UAAU motifs rather than a single UAAU. Cooperative action of the RRM and PUM-HD identifies a new mechanism by which multiple RNA-binding modules in a single protein collaborate to create a unique RNA-binding specificity.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert C Dutcher
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Douglas F Porter
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yoav Arava
- Department of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Correspondence may also be addressed to Marvin Wickens. Tel: +1 608 263 0858; Fax: +1 608 262 9108;
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA,To whom correspondence should be addressed. Tel: +1 984 287 3556; Fax: +1 310 480 3055;
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46
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Thore S, Fribourg S. Structural insights into the 3′-end mRNA maturation machinery: Snapshot on polyadenylation signal recognition. Biochimie 2019; 164:105-110. [DOI: 10.1016/j.biochi.2019.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/26/2019] [Indexed: 12/22/2022]
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47
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Yang W, Hsu PL, Yang F, Song JE, Varani G. Reconstitution of the CstF complex unveils a regulatory role for CstF-50 in recognition of 3'-end processing signals. Nucleic Acids Res 2019; 46:493-503. [PMID: 29186539 PMCID: PMC5778602 DOI: 10.1093/nar/gkx1177] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/13/2017] [Indexed: 01/18/2023] Open
Abstract
Cleavage stimulation factor (CstF) is a highly conserved protein complex composed of three subunits that recognizes G/U-rich sequences downstream of the polyadenylation signal of eukaryotic mRNAs. While CstF has been identified over 25 years ago, the architecture and contribution of each subunit to RNA recognition have not been fully understood. In this study, we provide a structural basis for the recruitment of CstF-50 to CstF via interaction with CstF-77 and establish that the hexameric assembly of CstF creates a high affinity platform to target various G/U-rich sequences. We further demonstrate that CstF-77 boosts the affinity of the CstF-64 RRM to the RNA targets and CstF-50 fine tunes the ability of the complex to recognize G/U sequences of certain lengths and content.
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Affiliation(s)
- Wen Yang
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Peter L Hsu
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Jae-Eun Song
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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48
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Abstract
Most human genes have multiple sites at which RNA 3' end cleavage and polyadenylation can occur, enabling the expression of distinct transcript isoforms under different conditions. Novel methods to sequence RNA 3' ends have generated comprehensive catalogues of polyadenylation (poly(A)) sites; their analysis using innovative computational methods has revealed how poly(A) site choice is regulated by core RNA 3' end processing factors, such as cleavage factor I and cleavage and polyadenylation specificity factor, as well as by other RNA-binding proteins, particularly splicing factors. Here, we review the experimental and computational methods that have enabled the global mapping of mRNA and of long non-coding RNA 3' ends, quantification of the resulting isoforms and the discovery of regulators of alternative cleavage and polyadenylation (APA). We highlight the different types of APA-derived isoforms and their functional differences, and illustrate how APA contributes to human diseases, including cancer and haematological, immunological and neurological diseases.
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49
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Bogard N, Linder J, Rosenberg AB, Seelig G. A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation. Cell 2019; 178:91-106.e23. [PMID: 31178116 PMCID: PMC6599575 DOI: 10.1016/j.cell.2019.04.046] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 03/18/2019] [Accepted: 04/29/2019] [Indexed: 12/22/2022]
Abstract
Alternative polyadenylation (APA) is a major driver of transcriptome diversity in human cells. Here, we use deep learning to predict APA from DNA sequence alone. We trained our model (APARENT, APA REgression NeT) on isoform expression data from over 3 million APA reporters. APARENT's predictions are highly accurate when tasked with inferring APA in synthetic and human 3'UTRs. Visualizing features learned across all network layers reveals that APARENT recognizes sequence motifs known to recruit APA regulators, discovers previously unknown sequence determinants of 3' end processing, and integrates these features into a comprehensive, interpretable, cis-regulatory code. We apply APARENT to forward engineer functional polyadenylation signals with precisely defined cleavage position and isoform usage and validate predictions experimentally. Finally, we use APARENT to quantify the impact of genetic variants on APA. Our approach detects pathogenic variants in a wide range of disease contexts, expanding our understanding of the genetic origins of disease.
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Affiliation(s)
- Nicholas Bogard
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Johannes Linder
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alexander B Rosenberg
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA.
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50
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Jafari Najaf Abadi MH, Shafabakhsh R, Asemi Z, Mirzaei HR, Sahebnasagh R, Mirzaei H, Hamblin MR. CFIm25 and alternative polyadenylation: Conflicting roles in cancer. Cancer Lett 2019; 459:112-121. [PMID: 31181319 DOI: 10.1016/j.canlet.2019.114430] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/01/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022]
Abstract
Alternative polyadenylation (APA) is now widely recognized to regulate gene expression. APA is an RNA-processing mechanism that generates distinct 3' termini on mRNAs, producing mRNA isoforms. Different factors influence the initiation and development of this process. CFIm25 (among others) is a cleavage and polyadenylation factor that plays a key role in the regulation of APA. Shortening of the 3'UTRs on mRNAs leads to enhanced cellular proliferation and tumorigenicity. One reason may be the up-regulation of growth promoting factors, such as Cyclin D1. Different studies have reported a dual role of CFIm25 in cancer (both oncogenic and tumor suppressor). microRNAs (miRNAs) may be involved in CFIm25 function as well as competing endogenous RNAs (ceRNAs). The present review focuses on the role of CFIm25 in cancer, cancer treatment, and possible involvement in other human diseases. We highlight the involvement of miRNAs and ceRNAs in the function of CFIm25 to affect gene expression. The lack of understanding of the mechanisms and regulation of CFIm25 and APA has underscored the need for further research regarding their role in cancer and other diseases.
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Affiliation(s)
| | - Rana Shafabakhsh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran.
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Roxana Sahebnasagh
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran.
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA, 02114, USA.
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