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Nanavaty V, Abrash EW, Hong C, Park S, Fink EE, Li Z, Sweet TJ, Bhasin JM, Singuri S, Lee BH, Hwang TH, Ting AH. DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex. Mol Cell 2020; 78:752-764.e6. [PMID: 32333838 PMCID: PMC7245569 DOI: 10.1016/j.molcel.2020.03.024] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 02/06/2020] [Accepted: 03/16/2020] [Indexed: 02/03/2023]
Abstract
Dysregulation of DNA methylation and mRNA alternative cleavage and polyadenylation (APA) are both prevalent in cancer and have been studied as independent processes. We discovered a DNA methylation-regulated APA mechanism when we compared genome-wide DNA methylation and polyadenylation site usage between DNA methylation-competent and DNA methylation-deficient cells. Here, we show that removal of DNA methylation enables CTCF binding and recruitment of the cohesin complex, which, in turn, form chromatin loops that promote proximal polyadenylation site usage. In this DNA demethylated context, either deletion of the CTCF binding site or depletion of RAD21 cohesin complex protein can recover distal polyadenylation site usage. Using data from The Cancer Genome Atlas, we authenticated the relationship between DNA methylation and mRNA polyadenylation isoform expression in vivo. This DNA methylation-regulated APA mechanism demonstrates how aberrant DNA methylation impacts transcriptome diversity and highlights the potential sequelae of global DNA methylation inhibition as a cancer treatment.
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Affiliation(s)
- Vishal Nanavaty
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Elizabeth W Abrash
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Changjin Hong
- Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sunho Park
- Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Emily E Fink
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zhuangyue Li
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Thomas J Sweet
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for RNA Sciences and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jeffrey M Bhasin
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Srinidhi Singuri
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Byron H Lee
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Tae Hyun Hwang
- Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Angela H Ting
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA.
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202
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Sudheesh AP, Mohan N, Francis N, Laishram RS, Anderson RA. Star-PAP controlled alternative polyadenylation coupled poly(A) tail length regulates protein expression in hypertrophic heart. Nucleic Acids Res 2020; 47:10771-10787. [PMID: 31598705 PMCID: PMC6847588 DOI: 10.1093/nar/gkz875] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 09/08/2019] [Accepted: 10/05/2019] [Indexed: 12/31/2022] Open
Abstract
Alternative polyadenylation (APA)-mediated 3′-untranslated region (UTR) shortening is known to increase protein expression due to the loss of miRNA regulatory sites. Yet, mRNAs with longer 3′-UTR also show enhanced protein expression. Here, we identify a mechanism by which longer transcripts generated by the distal-most APA site leads to increased protein expression compared to the shorter transcripts and the longer transcripts are positioned to regulate heart failure (HF). A Star-PAP target gene, NQO1 has three poly(A) sites (PA-sites) at the terminal exon on the pre-mRNA. Star-PAP selects the distal-most site that results in the expression of the longest isoform. We show that the NQO1 distal-specific mRNA isoform accounts for the majority of cellular NQO1 protein. Star-PAP control of the distal-specific isoform is stimulated by oxidative stress and the toxin dioxin. The longest NQO1 transcript has increased poly(A) tail (PA-tail) length that accounts for the difference in translation potentials of the three NQO1 isoforms. This mechanism is involved in the regulation of cardiac hypertrophy (CH), an antecedent condition to HF where NQO1 downregulation stems from the loss of the distal-specific transcript. The loss of NQO1 during hypertrophy was rescued by ectopic expression of the distal- but not the proximal- or middle-specific NQO1 mRNA isoforms in the presence of Star-PAP expression, and reverses molecular events of hypertrophy in cardiomyocytes.
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Affiliation(s)
- A P Sudheesh
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Nimmy Mohan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Nimmy Francis
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India
| | - Richard A Anderson
- School of Medicine and Public Health, University of Wisconsin, MD 53726, USA
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203
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Huang AZ, Delaidelli A, Sorensen PH. RNA modifications in brain tumorigenesis. Acta Neuropathol Commun 2020; 8:64. [PMID: 32375856 PMCID: PMC7204278 DOI: 10.1186/s40478-020-00941-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023] Open
Abstract
RNA modifications are emerging as critical regulators in cancer biology, thanks to their ability to influence gene expression and the predominant protein isoforms expressed during cell proliferation, migration, and other pro-oncogenic properties. The reversibility and dynamic nature of post-transcriptional RNA modifications allow cells to quickly adapt to microenvironmental changes. Recent literature has revealed that the deregulation of RNA modifications can promote a plethora of developmental diseases, including tumorigenesis. In this review, we will focus on four key post-transcriptional RNA modifications which have been identified as contributors to the pathogenesis of brain tumors: m6A, alternative polyadenylation, alternative splicing and adenosine to inosine modifications. In addition to the role of RNA modifications in brain tumor progression, we will also discuss potential opportunities to target these processes to improve the dismal prognosis for brain tumors.
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Affiliation(s)
- Albert Z Huang
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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204
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Characterization and Functional Analysis of Polyadenylation Sites in Fast and Slow Muscles. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2626584. [PMID: 32258109 PMCID: PMC7102456 DOI: 10.1155/2020/2626584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/01/2019] [Accepted: 01/16/2020] [Indexed: 12/05/2022]
Abstract
Many increasing documents have proved that alternative polyadenylation (APA) events with different polyadenylation sites (PAS) contribute to posttranscriptional regulation. However, little is known about the detailed molecular features of PASs and its role in porcine fast and slow skeletal muscles through microRNAs (miRNAs) and RNA binding proteins (RBPs). In this study, we combined single-molecule real-time sequencing and Illumina RNA-seq datasets to comprehensively analyze polyadenylation in pigs. We identified a total of 10,334 PASs, of which 8734 were characterized by reference genome annotation. 32.86% of PAS-associated genes were determined to have more than one PAS. Further analysis demonstrated that tissue-specific PASs between fast and slow muscles were enriched in skeletal muscle development pathways. In addition, we obtained 1407 target genes regulated by APA events through potential binding 69 miRNAs and 28 RBPs in variable 3′ UTR regions and some are involved in myofiber transformation. Furthermore, the de novo motif search confirmed that the most common usage of canonical motif AAUAAA and three types of PASs may be related to the strength of motifs. In summary, our results provide a useful annotation of PASs for pig transcriptome and suggest that APA may serve as a role in fast and slow muscle development under the regulation of miRNAs and RBPs.
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206
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Sommerkamp P, Altamura S, Renders S, Narr A, Ladel L, Zeisberger P, Eiben PL, Fawaz M, Rieger MA, Cabezas-Wallscheid N, Trumpp A. Differential Alternative Polyadenylation Landscapes Mediate Hematopoietic Stem Cell Activation and Regulate Glutamine Metabolism. Cell Stem Cell 2020; 26:722-738.e7. [PMID: 32229311 DOI: 10.1016/j.stem.2020.03.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 12/08/2019] [Accepted: 03/06/2020] [Indexed: 02/07/2023]
Abstract
Alternative polyadenylation (APA) is emerging as an important regulatory mechanism of RNA and protein isoform expression by controlling 3' untranslated region (3'-UTR) composition. The relevance of APA in stem cell hierarchies remains elusive. Here, we first demonstrate the requirement of the APA regulator Pabpn1 for hematopoietic stem cell (HSC) function. We then determine the genome-wide APA landscape (APAome) of HSCs and progenitors by performing low-input 3' sequencing paired with bioinformatic pipelines. This reveals transcriptome-wide dynamic APA patterns and an overall shortening of 3'-UTRs during differentiation and upon homeostatic or stress-induced transition from quiescence to proliferation. Specifically, we show that APA regulates activation-induced Glutaminase (Gls) isoform switching by Nudt21. This adaptation of the glutamine metabolism by increasing the GAC:KGA isoform ratio fuels versatile metabolic pathways necessary for HSC self-renewal and proper stress response. Our study establishes APA as a critical regulatory layer orchestrating HSC self-renewal, behavior, and commitment.
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Affiliation(s)
- Pia Sommerkamp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany
| | - Sandro Altamura
- Department of Pediatric Hematology, Oncology and Immunology, Heidelberg University Medical Center, 69120 Heidelberg, Germany
| | - Simon Renders
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Andreas Narr
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany
| | - Luisa Ladel
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - Petra Zeisberger
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - Paula Leonie Eiben
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - Malak Fawaz
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Michael A Rieger
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Frankfurt Cancer Institute, 60596 Frankfurt, Germany
| | - Nina Cabezas-Wallscheid
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.
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207
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Abdelfettah S, Boulay G, Dubuissez M, Spruyt N, Garcia SP, Rengarajan S, Loison I, Leroy X, Rivera MN, Leprince D. hPCL3S promotes proliferation and migration of androgen-independent prostate cancer cells. Oncotarget 2020; 11:1051-1074. [PMID: 32256978 PMCID: PMC7105160 DOI: 10.18632/oncotarget.27511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) allows the deposition of H3K27me3. PRC2 facultative subunits modulate its activity and recruitment such as hPCL3/PHF19, a human ortholog of Drosophila Polycomb-like protein (PCL). These proteins contain a TUDOR domain binding H3K36me3, two PHD domains and a “Winged-helix” domain involved in GC-rich DNA binding. The human PCL3 locus encodes the full-length hPCL3L protein and a shorter isoform, hPCL3S containing the TUDOR and PHD1 domains only. In this study, we demonstrated by RT-qPCR analyses of 25 prostate tumors that hPCL3S is frequently up-regulated. In addition, hPCL3S is overexpressed in the androgen-independent DU145 and PC3 cells, but not in the androgen-dependent LNCaP cells. hPCL3S knockdown decreased the proliferation and migration of DU145 and PC3 whereas its forced expression into LNCaP increased these properties. A mutant hPCL3S unable to bind H3K36me3 (TUDOR-W50A) increased proliferation and migration of LNCaP similarly to wt hPCL3S whereas inactivation of its PHD1 domain decreased proliferation. These effects partially relied on the up-regulation of genes known to be important for the proliferation and/or migration of prostate cancer cells such as S100A16, PlexinA2, and Spondin1. Collectively, our results suggest hPCL3S as a new potential therapeutic target in castration resistant prostate cancers.
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Affiliation(s)
- Souhila Abdelfettah
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Gaylor Boulay
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Marion Dubuissez
- Present Address: Maisonneuve-Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 3W5, Canada
| | - Nathalie Spruyt
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Sara P Garcia
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Shruthi Rengarajan
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ingrid Loison
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Xavier Leroy
- Department of Pathology, University de Lille, CHU de Lille, F-59000 Lille, France
| | - Miguel N Rivera
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Dominique Leprince
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
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208
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Conesa CM, Saez A, Navarro-Neila S, de Lorenzo L, Hunt AG, Sepúlveda EB, Baigorri R, Garcia-Mina JM, Zamarreño AM, Sacristán S, del Pozo JC. Alternative Polyadenylation and Salicylic Acid Modulate Root Responses to Low Nitrogen Availability. PLANTS (BASEL, SWITZERLAND) 2020; 9:E251. [PMID: 32079121 PMCID: PMC7076428 DOI: 10.3390/plants9020251] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) is probably the most important macronutrient and its scarcity limits plant growth, development and fitness. N starvation response has been largely studied by transcriptomic analyses, but little is known about the role of alternative polyadenylation (APA) in such response. In this work, we show that N starvation modifies poly(A) usage in a large number of transcripts, some of them mediated by FIP1, a component of the polyadenylation machinery. Interestingly, the number of mRNAs isoforms with poly(A) tags located in protein-coding regions or 5'-UTRs significantly increases in response to N starvation. The set of genes affected by APA in response to N deficiency is enriched in N-metabolism, oxidation-reduction processes, response to stresses, and hormone responses, among others. A hormone profile analysis shows that the levels of salicylic acid (SA), a phytohormone that reduces nitrate accumulation and root growth, increase significantly upon N starvation. Meta-analyses of APA-affected and fip1-2-deregulated genes indicate a connection between the nitrogen starvation response and salicylic acid (SA) signaling. Genetic analyses show that SA may be important for preventing the overgrowth of the root system in low N environments. This work provides new insights on how plants interconnect different pathways, such as defense-related hormonal signaling and the regulation of genomic information by APA, to fine-tune the response to low N availability.
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Affiliation(s)
- Carlos M. Conesa
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (C.M.C.); (S.N.-N.)
- Centro de Biotecnología y Genómica de Plantas (CBGP) and Escuela Técnica Superior de Ingeniería Agronómica, Agroambiental y de Biosistemas (ETSIAAB), Universidad Polictécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain;
| | - Angela Saez
- DTD Development and Technical Department, Timac Agro Spain, 31580 Lodosa, Navarra, Spain; (A.S.); (R.B.)
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (C.M.C.); (S.N.-N.)
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, USA; (L.d.L.); (A.G.H.)
| | - Arthur G. Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, USA; (L.d.L.); (A.G.H.)
| | - Edgar B. Sepúlveda
- Departamento de Biotecnología y Bioingeniería CINVESTAV Instituto Politécnico Nacional, 07360 Ciudad de Mexico, Mexico;
| | - Roberto Baigorri
- DTD Development and Technical Department, Timac Agro Spain, 31580 Lodosa, Navarra, Spain; (A.S.); (R.B.)
| | - Jose M. Garcia-Mina
- Environmental Biology Department, University of Navarra, 31008 Navarra, Spain; (J.M.G.-M.); (A.M.Z.)
| | - Angel M. Zamarreño
- Environmental Biology Department, University of Navarra, 31008 Navarra, Spain; (J.M.G.-M.); (A.M.Z.)
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (CBGP) and Escuela Técnica Superior de Ingeniería Agronómica, Agroambiental y de Biosistemas (ETSIAAB), Universidad Polictécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain;
| | - Juan C. del Pozo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (C.M.C.); (S.N.-N.)
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209
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Zhou Z, Qu J, He L, Zhu Y, Yang SZ, Zhang F, Guo T, Peng H, Chen P, Zhou Y. Stiff matrix instigates type I collagen biogenesis by mammalian cleavage factor I complex-mediated alternative polyadenylation. JCI Insight 2020; 5:e133972. [PMID: 31935199 PMCID: PMC7098798 DOI: 10.1172/jci.insight.133972] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/08/2020] [Indexed: 12/20/2022] Open
Abstract
Alternative polyadenylation (APA) is a widespread and important mechanism in regulation of gene expression. Dysregulation of the 3' UTR cleavage and polyadenylation represents a common characteristic among many disease states, including lung fibrosis. In this study, we investigated the role of mammalian cleavage factor I-mediated (CFIm-mediated) APA in regulating extracellular matrix production in response to mechanical stimuli from stiffened matrix simulating the fibrotic lungs. We found that stiff matrix downregulated expression of CFIm68, CFIm59 and CFIm25 subunits and promoted APA in favor of the proximal poly(A) site usage in the 3' UTRs of type I collagen (COL1A1) and fibronectin (FN1) in primary human lung fibroblasts. Knockdown and overexpression of each individual CFIm subunit demonstrated that CFIm68 and CFIm25 are indispensable attributes of stiff matrix-induced APA and overproduction of COL1A1, whereas CFIm did not appear to mediate stiffness-regulated FN1 APA. Furthermore, expression of the CFIm subunits was associated with matrix stiffness in vivo in a bleomycin-induced mouse model of pulmonary fibrosis. These data suggest that stiff matrix instigates type I collagen biogenesis by selectively targeting mRNA transcripts for 3' UTR shortening. The current study uncovered a potential mechanism for regulation of the CFIm complex by mechanical cues under fibrotic conditions.
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Affiliation(s)
- Zijing Zhou
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Respiratory Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jing Qu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Li He
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yi Zhu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shan-Zhong Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Feng Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ting Guo
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Respiratory Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Hong Peng
- Department of Respiratory Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ping Chen
- Department of Respiratory Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yong Zhou
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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210
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Zhang J, Gu H, Dai H, Zhang Z, Miao M. Alternative polyadenylation of the stacyose synthase gene mediates source-sink regulation in cucumber. JOURNAL OF PLANT PHYSIOLOGY 2020; 245:153111. [PMID: 31926460 DOI: 10.1016/j.jplph.2019.153111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/24/2019] [Accepted: 12/24/2019] [Indexed: 05/24/2023]
Abstract
Alternative polyadenylation (APA) is a pervasive mechanism for gene regulation in eukaryotes. Stachyose is the main assimilate translocated in the cucumber phloem. Stachyose synthase (CsSTS) catalyzes the last step of stachyose biosynthesis in cucumber leaves and plays a key role in the regulation of assimilate partitioning between source and sink. In this study, three CsSTS mRNAs with the same open reading frame and the 5`untranslated region (UTR), but differing in their 3`UTRs, named CsSTS1 (short), CsSTS2 (medium), and CsSTS3 (long), were identified. Southern blot and sequence analysis of the cucumber genome confirmed that these transcripts are regulated through APA from a single gene. No significant difference of in vitro translation efficiency was found among three mRNAs. However, the relative stabilities of three transcripts varied among different tissues and different leaf development stages of cucumber. CsSTS1 expression in cucumber calli was up-regulated by the raffinose (substrate of CsSTS) and down-regulated by stachyose (product of CsSTS), respectively. In cucumber plants, all three isoforms have considerable expression in non-fruit node leaves. However, in fruit-carrying node leaves, the expression of CsSTS2 and CsSTS3 was severely inhibited and only CsSTS1 was highly expressed, indicating fruit setting has a remarkable effect on the relative expression level of three transcripts. This "fruit setting" effect could be observed until at least 36 h after the fruit was removed from the node. Our results suggest that abundant expression of CsSTS1 is beneficial for stachyose loading in source leaves, and APA is a delicate mechanism for CsSTS to regulate cucumber source-sink balance.
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Affiliation(s)
- Jinji Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
| | - Hao Gu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
| | - Haibo Dai
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
| | - Zhiping Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
| | - Minmin Miao
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
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211
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Oh JM, Venters CC, Di C, Pinto AM, Wan L, Younis I, Cai Z, Arai C, So BR, Duan J, Dreyfuss G. U1 snRNP regulates cancer cell migration and invasion in vitro. Nat Commun 2020; 11:1. [PMID: 31911652 PMCID: PMC6946686 DOI: 10.1038/s41467-019-13993-7] [Citation(s) in RCA: 3406] [Impact Index Per Article: 681.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
Stimulated cells and cancer cells have widespread shortening of mRNA 3'-untranslated regions (3'UTRs) and switches to shorter mRNA isoforms due to usage of more proximal polyadenylation signals (PASs) in introns and last exons. U1 snRNP (U1), vertebrates' most abundant non-coding (spliceosomal) small nuclear RNA, silences proximal PASs and its inhibition with antisense morpholino oligonucleotides (U1 AMO) triggers widespread premature transcription termination and mRNA shortening. Here we show that low U1 AMO doses increase cancer cells' migration and invasion in vitro by up to 500%, whereas U1 over-expression has the opposite effect. In addition to 3'UTR length, numerous transcriptome changes that could contribute to this phenotype are observed, including alternative splicing, and mRNA expression levels of proto-oncogenes and tumor suppressors. These findings reveal an unexpected role for U1 homeostasis (available U1 relative to transcription) in oncogenic and activated cell states, and suggest U1 as a potential target for their modulation.
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Affiliation(s)
- Jung-Min Oh
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA
| | - Christopher C Venters
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA
| | - Chao Di
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA
| | - Anna Maria Pinto
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA
| | - Lili Wan
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA
| | - Ihab Younis
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA
| | - Zhiqiang Cai
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA
| | - Chie Arai
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA
| | - Byung Ran So
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA
| | - Jingqi Duan
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA
| | - Gideon Dreyfuss
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA.
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212
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Wang PH, Kumar S, Zeng J, McEwan R, Wright TR, Gupta M. Transcription Terminator-Mediated Enhancement in Transgene Expression in Maize: Preponderance of the AUGAAU Motif Overlapping With Poly(A) Signals. FRONTIERS IN PLANT SCIENCE 2020; 11:570778. [PMID: 33178242 PMCID: PMC7591816 DOI: 10.3389/fpls.2020.570778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/11/2020] [Indexed: 05/08/2023]
Abstract
The selection of transcription terminators (TTs) for pairing with high expressing constitutive promoters in chimeric constructs is crucial to deliver optimal transgene expression in plants. In this study, the use of the native combinations of four polyubiquitin gene promoters and corresponding TTs resulted in up to >3-fold increase in transgene expression in maize. Of the eight polyubiquitin promoter and TT regulatory elements utilized, seven were novel and identified from the polyubiquitin genes of Brachypodium distachyon, Setaria italica, and Zea mays. Furthermore, gene expression driven by the Cassava mosaic virus promoter was studied by pairing the promoter with distinct TTs derived from the high expressing genes of Arabidopsis. Of the three TTs studied, the polyubiquitin10 gene TT produced the highest transgene expression in maize. Polyadenylation patterns and mRNA abundance from eight distinct TTs were analyzed using 3'-RACE and next-generation sequencing. The results exhibited one to three unique polyadenylation sites in the TTs. The poly(A) site patterns for the StPinII TT were consistent when the same TT was deployed in chimeric constructs irrespective of the reporter gene and promoter used. Distal to the poly(A) sites, putative polyadenylation signals were identified in the near-upstream regions of the TTs based on previously reported mutagenesis and bioinformatics studies in rice and Arabidopsis. The putative polyadenylation signals were 9 to 11 nucleotides in length. Six of the eight TTs contained the putative polyadenylation signals that were overlaps of either canonical AAUAAA or AAUAAA-like polyadenylation signals and AUGAAU, a top-ranking-hexamer of rice and Arabidopsis gene near-upstream regions. Three of the polyubiquitin gene TTs contained the identical 9-nucleotide overlap, AUGAAUAAG, underscoring the functional significance of such overlaps in mRNA 3' end processing. In addition to identifying new combinations of regulatory elements for high constitutive trait gene expression in maize, this study demonstrated the importance of TTs for optimizing gene expression in plants. Learning from this study could be applied to other dicotyledonous and monocotyledonous plant species for transgene expression. Research on TTs is not limited to transgene expression but could be extended to the introduction of appropriate mutations into TTs via genome editing, paving the way for expression modulation of endogenous genes.
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Affiliation(s)
- Po-Hao Wang
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
| | - Sandeep Kumar
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
- *Correspondence: Sandeep Kumar,
| | - Jia Zeng
- Data Science & Informatics, Corteva Agriscience, Indianapolis, IN, United States
| | - Robert McEwan
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
| | - Terry R. Wright
- Trait Discovery, Corteva Agriscience, Indianapolis, IN, United States
| | - Manju Gupta
- Trait Product Development, Dow Agrosciences, Indianapolis, IN, United States
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213
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Iijima Y, Tanaka M, Suzuki S, Hauser D, Tanaka M, Okada C, Ito M, Ayukawa N, Sato Y, Ohtsuka M, Scheiffele P, Iijima T. SAM68-Specific Splicing Is Required for Proper Selection of Alternative 3' UTR Isoforms in the Nervous System. iScience 2019; 22:318-335. [PMID: 31805436 PMCID: PMC6909182 DOI: 10.1016/j.isci.2019.11.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/09/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022] Open
Abstract
Neuronal alternative splicing is a core mechanism for functional diversification. We previously found that STAR family proteins (SAM68, SLM1, SLM2) regulate spatiotemporal alternative splicing in the nervous system. However, the whole aspect of alternative splicing programs by STARs remains unclear. Here, we performed a transcriptomic analysis using SAM68 knockout and SAM68/SLM1 double-knockout midbrains. We revealed different alternative splicing activity between SAM68 and SLM1; SAM68 preferentially targets alternative 3′ UTR exons. SAM68 knockout causes a long-to-short isoform switch of a number of neuronal targets through the alteration in alternative last exon (ALE) selection or alternative polyadenylation. The altered ALE usage of a novel target, interleukin 1 receptor accessory protein (Il1rap), results in remarkable conversion from a membrane-bound type to a secreted type in Sam68KO brains. Proper ALE selection is necessary for IL1RAP neuronal function. Thus the SAM68-specific splicing program provides a mechanism for neuronal selection of alternative 3′ UTR isoforms. SAM68 and the related protein SLM1 exhibit distinct alternative splicing activity SAM68 specifically controls 3′ UTR selection of multiple neuronal genes Proper 3′ UTR selection is necessary for IL1RAP neuronal function Neuronal expression of SAM68 requires proper 3′ UTR selection in the nervous system
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Affiliation(s)
- Yoko Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Masami Tanaka
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Satoko Suzuki
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - David Hauser
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel 4056, Switzerland
| | - Masayuki Tanaka
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Chisa Okada
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Masatoshi Ito
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Noriko Ayukawa
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Yuji Sato
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Peter Scheiffele
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel 4056, Switzerland
| | - Takatoshi Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
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214
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Affiliation(s)
- Haibin Xi
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - April Pyle
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at University of California-Los Angeles, Los Angeles, CA 90095, USA.
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215
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Persson L, Brandman O. Finding the Right Finish Line in Eukaryotic Transcription. Biochemistry 2019; 58:4335-4336. [DOI: 10.1021/acs.biochem.9b00770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Laura Persson
- Department of Biology, Stanford University, Stanford, California 94305, United States
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
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216
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Yeh HS, Yong J. mTOR-coordinated Post-Transcriptional Gene Regulations: from Fundamental to Pathogenic Insights. J Lipid Atheroscler 2019; 9:8-22. [PMID: 32821719 PMCID: PMC7379075 DOI: 10.12997/jla.2020.9.1.8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/13/2019] [Accepted: 09/22/2019] [Indexed: 12/26/2022] Open
Abstract
Post-transcriptional regulations of mRNA transcripts such as alternative splicing and alternative polyadenylation can affect the expression of genes without changing the transcript levels. Recent studies have demonstrated that these post-transcriptional events can have significant physiological impacts on various biological systems and play important roles in the pathogenesis of a number of diseases, including cancers. Nevertheless, how cellular signaling pathways control these post-transcriptional processes in cells are not very well explored in the field yet. The mammalian target of rapamycin complex 1 (mTORC1) pathway plays a key role in sensing cellular nutrient and energy status and regulating the proliferation and growth of cells by controlling various anabolic and catabolic processes. Dysregulation of mTORC1 pathway can tip the metabolic balance of cells and is associated with a number of pathological conditions, including various types of cancers, diabetes, and cardiovascular diseases. Numerous reports have shown that mTORC1 controls its downstream pathways through translational and/or transcriptional regulation of the expression of key downstream effectors. And, recent studies have also shown that mTORC1 can control downstream pathways via post-transcriptional regulations. In this review, we will discuss the roles of post-transcriptional processes in gene expression regulations and how mTORC1-mediated post-transcriptional regulations contribute to cellular physiological changes. We highlight post-transcriptional regulation as an additional layer of gene expression control by mTORC1 to steer cellular biology. These emphasize the importance of studying post-transcriptional events in transcriptome datasets for gaining a fuller understanding of gene expression regulations in the biological systems of interest.
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Affiliation(s)
- Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
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217
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Leung MKK, Delong A, Frey BJ. Inference of the human polyadenylation code. Bioinformatics 2019; 34:2889-2898. [PMID: 29648582 PMCID: PMC6129302 DOI: 10.1093/bioinformatics/bty211] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 04/09/2018] [Indexed: 01/02/2023] Open
Abstract
Motivation Processing of transcripts at the 3′-end involves cleavage at a polyadenylation site followed by the addition of a poly(A)-tail. By selecting which site is cleaved, the process of alternative polyadenylation enables genes to produce transcript isoforms with different 3′-ends. To facilitate the identification and treatment of disease-causing mutations that affect polyadenylation and to understand the sequence determinants underlying this regulatory process, a computational model that can accurately predict polyadenylation patterns from genomic features is desirable. Results Previous works have focused on identifying candidate polyadenylation sites and classifying tissue-specific sites. By training on how multiple sites in genes are competitively selected for polyadenylation from 3′-end sequencing data, we developed a deep learning model that can predict the tissue-specific strength of a polyadenylation site in the 3′ untranslated region of the human genome given only its genomic sequence. We demonstrate the model’s broad utility on multiple tasks, without any application-specific training. The model can be used to predict which polyadenylation site is more likely to be selected in genes with multiple sites. It can be used to scan the 3′ untranslated region to find candidate polyadenylation sites. It can be used to classify the pathogenicity of variants near annotated polyadenylation sites in ClinVar. It can also be used to anticipate the effect of antisense oligonucleotide experiments to redirect polyadenylation. We provide analysis on how different features affect the model’s predictive performance and a method to identify sensitive regions of the genome at the single-based resolution that can affect polyadenylation regulation. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michael K K Leung
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada.,Deep Genomics, MaRS Centre, Toronto, Canada
| | - Andrew Delong
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada.,Deep Genomics, MaRS Centre, Toronto, Canada
| | - Brendan J Frey
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada.,Deep Genomics, MaRS Centre, Toronto, Canada.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
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218
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Xiong M, Chen L, Zhou L, Ding Y, Kazobinka G, Chen Z, Hou T. NUDT21 inhibits bladder cancer progression through ANXA2 and LIMK2 by alternative polyadenylation. Am J Cancer Res 2019; 9:7156-7167. [PMID: 31695759 PMCID: PMC6831288 DOI: 10.7150/thno.36030] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/09/2019] [Indexed: 11/25/2022] Open
Abstract
Purpose: Nudix Hydrolase 21 (NUDT21) is a crucial mediator involved in alternative polyadenylation (APA), and this molecule has been reported to be a tumor suppressor in human cancers. However, neither the role NUDT21 plays in bladder cancer (BC) nor the mechanisms which are involved have been investigated. Methods: Expression levels of NUDT21 in BC were evaluated with real-time PCR, western blotting, and immunohistochemistry (IHC). In vitro and in vivo assays were performed to investigate the function of NUDT21 in tumorigenesis in bladder cancer cells. The TOP/FOP flash reporter assay, western blot, and global APA site profiling analysis were used to identify the pathway which mediates the biologic roles of NUDT21 in BC. Results: NUDT21 expression is reduced in BC tissue and cells, and BC patients with lower NUDT21 expression have shorter overall and recurrent-free survival than patients with higher NUDT21 expression. NUDT21 ectopic expression or knockdown respectively profoundly inhibited or promoted the capacity of BC cells for proliferation, migration and invasion. We also identified a number of genes with shortened 3'UTRs through modulation of NUDT21 expression, and further characterized the NUDT21-regulated genes ANXA2 and LIMK2. We found NUDT21 modulates the expression of ANXA2 and LIMK2 in the Wnt/β-catenin and NF-κB signaling pathways. Conclusions: These findings show NUDT21 plays a crucial role in BC progression, at least in part through ANXA2 and LIMK2 which act by alternative polyadenylation. NUDT21 may thus have potential as a diagnostic and therapeutic target in treatment of BC.
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219
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Park J, Seo JW, Ahn N, Park S, Hwang J, Nam JW. UPF1/SMG7-dependent microRNA-mediated gene regulation. Nat Commun 2019; 10:4181. [PMID: 31519907 PMCID: PMC6744440 DOI: 10.1038/s41467-019-12123-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 08/20/2019] [Indexed: 12/16/2022] Open
Abstract
The stability and quality of metazoan mRNAs are under microRNA (miRNA)-mediated and nonsense-mediated control. Although UPF1, a core mediator of nonsense-mediated mRNA decay (NMD), mediates the decay of target mRNA in a 3′UTR-length-dependent manner, the detailed mechanism remains unclear. Here, we suggest that 3′UTR-length-dependent mRNA decay is not mediated by nonsense mRNAs but rather by miRNAs that downregulate target mRNAs via Ago-associated UPF1/SMG7. Global analyses of mRNAs in response to UPF1 RNA interference in miRNA-deficient cells reveal that 3′UTR-length-dependent mRNA decay by UPF1 requires canonical miRNA targeting. The destabilization of miRNA targets is accomplished by the combination of Ago2 and UPF1/SMG7, which may recruit the CCR4-NOT deadenylase complex. Indeed, loss of the SMG7-deadenylase complex interaction increases the levels of transcripts regulated by UPF1-SMG7. This UPF1/SMG7-dependent miRNA-mediated mRNA decay pathway may enable miRNA targeting to become more predictable and expand the miRNA-mRNA regulatory network. UPF1 mediates the decay of target mRNA in a 3′ untranslated region (UTR)-length-dependent manner. Here the authors reveal that the 3′UTR-length-dependent regulation of UPF1-dependent mRNA decay occurs through EJC-independent but miRNA-dependent regulation.
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Affiliation(s)
- Jungyun Park
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul, Republic of Korea
| | - Jwa-Won Seo
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Narae Ahn
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul, Republic of Korea
| | - Seokju Park
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Jungwook Hwang
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul, Republic of Korea. .,Department of Medical Genetics, College of Medicine, Hanyang University, Seoul, Republic of Korea.
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea. .,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, Republic of Korea.
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220
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Ko J, Mills T, Huang J, Chen NY, Mertens TCJ, Collum SD, Lee G, Xiang Y, Han L, Zhou Y, Lee CG, Elias JA, Jyothula SSK, Rajagopal K, Karmouty-Quintana H, Blackburn MR. Transforming growth factor β1 alters the 3'-UTR of mRNA to promote lung fibrosis. J Biol Chem 2019; 294:15781-15794. [PMID: 31488543 DOI: 10.1074/jbc.ra119.009148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 08/27/2019] [Indexed: 12/18/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic disease characterized by the pathological remodeling of air sacs as a result of excessive accumulation of extracellular matrix (ECM) proteins, but the mechanism governing the robust protein expression is poorly understood. Our recent findings demonstrate that alternative polyadenylation (APA) caused by NUDT21 reduction is important for the increased expression of fibrotic mediators and ECM proteins in lung fibroblasts by shortening the 3'-untranslated regions (3'-UTRs) of mRNAs and stabilizing their transcripts, therefore activating pathological signaling pathways. Despite the importance of NUDT21 reduction in the regulation of fibrosis, the underlying mechanisms for the depletion are unknown. We demonstrate here that NUDT21 is depleted by TGFβ1. We found that miR203, which is increased in IPF, was induced by TGFβ1 to target the NUDT21 3'-UTR, thus depleting NUDT21 in human and mouse lung fibroblasts. TGFβ1-mediated NUDT21 reduction was attenuated by the miR203 inhibitor antagomiR203 in fibroblasts. TGFβ1 transgenic mice revealed that TGFβ1 down-regulates NUDT21 in fibroblasts in vivo Furthermore, TGFβ1 promoted differential APA of fibrotic genes, including FGF14, RICTOR, TMOD2, and UCP5, in association with increased protein expression. This unique differential APA signature was also observed in IPF fibroblasts. Altogether, our results identified TGFβ1 as an APA regulator through NUDT21 depletion amplifying pulmonary fibrosis.
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Affiliation(s)
- Junsuk Ko
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center, Houston, Texas 77030.,MD Anderson UTHealth Graduate School, the University of Texas Health Science Center, Houston, Texas 77030
| | - Tingting Mills
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center, Houston, Texas 77030
| | - Jingjing Huang
- Department of Geriatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003 Jiangsu, China
| | - Ning-Yuan Chen
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center, Houston, Texas 77030
| | - Tinne C J Mertens
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center, Houston, Texas 77030
| | - Scott D Collum
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center, Houston, Texas 77030.,MD Anderson UTHealth Graduate School, the University of Texas Health Science Center, Houston, Texas 77030
| | - Garam Lee
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center, Houston, Texas 77030
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center, Houston, Texas 77030
| | - Leng Han
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center, Houston, Texas 77030.,MD Anderson UTHealth Graduate School, the University of Texas Health Science Center, Houston, Texas 77030
| | - Yang Zhou
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912
| | - Chun Geun Lee
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912
| | - Jack A Elias
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912
| | - Soma S K Jyothula
- Department of Internal Medicine, McGovern Medical School, the University of Texas Health Science Center, Houston, Texas 77030
| | - Keshava Rajagopal
- Department of Internal Medicine, McGovern Medical School, the University of Texas Health Science Center, Houston, Texas 77030
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center, Houston, Texas 77030.,MD Anderson UTHealth Graduate School, the University of Texas Health Science Center, Houston, Texas 77030
| | - Michael R Blackburn
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center, Houston, Texas 77030 .,MD Anderson UTHealth Graduate School, the University of Texas Health Science Center, Houston, Texas 77030
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221
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Téllez-Robledo B, Manzano C, Saez A, Navarro-Neila S, Silva-Navas J, de Lorenzo L, González-García MP, Toribio R, Hunt AG, Baigorri R, Casimiro I, Brady SM, Castellano MM, Del Pozo JC. The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1203-1219. [PMID: 31111599 DOI: 10.1111/tpj.14416] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 05/28/2023]
Abstract
Root development and its response to environmental changes is crucial for whole plant adaptation. These responses include changes in transcript levels. Here, we show that the alternative polyadenylation (APA) of mRNA is important for root development and responses. Mutations in FIP1, a component of polyadenylation machinery, affects plant development, cell division and elongation, and response to different abiotic stresses. Salt treatment increases the amount of poly(A) site usage within the coding region and 5' untranslated regions (5'-UTRs), and the lack of FIP1 activity reduces the poly(A) site usage within these non-canonical sites. Gene ontology analyses of transcripts displaying APA in response to salt show an enrichment in ABA signaling, and in the response to stresses such as salt or cadmium (Cd), among others. Root growth assays show that fip1-2 is more tolerant to salt but is hypersensitive to ABA or Cd. Our data indicate that FIP1-mediated alternative polyadenylation is important for plant development and stress responses.
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Affiliation(s)
- Barbara Téllez-Robledo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Concepcion Manzano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Angela Saez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- DTD, Timac Agro Spain, Lodosa, 31580, Navarra, Spain
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Javier Silva-Navas
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Mary-Paz González-García
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - René Toribio
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | | | - Ilda Casimiro
- Facultad de Ciencias, Department de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, 06006, Badajoz, Spain
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - J Carlos Del Pozo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
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222
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Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences. G3-GENES GENOMES GENETICS 2019; 9:2749-2760. [PMID: 31239292 PMCID: PMC6686930 DOI: 10.1534/g3.119.400196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Polyadenylation is an essential post-transcriptional modification of eukaryotic transcripts that plays critical role in transcript stability, localization, transport, and translational efficiency. About 70% genes in plants contain alternative polyadenylation (APA) sites. Despite availability of vast amount of sequencing data, to date, a comprehensive map of the polyadenylation events in maize is not available. Here, 9.48 billion RNA-Seq reads were analyzed to characterize 95,345 Poly(A) Clusters (PAC) in 23,705 (51%) maize genes. Of these, 76% were APA genes. However, most APA genes (55%) expressed a dominant PAC rather than favoring multiple PACs equally. The lincRNA genes with PACs were significantly longer in length than the genes without any PAC and about 48% genes had APA sites. Heterogeneity was observed in 52% of the PACs supporting the imprecise nature of the polyadenylation process. Genomic distribution revealed that the majority of the PACs (78%) were located in the genic regions. Unlike previous studies, large number of PACs were observed in the intergenic (n = 21,264), 5′-UTR (735), CDS (2,542), and the intronic regions (12,841). The CDS and introns with PACs were longer in length than without PACs, whereas intergenic PACs were more often associated with transcripts that lacked annotated 3′-UTRs. Nucleotide composition around PACs demonstrated AT-richness and the common upstream motif was AAUAAA, which is consistent with other plants. According to this study, only 2,830 genes still maintained the use of AAUAAA motif. This large-scale data provides useful insights about the gene expression regulation and could be utilized as evidence to validate the annotation of transcript ends.
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223
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Feng X, Li L, Wagner EJ, Li W. TC3A: The Cancer 3' UTR Atlas. Nucleic Acids Res 2019; 46:D1027-D1030. [PMID: 30053266 PMCID: PMC5753254 DOI: 10.1093/nar/gkx892] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 09/22/2017] [Indexed: 11/13/2022] Open
Abstract
Widespread alternative polyadenylation (APA) occurs during enhanced cellular proliferation and transformation. Recently, we demonstrated that CFIm25-mediated 3′ UTR shortening through APA promotes glioblastoma tumor growth in vitro and in vivo, further underscoring its significance to tumorigenesis. Here, we report The Cancer 3′ UTR Atlas (TC3A), a comprehensive resource of APA usage for 10,537 tumors across 32 cancer types. These APA events represent potentially novel prognostic biomarkers and may uncover novel mechanisms for the regulation of cancer driver genes. TC3A is built on top of the now de facto standard cBioPortal. Therefore, the large community of existing cBioPortal users and clinical researchers will find TC3A familiar and immediately usable. TC3A is currently fully functional and freely available at http://tc3a.org.
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Affiliation(s)
- Xin Feng
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric J Wagner
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Wei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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224
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Abstract
Modifications of RNA affect its function and stability. RNA editing is unique among these modifications because it not only alters the cellular fate of RNA molecules but also alters their sequence relative to the genome. The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. Recent transcriptomic studies have identified a number of 'recoding' sites at which A-to-I editing results in non-synonymous substitutions in protein-coding sequences. Many of these recoding sites are conserved within (but not usually across) lineages, are under positive selection and have functional and evolutionary importance. However, systematic mapping of the editome across the animal kingdom has revealed that most A-to-I editing sites are located within mobile elements in non-coding parts of the genome. Editing of these non-coding sites is thought to have a critical role in protecting against activation of innate immunity by self-transcripts. Both recoding and non-coding events have implications for genome evolution and, when deregulated, may lead to disease. Finally, ADARs are now being adapted for RNA engineering purposes.
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225
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Chen JL, Moss WN, Spencer A, Zhang P, Childs-Disney JL, Disney MD. The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology. PLoS One 2019; 14:e0219210. [PMID: 31291322 PMCID: PMC6619747 DOI: 10.1371/journal.pone.0219210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/18/2019] [Indexed: 12/31/2022] Open
Abstract
Tauopathies are neurodegenerative diseases that affect millions of people worldwide including those with Alzheimer’s disease. While many efforts have focused on understanding the role of tau protein in neurodegeneration, there has been little done to systematically analyze and study the structures within tau’s encoding RNA and their connection to disease pathology. Knowledge of RNA structure can provide insights into disease mechanisms and how to affect protein production for therapeutic benefit. Using computational methods based on thermodynamic stability and evolutionary conservation, we identified structures throughout the tau pre-mRNA, especially at exon-intron junctions and within the 5′ and 3′ untranslated regions (UTRs). In particular, structures were identified at twenty exon-intron junctions. The 5′ UTR contains one structured region, which lies within a known internal ribosome entry site. The 3′ UTR contains eight structured regions, including one that contains a polyadenylation signal. A series of functional experiments were carried out to assess the effects of mutations associated with mis-regulation of alternative splicing of exon 10 and to identify regions of the 3′ UTR that contain cis-regulatory elements. These studies defined novel structural regions within the mRNA that affect stability and pre-mRNA splicing and may lead to new therapeutic targets for treating tau-associated diseases.
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Affiliation(s)
- Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Adam Spencer
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Peiyuan Zhang
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Jessica L. Childs-Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, United States of America
- * E-mail:
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226
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Shi J, Deng Y, Huang S, Huang C, Wang J, Xiang AP, Yao C. Suboptimal RNA-RNA interaction limits U1 snRNP inhibition of canonical mRNA 3' processing. RNA Biol 2019; 16:1448-1460. [PMID: 31242075 DOI: 10.1080/15476286.2019.1636596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
It is increasingly appreciated that U1 snRNP transcriptomically suppresses the usage of intronic polyadenylation site (PAS) of mRNAs, an outstanding question is why frequently used PASs are not suppressed. Here we found that U1 snRNP could be transiently associated with sequences upstream of actionable PASs in human cells, and RNA-RNA interaction might contribute to the association. By focusing on individual PAS, we showed that the stable assembly of U1 snRNP near PAS might be generally required for U1 inhibition of mRNA 3' processing. Therefore, actionable PASs that often lack optimal U1 snRNP docking site nearby is free from U1 inhibitory effect. Consistently, natural 5' splicing site (5'-SS) is moderately enriched ~250 nt upstream of intronic PASs whose usage is sensitive to functional knockdown of U1 snRNA. Collectively, our results provided an insight into how U1 snRNP selectively inhibits the usage of PASs in a cellular context, and supported a prevailing model that U1 snRNP scans pre-mRNA through RNA-RNA interaction to find a stable interaction site to exercise its function in pre-mRNA processing, including repressing the usage of cryptic PASs.
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Affiliation(s)
- Junjie Shi
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Yanhui Deng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Shanshan Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Chunliu Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Jinkai Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China.,RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou , China.,Center for Precision Medicine, Sun Yat-sen University , Guangzhou , China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China.,Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University , Guangzhou , China
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227
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Zhu S, Wu X, Fu H, Ye C, Chen M, Jiang Z, Ji G. Modeling of Genome-Wide Polyadenylation Signals in Xenopus tropicalis. Front Genet 2019; 10:647. [PMID: 31333724 PMCID: PMC6616101 DOI: 10.3389/fgene.2019.00647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/18/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative polyadenylation (APA) is an important post-transcriptional modification event to process messenger RNA (mRNA) for transcriptional termination, transport, and translation. In the present study, we characterized poly(A) signals in Xenopus tropicalis using 70,918 highly confident poly(A) sites derived from 16,511 protein-coding genes to understand their roles in the regulation of embryo development and gender difference. We examined potential factors, including the gene length, the number of introns in a gene, and the intron length, that may affect the prevalence of APA. We observed 12 prominent poly(A) signal patterns, which accounted for approximately 92% of total APA sites in Xenopus tropicalis. Among them, three patterns are specific to X. tropicalis, so they are absent in other animals such as humans or mice. We catalogued APA sites based on their genomic regions and developed a bioinformatics pipeline to identify over-represented signal patterns for each class. Then the schema of cis elements for APA sites in each genomic region was proposed. More importantly, APA usage is dramatically dynamic in embryos along five developmental stages and well-coordinated with the maternal-to-zygotic transition event. We used an entropy-based method to identify developmental stage-specific APA sites and identified significant signal patterns around specific sites and constitutive sites. We found that the APA frequency in different genomic regions varies with developmental stages and that those sites located in intron or coding sequence regions contribute most to the dynamics of gene expression during developmental stages. This study deciphers the characteristics and poly(A) signal patterns for both canonical APA sites and non-canonical APA sites across different developmental stages and gender dimorphisms in X. tropicalis, providing new insights into the dynamic regulation of distal and proximal APA.
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Affiliation(s)
- Sheng Zhu
- Department of Automation, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Hongjuan Fu
- Department of Automation, Xiamen University, Xiamen, China
| | - Congting Ye
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Moliang Chen
- Department of Automation, Xiamen University, Xiamen, China
| | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
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228
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Chen M, Ji G, Fu H, Lin Q, Ye C, Ye W, Su Y, Wu X. A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data. Brief Bioinform 2019; 21:1261-1276. [PMID: 31267126 DOI: 10.1093/bib/bbz068] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022] Open
Abstract
Alternative polyadenylation (APA) has been implicated to play an important role in post-transcriptional regulation by regulating mRNA abundance, stability, localization and translation, which contributes considerably to transcriptome diversity and gene expression regulation. RNA-seq has become a routine approach for transcriptome profiling, generating unprecedented data that could be used to identify and quantify APA site usage. A number of computational approaches for identifying APA sites and/or dynamic APA events from RNA-seq data have emerged in the literature, which provide valuable yet preliminary results that should be refined to yield credible guidelines for the scientific community. In this review, we provided a comprehensive overview of the status of currently available computational approaches. We also conducted objective benchmarking analysis using RNA-seq data sets from different species (human, mouse and Arabidopsis) and simulated data sets to present a systematic evaluation of 11 representative methods. Our benchmarking study showed that the overall performance of all tools investigated is moderate, reflecting that there is still lot of scope to improve the prediction of APA site or dynamic APA events from RNA-seq data. Particularly, prediction results from individual tools differ considerably, and only a limited number of predicted APA sites or genes are common among different tools. Accordingly, we attempted to give some advice on how to assess the reliability of the obtained results. We also proposed practical recommendations on the appropriate method applicable to diverse scenarios and discussed implications and future directions relevant to profiling APA from RNA-seq data.
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Affiliation(s)
- Moliang Chen
- Department of Automation, Xiamen University, Xiamen 361005, China.,Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen 361005, China.,Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China
| | - Hongjuan Fu
- Department of Automation, Xiamen University, Xiamen 361005, China.,Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China
| | - Qianmin Lin
- Xiang' an hospital of Xiamen university, Xiamen 361005, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Wenbin Ye
- Department of Automation, Xiamen University, Xiamen 361005, China.,Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China
| | - Yaru Su
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou 350116, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen 361005, China.,Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China
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229
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MacDonald CC. Tissue-specific mechanisms of alternative polyadenylation: Testis, brain, and beyond (2018 update). WILEY INTERDISCIPLINARY REVIEWS. RNA 2019; 10:e1526. [PMID: 30816016 PMCID: PMC6617714 DOI: 10.1002/wrna.1526] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/05/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022]
Abstract
Alternative polyadenylation (APA) is how genes choose different sites for 3' end formation for mRNAs during transcription. APA often occurs in a tissue- or developmental stage-specific manner that can significantly affect gene activity by changing the protein product generated, the stability of the transcript, its localization within the cell, or its translatability. Despite the important regulatory effects that APA has on tissue-specific gene expression, only a few examples have been characterized mechanistically. In this 2018 update to our 2010 review, we examine mechanisms for the control of APA and update our understanding of the older mechanisms since 2010. We once postulated the existence of tissue-specific factors in APA. However, while a few tissue-specific polyadenylation factors are known, the emerging conclusion is that the majority of APA is accomplished by altering levels of core polyadenylation proteins. Examples of those core proteins include CSTF2, CPSF1, and subunits of mammalian cleavage factor I. But despite support for these mechanisms, no one has yet documented any of these proteins changing in either a tissue-specific or developmental manner. Given the profound effect that APA can have on gene expression and human health, improved understanding of tissue-specific APA could lead to numerous advances in gene activity control. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Clinton C. MacDonald
- Department of Cell Biology & BiochemistryTexas Tech University Health Sciences CenterLubbockTexas
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230
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Genome-wide transcriptome profiling of the medicinal plant Zanthoxylum planispinum using a single-molecule direct RNA sequencing approach. Genomics 2019; 111:973-979. [DOI: 10.1016/j.ygeno.2018.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/13/2018] [Accepted: 06/24/2018] [Indexed: 01/01/2023]
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231
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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: 126] [Impact Index Per Article: 21.0] [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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232
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Ye C, Long Y, Ji G, Li QQ, Wu X. APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. Bioinformatics 2019; 34:1841-1849. [PMID: 29360928 DOI: 10.1093/bioinformatics/bty029] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/17/2018] [Indexed: 12/28/2022] Open
Abstract
Motivation Alternative polyadenylation (APA) has been increasingly recognized as a crucial mechanism that contributes to transcriptome diversity and gene expression regulation. As RNA-seq has become a routine protocol for transcriptome analysis, it is of great interest to leverage such unprecedented collection of RNA-seq data by new computational methods to extract and quantify APA dynamics in these transcriptomes. However, research progress in this area has been relatively limited. Conventional methods rely on either transcript assembly to determine transcript 3' ends or annotated poly(A) sites. Moreover, they can neither identify more than two poly(A) sites in a gene nor detect dynamic APA site usage considering more than two poly(A) sites. Results We developed an approach called APAtrap based on the mean squared error model to identify and quantify APA sites from RNA-seq data. APAtrap is capable of identifying novel 3' UTRs and 3' UTR extensions, which contributes to locating potential poly(A) sites in previously overlooked regions and improving genome annotations. APAtrap also aims to tally all potential poly(A) sites and detect genes with differential APA site usages between conditions. Extensive comparisons of APAtrap with two other latest methods, ChangePoint and DaPars, using various RNA-seq datasets from simulation studies, human and Arabidopsis demonstrate the efficacy and flexibility of APAtrap for any organisms with an annotated genome. Availability and implementation Freely available for download at https://apatrap.sourceforge.io. Contact liqq@xmu.edu.cn or xhuister@xmu.edu.cn. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Yuqi Long
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China
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233
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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: 26] [Impact Index Per Article: 4.3] [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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234
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Modic M, Grosch M, Rot G, Schirge S, Lepko T, Yamazaki T, Lee FCY, Rusha E, Shaposhnikov D, Palo M, Merl-Pham J, Cacchiarelli D, Rogelj B, Hauck SM, von Mering C, Meissner A, Lickert H, Hirose T, Ule J, Drukker M. Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition. Mol Cell 2019; 74:951-965.e13. [PMID: 31047794 PMCID: PMC6561722 DOI: 10.1016/j.molcel.2019.03.041] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 02/12/2019] [Accepted: 03/28/2019] [Indexed: 01/22/2023]
Abstract
RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expression, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment "paraspeckles," are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR-21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation.
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Affiliation(s)
- Miha Modic
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Markus Grosch
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Gregor Rot
- Institute of Molecular Life Sciences of the University of Zurich and Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
| | - Silvia Schirge
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tjasa Lepko
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Flora C Y Lee
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ejona Rusha
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Dmitry Shaposhnikov
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Michael Palo
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 80939 Munich, Germany
| | - Davide Cacchiarelli
- Broad Institute of Harvard University/MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Telethon Institute of Genetics and Medicine (TIGEM), NA 80078 Pozzuoli, Italy
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia; Biomedical Research Institute BRIS, 1000 Ljubljana, Slovenia
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 80939 Munich, Germany
| | - Christian von Mering
- Institute of Molecular Life Sciences of the University of Zurich and Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
| | - Alexander Meissner
- Broad Institute of Harvard University/MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Heiko Lickert
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Jernej Ule
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK.
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Comprehensive Pneumology Center (CPC-M), Ludwig-Maximilians-Universität München, Asklepios Fachkliniken München-Gauting und Helmholtz Zentrum München, Max-Lebsche-Platz 31, 81377 Munich, Germany.
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235
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Cardon T, Salzet M, Franck J, Fournier I. Nuclei of HeLa cells interactomes unravel a network of ghost proteins involved in proteins translation. Biochim Biophys Acta Gen Subj 2019; 1863:1458-1470. [PMID: 31128158 DOI: 10.1016/j.bbagen.2019.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/18/2019] [Accepted: 05/14/2019] [Indexed: 11/29/2022]
Abstract
Ghost proteins are issued from alternative Open Reading Frames (ORFs) and are missing a genome annotation. Indeed, historical filters applied for the detection of putative translated ORFs led to a wrong classification of transcripts considered as non-coding although translated proteins can be detected by proteomics. This Ghost (also called Alternative) proteome was neglected, and one major issue is to identify the implication of the Ghost proteins in the biological processes. In this context, we aimed to identify the protein-protein interactions (PPIs) of the Ghost proteins. For that, we re-explored a cross-link MS study performed on nuclei of HeLa cells using cross-linking mass spectrometry (XL-MS) associated with the HaltOrf database. Among 1679 cross-link interactions identified, 292 are involving Ghost Proteins. Forty-Four of these Ghost proteins are found to interact with 7 Reference proteins related to ribonucleoproteins, ribosome subunits and zinc finger proteins network. We, thus, have focused our attention on the heterotrimer between the RE/poly(U)-binding/degradation factor 1 (AUF1), the Ribosomal protein 10 (RPL10) and AltATAD2. Using I-Tasser software we performed docking models from which we could suggest the attachment of AUF1 on the external part of RPL10 and the interaction of AltATAD2 on the RPL10 region interacting with 5S ribosomal RNA as a mechanism of regulation of the ribosome. Taken together, these results reveal the importance of Ghost Proteins within known protein interaction networks.
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Affiliation(s)
- Tristan Cardon
- Inserm, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Michel Salzet
- Inserm, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France.
| | - Julien Franck
- Inserm, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France.
| | - Isabelle Fournier
- Inserm, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France.
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236
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Kim N, Chung W, Eum HH, Lee HO, Park WY. Alternative polyadenylation of single cells delineates cell types and serves as a prognostic marker in early stage breast cancer. PLoS One 2019; 14:e0217196. [PMID: 31100099 PMCID: PMC6524824 DOI: 10.1371/journal.pone.0217196] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 05/08/2019] [Indexed: 12/15/2022] Open
Abstract
Alternative polyadenylation (APA) in 3’ untranslated regions (3’ UTR) plays an important role in regulating transcript abundance, localization, and interaction with microRNAs. Length-variation of 3’UTRs by APA contributes to efficient proliferation of cancer cells. In this study, we investigated APA in single cancer cells and tumor microenvironment cells to understand the physiological implication of APA in different cell types. We analyzed APA patterns and the expression level of genes from the 515 single-cell RNA sequencing (scRNA-seq) dataset from 11 breast cancer patients. Although the overall 3’UTR length of individual genes was distributed equally in tumor and non-tumor cells, we found a differential pattern of polyadenylation in gene sets between tumor and non-tumor cells. In addition, we found a differential pattern of APA across tumor types using scRNA-seq data from 3 glioblastoma patients and 1 renal cell carcinoma patients. In detail, 1,176 gene sets and 53 genes showed the distinct pattern of 3’UTR shortening and over-expression as signatures for five cell types including B lymphocytes, T lymphocytes, myeloid cells, stromal cells, and breast cancer cells. Functional categories of gene sets for cellular proliferation demonstrated concordant regulation of APA and gene expression specific to cell types. The expression of APA genes in breast cancer was significantly correlated with the clinical outcome of earlier stage breast cancer patients. We identified cell type-specific APA in single cells, which allows the identification of cell types based on 3’UTR length variation in combination with gene expression. Specifically, an immune-specific APA signature in breast cancer could be utilized as a prognostic marker of early stage breast cancer.
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Affiliation(s)
- Nayoung Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Woosung Chung
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Hye Hyeon Eum
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Hae-Ock Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences &Technology, Sungkyunkwan University, Seoul, South Korea
- * E-mail: (HOL); (WYP)
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences &Technology, Sungkyunkwan University, Seoul, South Korea
- GENINUS Inc., Seoul, South Korea
- * E-mail: (HOL); (WYP)
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237
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Zhang J, Sun W, Ren C, Kong X, Yan W, Chen X. A PolH Transcript with a Short 3'UTR Enhances PolH Expression and Mediates Cisplatin Resistance. Cancer Res 2019; 79:3714-3724. [PMID: 31064846 DOI: 10.1158/0008-5472.can-18-3928] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/22/2019] [Accepted: 04/30/2019] [Indexed: 12/14/2022]
Abstract
Platinum-based anticancer drugs are widely used as a first-line drug for cancers, such as non-small cell lung carcinoma (NSCLC) and bladder cancer. However, the efficacy is limited due to intrinsic or acquired resistance to these drugs. DNA polymerase eta (PolH, Polη) belongs to the Y-family of DNA polymerases and mediates DNA translesion synthesis, a major mechanism for DNA damage tolerance. Here, we showed that a high level of PolH is associated with cisplatin resistance in lung and bladder cancer. Consistent with this, loss of PolH markedly attenuates cisplatin resistance in both cisplatin-sensitive and cisplatin-resistant lung cancer cells. Interestingly, we found that due to the presence of multiple polyadenylation sites, alternative polyadenylation (APA) produces three major PolH transcripts with various lengths of 3'untranslated region (3'UTR; 427-/2516-/6245-nt). We showed that the short PolH transcript with 427-nt 3'UTR is responsible for high expression of PolH in various cisplatin-resistant lung and bladder cancer cell lines. Importantly, loss of the short PolH transcript significantly sensitizes cancer cells to cisplatin treatment. Moreover, we found that miR-619 selectively inhibits the ability of the long PolH transcript with 6245-nt 3'UTR to produce PolH protein and, subsequently, PolH-dependent cell growth. Together, our data suggest that PolH expression is controlled by APA and that the short PolH transcript produced by APA can escape miR-619-mediated repression and, subsequently, confers PolH-mediated cisplatin resistance. SIGNIFICANCE: A short PolH transcript produced by alternative polyadenylation escapes repression by miR-619 and confers resistance to cisplatin.
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Affiliation(s)
- Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California.
| | - Wenqiang Sun
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Cong Ren
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Xiangmudong Kong
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Wensheng Yan
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California.
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238
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Sadek J, Omer A, Hall D, Ashour K, Gallouzi IE. Alternative polyadenylation and the stress response. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1540. [DOI: 10.1002/wrna.1540] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 03/18/2019] [Accepted: 04/02/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Jason Sadek
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Amr Omer
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Derek Hall
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Kholoud Ashour
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Imed Eddine Gallouzi
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
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239
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Ganapathi Sankaran D, Stemm-Wolf AJ, Pearson CG. CEP135 isoform dysregulation promotes centrosome amplification in breast cancer cells. Mol Biol Cell 2019; 30:1230-1244. [PMID: 30811267 PMCID: PMC6724517 DOI: 10.1091/mbc.e18-10-0674] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022] Open
Abstract
The centrosome, composed of two centrioles surrounded by pericentriolar material, is the cell's central microtubule-organizing center. Centrosome duplication is coupled with the cell cycle such that centrosomes duplicate once in S phase. Loss of such coupling produces supernumerary centrosomes, a condition called centrosome amplification (CA). CA promotes cell invasion and chromosome instability, two hallmarks of cancer. We examined the contribution of centriole overduplication to CA and the consequences for genomic stability in breast cancer cells. CEP135, a centriole assembly protein, is dysregulated in some breast cancers. We previously identified a short isoform of CEP135, CEP135mini, that represses centriole duplication. Here, we show that the relative level of full-length CEP135 (CEP135full) to CEP135mini (the CEP135full:mini ratio) is increased in breast cancer cell lines with high CA. Inducing expression of CEP135full in breast cancer cells increases the frequency of CA, multipolar spindles, anaphase-lagging chromosomes, and micronuclei. Conversely, inducing expression of CEP135mini reduces centrosome number. The differential expression of the CEP135 isoforms in vivo is generated by alternative polyadenylation. Directed genetic mutations near the CEP135mini alternative polyadenylation signal reduces the CEP135full:mini ratio and decreases CA. We conclude that dysregulation of CEP135 isoforms promotes centriole overduplication and contributes to chromosome segregation errors in breast cancer cells.
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Affiliation(s)
- Divya Ganapathi Sankaran
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045-2537
| | - Alexander J. Stemm-Wolf
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045-2537
| | - Chad G. Pearson
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045-2537
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240
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Polyadenylation sites and their characteristics in the genome of channel catfish (Ictalurus punctatus) as revealed by using RNA-Seq data. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 30:248-255. [PMID: 30952021 DOI: 10.1016/j.cbd.2019.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/24/2019] [Accepted: 03/24/2019] [Indexed: 11/21/2022]
Abstract
Polyadenylation plays important roles in gene expression regulation in eukaryotes, which typically involves cleavage and poly(A) tail addition at the polyadenylation site (PAS) of the pre-mature mRNA. Many eukaryotic genes contain more than one PASs, termed as alternative polyadenylation (APA). As a crucial post-transcriptional regulation, polyadenylation affects various aspects of RNA metabolism such as mRNA stability, translocation, and translation. However, polyadenylation has been rarely studied in teleosts. Here we conducted polyadenylation analysis in channel catfish, a commercially important aquaculture species around the world. Using RNA-Seq data, we identified 20,320 PASs which were classified into 14,500 clusters by merging adjacent PASs. Most of the PASs were found in 3' UTRs, followed by intron regions based on the annotation of channel catfish reference genome. No apparent difference in PAS distribution was observed between the sense and antisense strand of the channel catfish genome. The sequence analysis of nucleotide composition and motif around PASs yielded a highly similar profile among various organisms, suggesting the conservation and importance of polyadenylation in evolution. Using APA genes with more than two PASs, gene ontology enrichment revealed genes particularly involved in RNA binding. Reactome pathway analysis showed the enrichment of the innate immune system, especially neutrophil degranulation.
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241
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Abstract
The mechanisms underlying rapid adaptation to changing environments in species with reduced genetic variation, referred to as the “genetic paradox of invasion,” are unknown. We report that transposable elements (TEs) are highly enriched in the gene promoter regions of Capsella rubella compared with its outcrossing sister species Capsella grandiflora. We also show that a number of polymorphic TEs in C. rubella are associated with changes in gene expression. Frequent TE insertions at FLOWERING LOCUS C of C. rubella affect flowering-time variation, an important life history trait correlated with fitness. These results indicate that TE insertions drive rapid phenotypic variation, which could potentially help adapting to novel environments in species with limited genetic variation. Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown. Capsella rubella, an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (i) highly enriched in C. rubella compared with its outcrossing sister species Capsella grandiflora, and (ii) 4.2% of polymorphic TEs in C. rubella are associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions at FLOWERING LOCUS C (FLC) in natural populations of C. rubella could explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3′ UTR of FLC affects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.
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242
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Harrison BJ, Park JW, Gomes C, Petruska JC, Sapio MR, Iadarola MJ, Chariker JH, Rouchka EC. Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs. Front Genet 2019; 10:182. [PMID: 30915105 PMCID: PMC6422928 DOI: 10.3389/fgene.2019.00182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/19/2019] [Indexed: 01/08/2023] Open
Abstract
The length of untranslated regions at the 3' end of transcripts (3'UTRs) is regulated by alternate polyadenylation (APA). 3'UTRs contain regions that harbor binding motifs for regulatory molecules. However, the mechanisms that coordinate the 3'UTR length of specific groups of transcripts are not well-understood. We therefore developed a method, CSI-UTR, that models 3'UTR structure as tandem segments between functional alternative-polyadenylation sites (termed cleavage site intervals-CSIs). This approach facilitated (1) profiling of 3'UTR isoform expression changes and (2) statistical enrichment of putative regulatory motifs. CSI-UTR analysis is UTR-annotation independent and can interrogate legacy data generated from standard RNA-Seq libraries. CSI-UTR identified a set of CSIs in human and rodent transcriptomes. Analysis of RNA-Seq datasets from neural tissue identified differential expression events within 3'UTRs not detected by standard gene-based differential expression analyses. Further, in many instances 3'UTR and CDS from the same gene were regulated differently. This modulation of motifs for RNA-interacting molecules with potential condition-dependent and tissue-specific RNA binding partners near the polyA signal and CSI junction may play a mechanistic role in the specificity of alternative polyadenylation. Source code, CSI BED files and example datasets are available at: https://github.com/UofLBioinformatics/CSI-UTR.
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Affiliation(s)
- Benjamin J Harrison
- Department of Biomedical Sciences, Center for Excellence in the Neurosciences, College of Osteopathic Medicine, University of New England, Biddeford, ME, United States.,Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States
| | - Juw Won Park
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States.,Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Louisville, KY, United States
| | - Cynthia Gomes
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States
| | - Jeffrey C Petruska
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, United States.,Department of Neurological Surgery, University of Louisville, Louisville, KY, United States
| | - Matthew R Sapio
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Julia H Chariker
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States.,Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Louisville, KY, United States
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243
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Peck SA, Hughes KD, Victorino JF, Mosley AL. Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1529. [PMID: 30848101 PMCID: PMC6570551 DOI: 10.1002/wrna.1529] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/27/2018] [Accepted: 02/07/2019] [Indexed: 12/20/2022]
Abstract
Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein-protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co-transcriptionally. This review focuses specifically on the intricate balance between 3' end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Sarah A Peck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Katlyn D Hughes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jose F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
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244
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Xiang Y, Ye Y, Lou Y, Yang Y, Cai C, Zhang Z, Mills T, Chen NY, Kim Y, Muge Ozguc F, Diao L, Karmouty-Quintana H, Xia Y, Kellems RE, Chen Z, Blackburn MR, Yoo SH, Shyu AB, Mills GB, Han L. Comprehensive Characterization of Alternative Polyadenylation in Human Cancer. J Natl Cancer Inst 2019; 110:379-389. [PMID: 29106591 DOI: 10.1093/jnci/djx223] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 09/20/2017] [Indexed: 12/16/2022] Open
Abstract
Background Alternative polyadenylation (APA) is emerging as a major post-transcriptional mechanism for gene regulation, and dysregulation of APA contributes to several human diseases. However, the functional consequences of APA in human cancer are not fully understood. Particularly, there is no large-scale analysis in cancer cell lines. Methods We characterized the global APA profiles of 6398 patient samples across 17 cancer types from The Cancer Genome Atlas and 739 cancer cell lines from the Cancer Cell Line Encyclopedia. We built a linear regression model to explore the correlation between APA factors and APA events across different cancer types. We used Spearman correlation to assess the effects of APA events on drug sensitivity and the Wilcoxon rank-sum test or Cox proportional hazards model to identify clinically relevant APA events. Results We revealed a striking global 3'UTR shortening in cancer cell lines compared with tumor samples. Our analysis further suggested PABPN1 as the master regulator in regulating APA profile across different cancer types. Furthermore, we showed that APA events could affect drug sensitivity, especially of drugs targeting chromatin modifiers. Finally, we identified 1971 clinically relevant APA events, as well as alterations of APA in clinically actionable genes, suggesting that analysis of the complexity of APA profiles could have clinical utility. Conclusions Our study highlights important roles for APA in human cancer, including reshaping cellular pathways and regulating specific gene expression, exemplifying the complex interplay between APA and other biological processes and yielding new insights into the action mechanism of cancer drugs.
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Affiliation(s)
- Yu Xiang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Yanyan Lou
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL
| | - Yang Yang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chunyan Cai
- Department of Internal Medicine, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Tingting Mills
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Ning-Yuan Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Yoonjin Kim
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Fatma Muge Ozguc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Yang Xia
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Rodney E Kellems
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Michael R Blackburn
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
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Weng T, Ko J, Masamha CP, Xia Z, Xiang Y, Chen NY, Molina JG, Collum S, Mertens TC, Luo F, Philip K, Davies J, Huang J, Wilson C, Thandavarayan RA, Bruckner BA, Jyothula SS, Volcik KA, Li L, Han L, Li W, Assassi S, Karmouty-Quintana H, Wagner EJ, Blackburn MR. Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation. J Clin Invest 2019; 129:1984-1999. [PMID: 30830875 DOI: 10.1172/jci122106] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and deadly disease with a poor prognosis and few treatment options. Pathological remodeling of the extracellular matrix (ECM) by myofibroblasts is a key factor that drives disease pathogenesis, although the underlying mechanisms remain unknown. Alternative polyadenylation (APA) has recently been shown to play a major role in cellular responses to stress by driving the expression of fibrotic factors and ECMs through altering microRNA sensitivity, but a connection to IPF has not been established. Here, we demonstrate that CFIm25, a global regulator of APA, is down-regulated in the lungs of patients with IPF and mice with pulmonary fibrosis, with its expression selectively reduced in alpha-smooth muscle actin (α-SMA) positive fibroblasts. Following the knockdown of CFIm25 in normal human lung fibroblasts, we identified 808 genes with shortened 3'UTRs, including those involved in the transforming growth factor-β signaling pathway, the Wnt signaling pathway, and cancer pathways. The expression of key pro-fibrotic factors can be suppressed by CFIm25 overexpression in IPF fibroblasts. Finally, we demonstrate that deletion of CFIm25 in fibroblasts or myofibroblast precursors using either the Col1a1 or the Foxd1 promoter enhances pulmonary fibrosis after bleomycin exposure in mice. Taken together, our results identified CFIm25 down-regulation as a novel mechanism to elevate pro-fibrotic gene expression in pulmonary fibrosis.
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Affiliation(s)
- Tingting Weng
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Junsuk Ko
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Chioniso P Masamha
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Zheng Xia
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine Houston, Texas, USA
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Ning-Yuan Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Jose G Molina
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Scott Collum
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Tinne C Mertens
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Fayong Luo
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Kemly Philip
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Jonathan Davies
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Jingjing Huang
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cory Wilson
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | | | - Brian A Bruckner
- Houston Methodist DeBakey Transplant Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Soma Sk Jyothula
- Department of Internal Medicine, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Kelly A Volcik
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Lei Li
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine Houston, Texas, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Wei Li
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine Houston, Texas, USA
| | - Shervin Assassi
- Department of Internal Medicine, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Michael R Blackburn
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas, USA
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246
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Geng G, Yu C, Li X, Yuan X. Variable 3'polyadenylation of Wheat yellow mosaic virus and its novel effects on translation and replication. Virol J 2019; 16:23. [PMID: 30786887 PMCID: PMC6383263 DOI: 10.1186/s12985-019-1130-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/13/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Polyadenylation influences many aspects of mRNA as well as viral RNA. variable polyadenylation at the 3' end have been reported in RNA viruses. It is interesting to identify the characteristic and potential role of 3' polyadenylation of Wheat yellow mosaic virus (WYMV), which has been reported to contain two genomic RNAs with 3' poly(A) tails and caused severe disease on wheat in East Asia region. METHODS 3' RACE was used to identify sequences of the 3' end in WYMV RNAs from naturally infected wheat by WYMV. In vitro translation assay was performed to analyze effect of UTRs of WYMV with or without 3'polyadenylation on translation. In vitro replication mediated by WYMV NIb protein were performed to evaluate effect of variable polyadenylation on replication. RESULTS Variable polyadenylation in WYMV RNAs was identified via 3' RACE. WYMV RNAs in naturally infected wheat in China simultaneously present with regions of long, short, or no adenylation at the 3' ends. The effects of variable polyadenylation on translation and replication of WYMV RNAs were evaluated. 5'UTR and 3'UTR of WYMV RNA1 or RNA2 synergistically enhanced the translation of the firefly luciferase (Fluc) gene in in vitro WGE system, whereas additional adenylates had an oppositive effect on this enhancement on translation mediated by UTRs of WYMV. Additional adenylates remarkably inhibited the synthesis of complementary strand from viral genome RNA during the in vitro replication mediated by WYMV NIb protein. CONCLUSIONS 3' end of WYMV RNAs present variable polyadenylation even no polyadenylation. 3' polyadenylation have opposite effect on translation mediated by UTRs of WYMV RNA1 or RNA2. 3' polyadenylation have negative effect on minus-strand synthesis of WYMV RNA in vitro. Variable polyadenylation of WYMV RNAs may provide sufficient selection on the template for translation and replication.
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Affiliation(s)
- Guowei Geng
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| | - Chengming Yu
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| | - Xiangdong Li
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| | - Xuefeng Yuan
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
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247
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It's all about the T: transcription termination in archaea. Biochem Soc Trans 2019; 47:461-468. [PMID: 30783016 DOI: 10.1042/bst20180557] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/06/2023]
Abstract
One of the most fundamental biological processes driving all life on earth is transcription. The, at first glance, relatively simple cycle is divided into three stages: initiation at the promoter site, elongation throughout the open reading frame, and finally termination and product release at the terminator. In all three processes, motifs of the template DNA and protein factors of the transcription machinery including the multisubunit polymerase itself as well as a broad range of associated transcription factors work together and mutually influence each other. Despite several decades of research, this interplay holds delicate mechanistic and structural details as well as interconnections yet to be explored. One of the surprising characteristics of archaeal biology is the use of eukaryotic-like information processing systems against a backdrop of a bacterial-like genome. Archaeal genomes usually comprise main chromosomes alongside chromosomal plasmids, and the genetic information is encoded in single transcriptional units as well as in multicistronic operons alike their bacterial counterparts. Moreover, archaeal genomes are densely packed and this necessitates a tight regulation of transcription and especially assured termination events in order to prevent read-through into downstream coding regions and the accumulation of antisense transcripts.
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248
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Ngo T, Corrales A, Bourne T, Elmojahid S, Lam KS, Díaz E. Alternative Splicing of MXD3 and Its Regulation of MXD3 Levels in Glioblastoma. Front Mol Biosci 2019; 6:5. [PMID: 30838212 PMCID: PMC6390498 DOI: 10.3389/fmolb.2019.00005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/30/2019] [Indexed: 12/12/2022] Open
Abstract
The transcription factor MXD3 is an atypical member of the MYC/MAX/MXD transcriptional network and has been previously shown to be an important regulator of cell proliferation. MXD3 has been shown to be overexpressed and to be required for medulloblastoma and acute lymphoblastic leukemia cell proliferation. In this study we leveraged datasets from The Cancer Genome Atlas to examine MXD3 across several cancers. We find that MXD3 transcripts are significantly overexpressed in ~72% of the available datasets. The gene itself is not frequently altered, while the promoter appears to be hypomethylated. We examine the possibility that aberrant regulation of the MXD3 message is the cause of abnormal MXD3 expression across cancers. Specifically, we looked at MXD3 alternative splicing in glioblastoma multiforme (GBM) and find notable functional differences between the splice variants. The 3′UTR confers differential message stability. Furthermore, the different coding sequences lead to different protein stabilities and localizations. Altogether, these data extend our knowledge of MXD3 in the context of human cancers while characterizing a previously unstudied splice variant of MXD3.
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Affiliation(s)
- Tin Ngo
- Department of Pharmacology, University of California Davis School of Medicine, Davis, CA, United States.,Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA, United States
| | - Abraham Corrales
- Department of Pharmacology, University of California Davis School of Medicine, Davis, CA, United States
| | - Traci Bourne
- Department of Pharmacology, University of California Davis School of Medicine, Davis, CA, United States
| | - Samir Elmojahid
- Department of Pharmacology, University of California Davis School of Medicine, Davis, CA, United States
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA, United States
| | - Elva Díaz
- Department of Pharmacology, University of California Davis School of Medicine, Davis, CA, United States
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249
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Fonseca S, Rubio V. Arabidopsis CRL4 Complexes: Surveying Chromatin States and Gene Expression. FRONTIERS IN PLANT SCIENCE 2019; 10:1095. [PMID: 31608079 PMCID: PMC6761389 DOI: 10.3389/fpls.2019.01095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/09/2019] [Indexed: 05/10/2023]
Abstract
CULLIN4 (CUL4) RING ligase (CRL4) complexes contain a CUL4 scaffold protein, associated to RBX1 and to DDB1 proteins and have traditionally been associated to protein degradation events. Through DDB1, these complexes can associate with numerous DCAF proteins, which directly interact with specific targets promoting their ubiquitination and subsequent degradation by the proteasome. A characteristic feature of the majority of DCAF proteins that associate with DDB1 is the presence of the DWD motif. DWD-containing proteins sum up to 85 in the plant model species Arabidopsis. In the last decade, numerous Arabidopsis DWD proteins have been studied and their molecular functions uncovered. Independently of whether their association with CRL4 has been confirmed or not, DWD proteins are often found as components of additional multimeric protein complexes that play key roles in essential nuclear events. For most of them, the significance of their complex partnership is still unexplored. Here, we summarize recent findings involving both confirmed and putative CRL4-associated DCAF proteins in regulating nuclei architecture remodelling, DNA damage repair, histone post-translational modification, mRNA processing and export, and ribosome biogenesis, that definitely have an impact in gene expression and de novo protein synthesis. We hypothesized that, by maintaining accurate levels of regulatory proteins through targeted degradation and transcriptional control, CRL4 complexes help to surveil nuclear processes essential for plant development and survival.
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Vasconez AE, Janetzko P, Oo JA, Pflüger-Müller B, Ratiu C, Gu L, Helin K, Geisslinger G, Fleming I, Schröder K, Fork C, Brandes RP, Leisegang MS. The histone demethylase Jarid1b mediates angiotensin II-induced endothelial dysfunction by controlling the 3'UTR of soluble epoxide hydrolase. Acta Physiol (Oxf) 2019; 225:e13168. [PMID: 30076673 DOI: 10.1111/apha.13168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/26/2018] [Accepted: 08/01/2018] [Indexed: 01/25/2023]
Abstract
AIM The histone demethylase Jarid1b limits gene expression by removing the active methyl mark from histone3 lysine4 at gene promoter regions. A vascular function of Jarid1b is unknown, but a vasoprotective function to inflammatory and hypertrophic stimuli, like angiotensin II (AngII) could be inferred. This hypothesis was tested using Jarid1b knockout mice and the inhibitor PBIT. METHODS Mice or aortic segments were treated with AngII to induce endothelial dysfunction. Aortae from WT and Jarid1b knockout were studied in organ chambers and endothelium-dependent dilator responses to acetylcholine and endothelium-independent responses to DetaNONOate were recorded after pre-constriction with phenylephrine in the presence or absence of the NO-synthase inhibitor nitro-L-arginine. Molecular mechanisms were investigated with chromatin immunoprecipitation, RNA-Seq, RNA-3'-adaptor-ligation, actinomycin D and RNA-immunoprecipitation. RESULTS Knockout or inhibition of Jarid1b prevented the development of endothelial dysfunction in response to AngII. This effect was not a consequence of altered nitrite oxide availability but accompanied by a loss of the inflammatory response to AngII. As Jarid1b mainly inhibits gene expression, an indirect effect should account for this observation. AngII induced the soluble epoxide hydrolase (sEH), which degrades anti-inflammatory lipids, and thus promotes inflammation. Knockout or inhibition of Jarid1b prevented the AngII-mediated sEH induction. Mechanistically, Jarid1b maintained the length of the 3'untranslated region of the sEH mRNA, thereby increasing its stability and thus sEH protein expression. Loss of Jarid1b activity therefore resulted in sEH mRNA destabilization. CONCLUSION Jarid1b contributes to the pro-inflammatory effects of AngII by stabilizing sEH expression. Jarid1b inhibition might be an option for future therapeutics against cardiovascular dysfunction.
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Affiliation(s)
- Andrea E. Vasconez
- Institute for Cardiovascular Physiology; Goethe-University; Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK); Partner site RheinMain, Frankfurt Germany
| | - Patrick Janetzko
- Institute for Cardiovascular Physiology; Goethe-University; Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK); Partner site RheinMain, Frankfurt Germany
| | - James A. Oo
- Institute for Cardiovascular Physiology; Goethe-University; Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK); Partner site RheinMain, Frankfurt Germany
| | - Beatrice Pflüger-Müller
- Institute for Cardiovascular Physiology; Goethe-University; Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK); Partner site RheinMain, Frankfurt Germany
| | - Corina Ratiu
- Institute for Cardiovascular Physiology; Goethe-University; Frankfurt am Main Germany
- Department of Functional Sciences - Pathophysiology; “Victor Babes” University of Medicine and Pharmacy Timisoara; Timisoara Romania
| | - Lunda Gu
- Institute for Cardiovascular Physiology; Goethe-University; Frankfurt am Main Germany
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC); University of Copenhagen; Copenhagen Denmark
- Centre for Epigenetics; University of Copenhagen; Copenhagen Denmark
| | - Gerd Geisslinger
- Pharmazentrum Frankfurt; Institute of Clinical Pharmacology; Goethe-University; Frankfurt Germany
| | - Ingrid Fleming
- German Center of Cardiovascular Research (DZHK); Partner site RheinMain, Frankfurt Germany
- Institute for Vascular Signalling; Centre for Molecular Medicine; Goethe-University; Frankfurt Germany
| | - Katrin Schröder
- Institute for Cardiovascular Physiology; Goethe-University; Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK); Partner site RheinMain, Frankfurt Germany
| | - Christian Fork
- Institute for Cardiovascular Physiology; Goethe-University; Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK); Partner site RheinMain, Frankfurt Germany
| | - Ralf P. Brandes
- Institute for Cardiovascular Physiology; Goethe-University; Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK); Partner site RheinMain, Frankfurt Germany
| | - Matthias S. Leisegang
- Institute for Cardiovascular Physiology; Goethe-University; Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK); Partner site RheinMain, Frankfurt Germany
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