1
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Ietswaart R, Smalec BM, Xu A, Choquet K, McShane E, Jowhar ZM, Guegler CK, Baxter-Koenigs AR, West ER, Fu BXH, Gilbert L, Floor SN, Churchman LS. Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle. Mol Cell 2024; 84:2765-2784.e16. [PMID: 38964322 PMCID: PMC11315470 DOI: 10.1016/j.molcel.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/15/2024] [Accepted: 06/11/2024] [Indexed: 07/06/2024]
Abstract
Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.
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Affiliation(s)
- Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ziad Mohamoud Jowhar
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chantal K Guegler
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Autum R Baxter-Koenigs
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emma R West
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Luke Gilbert
- Arc Institute, Palo Alto, CA 94305, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94518, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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2
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Kose C, Lindsey-Boltz LA, Sancar A, Jiang Y. Genome-wide analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans. PLoS Genet 2024; 20:e1011365. [PMID: 39028758 PMCID: PMC11290646 DOI: 10.1371/journal.pgen.1011365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 07/31/2024] [Accepted: 07/08/2024] [Indexed: 07/21/2024] Open
Abstract
Bulky DNA adducts such as those induced by ultraviolet light are removed from the genomes of multicellular organisms by nucleotide excision repair, which occurs through two distinct mechanisms, global repair, requiring the DNA damage recognition-factor XPC (xeroderma pigmentosum complementation group C), and transcription-coupled repair (TCR), which does not. TCR is initiated when elongating RNA polymerase II encounters DNA damage, and thus analysis of genome-wide excision repair in XPC-mutants only repairing by TCR provides a unique opportunity to map transcription events missed by methods dependent on capturing RNA transcription products and thus limited by their stability and/or modifications (5'-capping or 3'-polyadenylation). Here, we have performed eXcision Repair-sequencing (XR-seq) in the model organism Caenorhabditis elegans to generate genome-wide repair maps in a wild-type strain with normal excision repair, a strain lacking TCR (csb-1), and a strain that only repairs by TCR (xpc-1). Analysis of the intersections between the xpc-1 XR-seq repair maps with RNA-mapping datasets (RNA-seq, long- and short-capped RNA-seq) reveal previously unrecognized sites of transcription and further enhance our understanding of the genome of this important model organism.
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Affiliation(s)
- Cansu Kose
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Laura A. Lindsey-Boltz
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Yuchao Jiang
- Department of Statistics, College of Arts and Sciences, Texas A&M University, College Station, Texas, United States of America
- Department of Biology, College of Arts and Sciences, Texas A&M University, College Station, Texas, United States of America
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, Texas, United States of America
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3
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Furugori K, Suzuki H, Abe R, Horiuchi K, Akiyama T, Hirose T, Toyoda A, Takahashi H. Chimera RNA transcribed from integrated HPV18 genome with adjacent host genomic region promotes oncogenic gene expression through condensate formation. Genes Cells 2024; 29:532-548. [PMID: 38715205 DOI: 10.1111/gtc.13121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 07/06/2024]
Abstract
Most cervical cancers are caused by human papillomavirus (HPV) infection. In HeLa cells, the HPV18 viral genome is integrated at chromosome 8q24.21 and activates transcription of the proto-oncogene c-Myc. However, the mechanism of how the integrated HPV genome and its transcribed RNAs exhibit transcription activation function has not been fully elucidated. In this study, we found that HPV18 transcripts contain an enhancer RNA-like function to activate proximal genes including CCAT1-5L and c-Myc. We showed that the human genome-integrated HPV18 genes are activated by transcription coregulators including BRD4 and Mediator. The transcribed HPV18 RNAs form a liquid-like condensate at chromosome 8q24.21 locus, which in turn accumulates RNA polymerase II. Moreover, we focused on a relatively uncharacterized transcript from the upstream region of CCAT1, named URC. The URC RNA is transcribed as a chimera RNA with HPV18 and is composed of the 3'-untranslated region of the HPV18 transcript. We experimentally showed that the URC contributes to stabilization of HPV18 RNAs by supplying a polyadenylation site for the HPV18 transcript. Our findings suggest that integrated HPV18 at 8q24.21 locus produces HPV18-URC chimera RNA and promotes tumorigenesis through RNA-based condensate formation.
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Affiliation(s)
- Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Tomonori Hirose
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
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4
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Han X, Xing L, Hong Y, Zhang X, Hao B, Lu JY, Huang M, Wang Z, Ma S, Zhan G, Li T, Hao X, Tao Y, Li G, Zhou S, Zheng Z, Shao W, Zeng Y, Ma D, Zhang W, Xie Z, Deng H, Yan J, Deng W, Shen X. Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence. Cell Stem Cell 2024; 31:694-716.e11. [PMID: 38631356 DOI: 10.1016/j.stem.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/01/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
Understanding cellular coordination remains a challenge despite knowledge of individual pathways. The RNA exosome, targeting a wide range of RNA substrates, is often downregulated in cellular senescence. Utilizing an auxin-inducible system, we observed that RNA exosome depletion in embryonic stem cells significantly affects the transcriptome and proteome, causing pluripotency loss and pre-senescence onset. Mechanistically, exosome depletion triggers acute nuclear RNA aggregation, disrupting nuclear RNA-protein equilibrium. This disturbance limits nuclear protein availability and hinders polymerase initiation and engagement, reducing gene transcription. Concurrently, it promptly disrupts nucleolar transcription, ribosomal processes, and nuclear exporting, resulting in a translational shutdown. Prolonged exosome depletion induces nuclear structural changes resembling senescent cells, including aberrant chromatin compaction, chromocenter disassembly, and intensified heterochromatic foci. These effects suggest that the dynamic turnover of nuclear RNA orchestrates crosstalk between essential processes to optimize cellular function. Disruptions in nuclear RNA homeostasis result in systemic functional decline, altering the cell state and promoting senescence.
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Affiliation(s)
- Xue Han
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Linqing Xing
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xuechun Zhang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Bo Hao
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - J Yuyang Lu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Mengyuan Huang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zuhui Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shaoqian Ma
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ge Zhan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Tong Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaowen Hao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yibing Tao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Guanwen Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Shuqin Zhou
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zheng Zheng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Wen Shao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yitian Zeng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Dacheng Ma
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiangwei Yan
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaohua Shen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China.
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5
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Rambout X, Maquat LE. Nuclear mRNA decay: regulatory networks that control gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00712-2. [PMID: 38637632 DOI: 10.1038/s41576-024-00712-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2024] [Indexed: 04/20/2024]
Abstract
Proper regulation of mRNA production in the nucleus is critical for the maintenance of cellular homoeostasis during adaptation to internal and environmental cues. Over the past 25 years, it has become clear that the nuclear machineries governing gene transcription, pre-mRNA processing, pre-mRNA and mRNA decay, and mRNA export to the cytoplasm are inextricably linked to control the quality and quantity of mRNAs available for translation. More recently, an ever-expanding diversity of new mechanisms by which nuclear RNA decay factors finely tune the expression of protein-encoding genes have been uncovered. Here, we review the current understanding of how mammalian cells shape their protein-encoding potential by regulating the decay of pre-mRNAs and mRNAs in the nucleus.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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6
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Mouzannar K, Schauer A, Liang TJ. The Post-Transcriptional Regulatory Element of Hepatitis B Virus: From Discovery to Therapy. Viruses 2024; 16:528. [PMID: 38675871 PMCID: PMC11055085 DOI: 10.3390/v16040528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The post-transcriptional regulatory element (PRE) is present in all HBV mRNAs and plays a major role in their stability, nuclear export, and enhancement of viral gene expression. Understanding PRE's structure, function, and mode of action is essential to leverage its potential as a therapeutic target. A wide range of PRE-based reagents and tools have been developed and assessed in preclinical and clinical settings for therapeutic and biotechnology applications. This manuscript aims to provide a systematic review of the characteristics and mechanism of action of PRE, as well as elucidating its current applications in basic and clinical research. Finally, we discuss the promising opportunities that PRE may provide to antiviral development, viral biology, and potentially beyond.
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Affiliation(s)
- Karim Mouzannar
- Liver Diseases Branch, National Institute of Diabetics and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | | | - T. Jake Liang
- Liver Diseases Branch, National Institute of Diabetics and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
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7
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Pérez-Ortín JE, García-Marcelo MJ, Delgado-Román I, Muñoz-Centeno MC, Chávez S. Influence of cell volume on the gene transcription rate. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195008. [PMID: 38246270 DOI: 10.1016/j.bbagrm.2024.195008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Cells vary in volume throughout their life cycle and in many other circumstances, while their genome remains identical. Hence, the RNA production factory must adapt to changing needs, while maintaining the same production lines. This paradox is resolved by different mechanisms in distinct cells and circumstances. RNA polymerases have evolved to cope with the particular circumstances of each case and the different characteristics of the several RNA molecule types, especially their stabilities. Here we review current knowledge on these issues. We focus on the yeast Saccharomyces cerevisiae, where many of the studies have been performed, although we compare and discuss the results obtained in other eukaryotes and propose several ideas and questions to be tested and solved in the future. TAKE AWAY.
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Affiliation(s)
- José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain.
| | - María J García-Marcelo
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain; Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Irene Delgado-Román
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - María C Muñoz-Centeno
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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8
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Zheng Y, Wang M, Yin J, Duan Y, Wu C, Xu Z, Bu Y, Wang J, Chen Q, Zhu G, Zhao K, Zhang L, Hua R, Xu Y, Hu X, Cheng X, Xia Y. Hepatitis B virus RNAs co-opt ELAVL1 for stabilization and CRM1-dependent nuclear export. PLoS Pathog 2024; 20:e1011999. [PMID: 38306394 PMCID: PMC10866535 DOI: 10.1371/journal.ppat.1011999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/14/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
Hepatitis B virus (HBV) chronically infects 296 million people worldwide, posing a major global health threat. Export of HBV RNAs from the nucleus to the cytoplasm is indispensable for viral protein translation and genome replication, however the mechanisms regulating this critical process remain largely elusive. Here, we identify a key host factor embryonic lethal, abnormal vision, Drosophila-like 1 (ELAVL1) that binds HBV RNAs and controls their nuclear export. Using an unbiased quantitative proteomics screen, we demonstrate direct binding of ELAVL1 to the HBV pregenomic RNA (pgRNA). ELAVL1 knockdown inhibits HBV RNAs posttranscriptional regulation and suppresses viral replication. Further mechanistic studies reveal ELAVL1 recruits the nuclear export receptor CRM1 through ANP32A and ANP32B to transport HBV RNAs to the cytoplasm via specific AU-rich elements, which can be targeted by a compound CMLD-2. Moreover, ELAVL1 protects HBV RNAs from DIS3+RRP6+ RNA exosome mediated nuclear RNA degradation. Notably, we find HBV core protein is dispensable for HBV RNA-CRM1 interaction and nuclear export. Our results unveil ELAVL1 as a crucial host factor that regulates HBV RNAs stability and trafficking. By orchestrating viral RNA nuclear export, ELAVL1 is indispensable for the HBV life cycle. Our study highlights a virus-host interaction that may be exploited as a new therapeutic target against chronic hepatitis B.
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Affiliation(s)
- Yingcheng Zheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
- School of Life Sciences, Hubei University, Wuhan, China
| | - Mengfei Wang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Jiatong Yin
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yurong Duan
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Chuanjian Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Zaichao Xu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yanan Bu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Jingjing Wang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Quan Chen
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Guoguo Zhu
- Department of Emergency, General Hospital of Central Theater Command of People’s Liberation Army of China, Wuhan, China
| | - Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Lu Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Rong Hua
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yanping Xu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Xiyu Hu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Xiaoming Cheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, China
- Pingyuan Laboratory, Henan, China
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9
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Zheng J, Lu Y, Lin Y, Si S, Guo B, Zhao X, Cui L. Epitranscriptomic modifications in mesenchymal stem cell differentiation: advances, mechanistic insights, and beyond. Cell Death Differ 2024; 31:9-27. [PMID: 37985811 PMCID: PMC10782030 DOI: 10.1038/s41418-023-01238-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/24/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023] Open
Abstract
RNA modifications, known as the "epitranscriptome", represent a key layer of regulation that influences a wide array of biological processes in mesenchymal stem cells (MSCs). These modifications, catalyzed by specific enzymes, often termed "writers", "readers", and "erasers", can dynamically alter the MSCs' transcriptomic landscape, thereby modulating cell differentiation, proliferation, and responses to environmental cues. These enzymes include members of the classes METTL, IGF2BP, WTAP, YTHD, FTO, NAT, and others. Many of these RNA-modifying agents are active during MSC lineage differentiation. This review provides a comprehensive overview of the current understanding of different RNA modifications in MSCs, their roles in regulating stem cell behavior, and their implications in MSC-based therapies. It delves into how RNA modifications impact MSC biology, the functional significance of individual modifications, and the complex interplay among these modifications. We further discuss how these intricate regulatory mechanisms contribute to the functional diversity of MSCs, and how they might be harnessed for therapeutic applications. The review also highlights current challenges and potential future directions in the study of RNA modifications in MSCs, emphasizing the need for innovative tools to precisely map these modifications and decipher their context-specific effects. Collectively, this work paves the way for a deeper understanding of the role of the epitranscriptome in MSC biology, potentially advancing therapeutic strategies in regenerative medicine and MSC-based therapies.
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Affiliation(s)
- Jiarong Zheng
- Department of Dentistry, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Ye Lu
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Yunfan Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Shanshan Si
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Bing Guo
- Department of Dentistry, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Xinyuan Zhao
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China.
| | - Li Cui
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China.
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, Los Angeles, 90095, CA, USA.
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10
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Torre D, Fstkchyan YS, Ho JSY, Cheon Y, Patel RS, Degrace EJ, Mzoughi S, Schwarz M, Mohammed K, Seo JS, Romero-Bueno R, Demircioglu D, Hasson D, Tang W, Mahajani SU, Campisi L, Zheng S, Song WS, Wang YC, Shah H, Francoeur N, Soto J, Salfati Z, Weirauch MT, Warburton P, Beaumont K, Smith ML, Mulder L, Villalta SA, Kessenbrock K, Jang C, Lee D, De Rubeis S, Cobos I, Tam O, Hammell MG, Seldin M, Shi Y, Basu U, Sebastiano V, Byun M, Sebra R, Rosenberg BR, Benner C, Guccione E, Marazzi I. Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Mol Cell 2023; 83:4255-4271.e9. [PMID: 37995687 PMCID: PMC10842741 DOI: 10.1016/j.molcel.2023.10.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/28/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Endogenous retroviruses (ERVs) are remnants of ancient parasitic infections and comprise sizable portions of most genomes. Although epigenetic mechanisms silence most ERVs by generating a repressive environment that prevents their expression (heterochromatin), little is known about mechanisms silencing ERVs residing in open regions of the genome (euchromatin). This is particularly important during embryonic development, where induction and repression of distinct classes of ERVs occur in short temporal windows. Here, we demonstrate that transcription-associated RNA degradation by the nuclear RNA exosome and Integrator is a regulatory mechanism that controls the productive transcription of most genes and many ERVs involved in preimplantation development. Disrupting nuclear RNA catabolism promotes dedifferentiation to a totipotent-like state characterized by defects in RNAPII elongation and decreased expression of long genes (gene-length asymmetry). Our results indicate that RNA catabolism is a core regulatory module of gene networks that safeguards RNAPII activity, ERV expression, cell identity, and developmental potency.
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Affiliation(s)
- Denis Torre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yesai S Fstkchyan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jessica Sook Yuin Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Youngseo Cheon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea; Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Roosheel S Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emma J Degrace
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Slim Mzoughi
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan Schwarz
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kevin Mohammed
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ji-Seon Seo
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Raquel Romero-Bueno
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Deniz Demircioglu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weijing Tang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sameehan U Mahajani
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura Campisi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Won-Suk Song
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nancy Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan Soto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zelda Salfati
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Peter Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristin Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Lubbertus Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - S Armando Villalta
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, The Mindich Child Health and Development Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Inma Cobos
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oliver Tam
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Marcus Seldin
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Yongsheng Shi
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA; Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Uttiya Basu
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Vittorio Sebastiano
- Institute for Stem Cell Biology and Regenerative Medicine and the Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minji Byun
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chris Benner
- Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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11
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Polák P, Garland W, Rathore O, Schmid M, Salerno-Kochan A, Jakobsen L, Gockert M, Gerlach P, Silla T, Andersen JS, Conti E, Jensen TH. Dual agonistic and antagonistic roles of ZC3H18 provide for co-activation of distinct nuclear RNA decay pathways. Cell Rep 2023; 42:113325. [PMID: 37889751 PMCID: PMC10720265 DOI: 10.1016/j.celrep.2023.113325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/19/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The RNA exosome is a versatile ribonuclease. In the nucleoplasm of mammalian cells, it is assisted by its adaptors the nuclear exosome targeting (NEXT) complex and the poly(A) exosome targeting (PAXT) connection. Via its association with the ARS2 and ZC3H18 proteins, NEXT/exosome is recruited to capped and short unadenylated transcripts. Conversely, PAXT/exosome is considered to target longer and adenylated substrates via their poly(A) tails. Here, mutational analysis of the core PAXT component ZFC3H1 uncovers a separate branch of the PAXT pathway, which targets short adenylated RNAs and relies on a direct ARS2-ZFC3H1 interaction. We further demonstrate that similar acidic-rich short linear motifs of ZFC3H1 and ZC3H18 compete for a common ARS2 epitope. Consequently, while promoting NEXT function, ZC3H18 antagonizes PAXT activity. We suggest that this organization of RNA decay complexes provides co-activation of NEXT and PAXT at loci with abundant production of short exosome substrates.
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Affiliation(s)
- Patrik Polák
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Om Rathore
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Anna Salerno-Kochan
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, Germany
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, Denmark
| | - Maria Gockert
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Piotr Gerlach
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, Germany
| | - Toomas Silla
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, Germany
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark.
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12
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Contreras X, Depierre D, Akkawi C, Srbic M, Helsmoortel M, Nogaret M, LeHars M, Salifou K, Heurteau A, Cuvier O, Kiernan R. PAPγ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs. Nat Commun 2023; 14:6745. [PMID: 37875486 PMCID: PMC10598014 DOI: 10.1038/s41467-023-42620-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/17/2023] [Indexed: 10/26/2023] Open
Abstract
Pervasive transcription of the human genome generates an abundance of RNAs that must be processed and degraded. The nuclear RNA exosome is the main RNA degradation machinery in the nucleus. However, nuclear exosome must be recruited to its substrates by targeting complexes, such as NEXT or PAXT. By proteomic analysis, we identify additional subunits of PAXT, including many orthologs of MTREC found in S. pombe. In particular, we show that polyA polymerase gamma (PAPγ) associates with PAXT. Genome-wide mapping of the binding sites of ZFC3H1, RBM27 and PAPγ shows that PAXT is recruited to the TSS of hundreds of genes. Loss of ZFC3H1 abolishes recruitment of PAXT subunits including PAPγ to TSSs and concomitantly increases the abundance of PROMPTs at the same sites. Moreover, PAPγ, as well as MTR4 and ZFC3H1, is implicated in the polyadenylation of PROMPTs. Our results thus provide key insights into the direct targeting of PROMPT ncRNAs by PAXT at their genomic sites.
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Affiliation(s)
- Xavier Contreras
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - David Depierre
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Charbel Akkawi
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Marina Srbic
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Marion Helsmoortel
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Maguelone Nogaret
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Matthieu LeHars
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Kader Salifou
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Alexandre Heurteau
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Olivier Cuvier
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Rosemary Kiernan
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France.
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13
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Kabzinski J, Kucharska-Lusina A, Majsterek I. RNA-Based Liquid Biopsy in Head and Neck Cancer. Cells 2023; 12:1916. [PMID: 37508579 PMCID: PMC10377854 DOI: 10.3390/cells12141916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Head and neck cancer (HNC) is a prevalent and diverse group of malignancies with substantial morbidity and mortality rates. Early detection and monitoring of HNC are crucial for improving patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, has emerged as a promising tool for cancer detection and monitoring. In this article, we review the application of RNA-based liquid biopsy in HNC. Various types of RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), circular RNA (circRNA) and PIWI-interacting RNA (piRNA), are explored as potential biomarkers in HNC liquid-based diagnostics. The roles of RNAs in HNC diagnosis, metastasis, tumor resistance to radio and chemotherapy, and overall prognosis are discussed. RNA-based liquid biopsy holds great promise for the early detection, prognosis, and personalized treatment of HNC. Further research and validation are necessary to translate these findings into clinical practice and improve patient outcomes.
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Affiliation(s)
- Jacek Kabzinski
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Aleksandra Kucharska-Lusina
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
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14
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Rodríguez‐Molina JB, Turtola M. Birth of a poly(A) tail: mechanisms and control of mRNA polyadenylation. FEBS Open Bio 2023; 13:1140-1153. [PMID: 36416579 PMCID: PMC10315857 DOI: 10.1002/2211-5463.13528] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022] Open
Abstract
During their synthesis in the cell nucleus, most eukaryotic mRNAs undergo a two-step 3'-end processing reaction in which the pre-mRNA is cleaved and released from the transcribing RNA polymerase II and a polyadenosine (poly(A)) tail is added to the newly formed 3'-end. These biochemical reactions might appear simple at first sight (endonucleolytic RNA cleavage and synthesis of a homopolymeric tail), but their catalysis requires a multi-faceted enzymatic machinery, the cleavage and polyadenylation complex (CPAC), which is composed of more than 20 individual protein subunits. The activity of CPAC is further orchestrated by Poly(A) Binding Proteins (PABPs), which decorate the poly(A) tail during its synthesis and guide the mRNA through subsequent gene expression steps. Here, we review the structure, molecular mechanism, and regulation of eukaryotic mRNA 3'-end processing machineries with a focus on the polyadenylation step. We concentrate on the CPAC and PABPs from mammals and the budding yeast, Saccharomyces cerevisiae, because these systems are the best-characterized at present. Comparison of their functions provides valuable insights into the principles of mRNA 3'-end processing.
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Affiliation(s)
| | - Matti Turtola
- Department of Life TechnologiesUniversity of TurkuFinland
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15
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García-Martínez J, Singh A, Medina D, Chávez S, Pérez-Ortín JE. Enhanced gene regulation by cooperation between mRNA decay and gene transcription. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194910. [PMID: 36731791 PMCID: PMC10663100 DOI: 10.1016/j.bbagrm.2023.194910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
It has become increasingly clear in the last few years that gene expression in eukaryotes is not a linear process from mRNA synthesis in the nucleus to translation and degradation in the cytoplasm, but works as a circular one where the mRNA level is controlled by crosstalk between nuclear transcription and cytoplasmic decay pathways. One of the consequences of this crosstalk is the approximately constant level of mRNA. This is called mRNA buffering and happens when transcription and mRNA degradation act at compensatory rates. However, if transcription and mRNA degradation act additively, enhanced gene expression regulation occurs. In this work, we analyzed new and previously published genomic datasets obtained for several yeast mutants related to either transcription or mRNA decay that are not known to play any role in the other process. We show that some, which were presumed only transcription factors (Sfp1) or only decay factors (Puf3, Upf2/3), may represent examples of RNA-binding proteins (RBPs) that make specific crosstalk to enhance the control of the mRNA levels of their target genes by combining additive effects on transcription and mRNA stability. These results were mathematically modeled to see the effects of RBPs when they have positive or negative effects on mRNA synthesis and decay rates. We found that RBPs can be an efficient way to buffer or enhance gene expression responses depending on their respective effects on transcription and mRNA stability.
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Affiliation(s)
- José García-Martínez
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Daniel Medina
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain; Dirección de Evaluación y Acreditación, Agencia Andaluza del Conocimiento, Doña Berenguela s/n, planta 3ª C.P. 14006, Córdoba, Spain
| | - José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain.
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16
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Ohguchi Y, Ohguchi H. DIS3: The Enigmatic Gene in Multiple Myeloma. Int J Mol Sci 2023; 24:ijms24044079. [PMID: 36835493 PMCID: PMC9958658 DOI: 10.3390/ijms24044079] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/01/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Recent studies have revealed the genetic aberrations involved in the initiation and progression of various cancers, including multiple myeloma (MM), via next-generation sequencing analysis. Notably, DIS3 mutations have been identified in approximately 10% of patients with MM. Moreover, deletions of the long arm of chromosome 13, that includes DIS3, are present in approximately 40% of patients with MM. Regardless of the high incidence of DIS3 mutations and deletions, their contribution to the pathogenesis of MM has not yet been determined. Herein, we summarize the molecular and physiological functions of DIS3, focusing on hematopoiesis, and discuss the characteristics and potential roles of DIS3 mutations in MM. Recent findings highlight the essential roles of DIS3 in RNA homeostasis and normal hematopoiesis and suggest that the reduced activity of DIS3 may be involved in myelomagenesis by increasing genome instability.
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Affiliation(s)
- Yasuyo Ohguchi
- Division of Disease Epigenetics, Institute of Resource Development and Analysis, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Hiroto Ohguchi
- Division of Disease Epigenetics, Institute of Resource Development and Analysis, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
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17
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Hughes AL, Szczurek AT, Kelley JR, Lastuvkova A, Turberfield AH, Dimitrova E, Blackledge NP, Klose RJ. A CpG island-encoded mechanism protects genes from premature transcription termination. Nat Commun 2023; 14:726. [PMID: 36759609 PMCID: PMC9911701 DOI: 10.1038/s41467-023-36236-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Transcription must be tightly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, by dissecting the function of the SET1 chromatin-modifying complexes that bind to CpG island-associated gene promoters, we discover that they play a specific and essential role in enabling the expression of low to moderately transcribed genes. Counterintuitively, this effect can occur independently of SET1 complex histone-modifying activity and instead relies on an interaction with the RNA Polymerase II-binding protein WDR82. Unexpectedly, we discover that SET1 complexes enable gene expression by antagonising premature transcription termination by the ZC3H4/WDR82 complex at CpG island-associated genes. In contrast, at extragenic sites of transcription, which typically lack CpG islands and SET1 complex occupancy, we show that the activity of ZC3H4/WDR82 is unopposed. Therefore, we reveal a gene regulatory mechanism whereby CpG islands are bound by a protein complex that specifically protects genic transcripts from premature termination, effectively distinguishing genic from extragenic transcription and enabling normal gene expression.
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Affiliation(s)
- Amy L Hughes
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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18
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Temporal-iCLIP captures co-transcriptional RNA-protein interactions. Nat Commun 2023; 14:696. [PMID: 36755023 PMCID: PMC9908952 DOI: 10.1038/s41467-023-36345-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 01/27/2023] [Indexed: 02/10/2023] Open
Abstract
Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding of this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking of RNA-protein complexes at serial timepoints. We apply tiCLIP to the RNA export adaptor, ALYREF; a component of the Nuclear Exosome Targeting (NEXT) complex, RBM7; and the nuclear cap binding complex (CBC). Regardless of function, all tested factors interact with nascent RNA as it exits RNAPII. Moreover, we demonstrate that the two transesterification steps of pre-mRNA splicing temporally separate ALYREF and RBM7 binding to splicing intermediates, and that exon-exon junction density drives RNA 5'end binding of ALYREF. Finally, we identify underappreciated steps in snoRNA 3'end processing performed by RBM7. Altogether, our data provide a temporal view of RNA-protein interactions during the early phases of transcription.
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19
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Revy P, Kannengiesser C, Bertuch AA. Genetics of human telomere biology disorders. Nat Rev Genet 2023; 24:86-108. [PMID: 36151328 DOI: 10.1038/s41576-022-00527-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2022] [Indexed: 01/24/2023]
Abstract
Telomeres are specialized nucleoprotein structures at the ends of linear chromosomes that prevent the activation of DNA damage response and repair pathways. Numerous factors localize at telomeres to regulate their length, structure and function, to avert replicative senescence or genome instability and cell death. In humans, Mendelian defects in several of these factors can result in abnormally short or dysfunctional telomeres, causing a group of rare heterogeneous premature-ageing diseases, termed telomeropathies, short-telomere syndromes or telomere biology disorders (TBDs). Here, we review the TBD-causing genes identified so far and describe their main functions associated with telomere biology. We present molecular aspects of TBDs, including genetic anticipation, phenocopy, incomplete penetrance and somatic genetic rescue, which underlie the complexity of these diseases. We also discuss the implications of phenotypic and genetic features of TBDs on fundamental aspects related to human telomere biology, ageing and cancer, as well as on diagnostic, therapeutic and clinical approaches.
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Affiliation(s)
- Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Nationale contre le Cancer, Paris, France.
- Université Paris Cité, Imagine Institute, Paris, France.
| | - Caroline Kannengiesser
- APHP Service de Génétique, Hôpital Bichat, Paris, France
- Inserm U1152, Université Paris Cité, Paris, France
| | - Alison A Bertuch
- Departments of Paediatrics and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
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20
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Alles J, Legnini I, Pacelli M, Rajewsky N. Rapid nuclear deadenylation of mammalian messenger RNA. iScience 2022; 26:105878. [PMID: 36691625 PMCID: PMC9860345 DOI: 10.1016/j.isci.2022.105878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/13/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Poly(A) tails protect RNAs from degradation and their deadenylation rates determine RNA stability. Although poly(A) tails are generated in the nucleus, deadenylation of tails has mostly been investigated within the cytoplasm. Here, we combined long-read sequencing with metabolic labeling, splicing inhibition and cell fractionation experiments to quantify, separately, the genesis and trimming of nuclear and cytoplasmic tails in vitro and in vivo. We present evidence for genome-wide, nuclear synthesis of tails longer than 200 nt, which are rapidly shortened after transcription. Our data suggests that rapid deadenylation is a nuclear process, and that different classes of transcripts and even transcript isoforms have distinct nuclear tail lengths. For example, many long-noncoding RNAs retain long poly(A) tails. Modeling deadenylation dynamics predicts nuclear deadenylation about 10 times faster than cytoplasmic deadenylation. In summary, our data suggests that nuclear deadenylation might be a key mechanism for regulating mRNA stability, abundance, and subcellular localization.
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Affiliation(s)
- Jonathan Alles
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany,Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099 Berlin, Germany
| | - Ivano Legnini
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Maddalena Pacelli
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany,Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099 Berlin, Germany,Corresponding author
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21
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Gorin G, Vastola JJ, Fang M, Pachter L. Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments. Nat Commun 2022; 13:7620. [PMID: 36494337 PMCID: PMC9734650 DOI: 10.1038/s41467-022-34857-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022] Open
Abstract
The question of how cell-to-cell differences in transcription rate affect RNA count distributions is fundamental for understanding biological processes underlying transcription. Answering this question requires quantitative models that are both interpretable (describing concrete biophysical phenomena) and tractable (amenable to mathematical analysis). This enables the identification of experiments which best discriminate between competing hypotheses. As a proof of principle, we introduce a simple but flexible class of models involving a continuous stochastic transcription rate driving a discrete RNA transcription and splicing process, and compare and contrast two biologically plausible hypotheses about transcription rate variation. One assumes variation is due to DNA experiencing mechanical strain, while the other assumes it is due to regulator number fluctuations. We introduce a framework for numerically and analytically studying such models, and apply Bayesian model selection to identify candidate genes that show signatures of each model in single-cell transcriptomic data from mouse glutamatergic neurons.
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Affiliation(s)
- Gennady Gorin
- grid.20861.3d0000000107068890Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - John J. Vastola
- grid.38142.3c000000041936754XDepartment of Neurobiology, Harvard Medical School, Boston, MA 02115 USA
| | - Meichen Fang
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Lior Pachter
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA ,grid.20861.3d0000000107068890Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125 USA
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22
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Gómez-Liñán C, Gómez-Díaz E, Ceballos-Pérez G, Fernández-Moya S, Estévez AM. The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes. Nucleic Acids Res 2022; 50:12251-12265. [PMID: 36454008 PMCID: PMC9757043 DOI: 10.1093/nar/gkac1123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022] Open
Abstract
In-depth analysis of the transcriptomes of several model organisms has revealed that genomes are pervasively transcribed, giving rise to an abundance of non-canonical and mainly antisense RNA polymerase II-derived transcripts that are produced from almost any genomic context. Pervasive RNAs are degraded by surveillance mechanisms, but the repertoire of proteins that control the fate of these non-productive transcripts is still incomplete. Trypanosomes are single-celled eukaryotes that show constitutive RNA polymerase II transcription and in which initiation and termination of transcription occur at a limited number of sites per chromosome. It is not known whether pervasive transcription exists in organisms with unregulated RNA polymerase II activity, and which factors could be involved in the process. We show here that depletion of RBP33 results in overexpression of ∼40% of all annotated genes in the genome, with a marked accumulation of sense and antisense transcripts derived from silenced regions. RBP33 loss does not result in a significant increase in chromatin accessibility. Finally, we have found that transcripts that increase in abundance upon RBP33 knockdown are significantly more stable in RBP33-depleted trypanosomes, and that the exosome complex is responsible for their degradation. Our results provide strong evidence that RBP33 dampens non-productive transcription in trypanosomes.
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Affiliation(s)
- Claudia Gómez-Liñán
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Gloria Ceballos-Pérez
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Sandra M Fernández-Moya
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Antonio M Estévez
- To whom correspondence should be addressed. Tel: +34 958 181652; Fax: +34 958 181632;
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23
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Ponting CP, Haerty W. Genome-Wide Analysis of Human Long Noncoding RNAs: A Provocative Review. Annu Rev Genomics Hum Genet 2022; 23:153-172. [PMID: 35395170 DOI: 10.1146/annurev-genom-112921-123710] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Do long noncoding RNAs (lncRNAs) contribute little or substantively to human biology? To address how lncRNA loci and their transcripts, structures, interactions, and functions contribute to human traits and disease, we adopt a genome-wide perspective. We intend to provoke alternative interpretation of questionable evidence and thorough inquiry into unsubstantiated claims. We discuss pitfalls of lncRNA experimental and computational methods as well as opposing interpretations of their results. The majority of evidence, we argue, indicates that most lncRNA transcript models reflect transcriptional noise or provide minor regulatory roles, leaving relatively few human lncRNAs that contribute centrally to human development, physiology, or behavior. These important few tend to be spliced and better conserved but lack a simple syntax relating sequence to structure and mechanism, and so resist simple categorization. This genome-wide view should help investigators prioritize individual lncRNAs based on their likely contribution to human biology.
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Affiliation(s)
- Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom;
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24
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Post-Transcriptional Control of mRNA Metabolism and Protein Secretion: The Third Level of Regulation within the NF-κB System. Biomedicines 2022; 10:biomedicines10092108. [PMID: 36140209 PMCID: PMC9495616 DOI: 10.3390/biomedicines10092108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
The NF-κB system is a key transcriptional pathway that regulates innate and adaptive immunity because it triggers the activation and differentiation processes of lymphocytes and myeloid cells during immune responses. In most instances, binding to cytoplasmic inhibitory IκB proteins sequesters NF-κB into an inactive state, while a plethora of external triggers activate three complex signaling cascades that mediate the release and nuclear translocation of the NF-κB DNA-binding subunits. In addition to these cytosolic steps (level 1 of NF-κB regulation), NF-κB activity is also controlled in the nucleus by signaling events, cofactors and the chromatin environment to precisely determine chromatin recruitment and the specificity and timing of target gene transcription (level 2 of NF-κB regulation). Here, we discuss an additional layer of the NF-κB system that manifests in various steps of post-transcriptional gene expression and protein secretion. This less-studied regulatory level allows reduction of (transcriptional) noise and signal integration and endows time-shifted control of the secretion of inflammatory mediators. Detailed knowledge of these steps is important, as dysregulated post-transcriptional NF-κB signaling circuits are likely to foster chronic inflammation and contribute to the formation and maintenance of a tumor-promoting microenvironment.
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25
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Foucher AE, Touat-Todeschini L, Juarez-Martinez AB, Rakitch A, Laroussi H, Karczewski C, Acajjaoui S, Soler-López M, Cusack S, Mackereth CD, Verdel A, Kadlec J. Structural analysis of Red1 as a conserved scaffold of the RNA-targeting MTREC/PAXT complex. Nat Commun 2022; 13:4969. [PMID: 36002457 PMCID: PMC9402713 DOI: 10.1038/s41467-022-32542-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/04/2022] [Indexed: 11/09/2022] Open
Abstract
To eliminate specific or aberrant transcripts, eukaryotes use nuclear RNA-targeting complexes that deliver them to the exosome for degradation. S. pombe MTREC, and its human counterpart PAXT, are key players in this mechanism but inner workings of these complexes are not understood in sufficient detail. Here, we present an NMR structure of an MTREC scaffold protein Red1 helix-turn-helix domain bound to the Iss10 N-terminus and show this interaction is required for proper cellular growth and meiotic mRNA degradation. We also report a crystal structure of a Red1-Ars2 complex explaining mutually exclusive interactions of hARS2 with various ED/EGEI/L motif-possessing RNA regulators, including hZFC3H1 of PAXT, hFLASH or hNCBP3. Finally, we show that both Red1 and hZFC3H1 homo-dimerize via their coiled-coil regions indicating that MTREC and PAXT likely function as dimers. Our results, combining structures of three Red1 interfaces with in vivo studies, provide mechanistic insights into conserved features of MTREC/PAXT architecture.
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Affiliation(s)
| | - Leila Touat-Todeschini
- Institut for Advanced Biosciences, UMR Inserm U1209/CNRS 5309/University Grenoble Alpes, La Tronche, France
| | | | - Auriane Rakitch
- Institut for Advanced Biosciences, UMR Inserm U1209/CNRS 5309/University Grenoble Alpes, La Tronche, France
| | - Hamida Laroussi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Claire Karczewski
- Institut for Advanced Biosciences, UMR Inserm U1209/CNRS 5309/University Grenoble Alpes, La Tronche, France
| | - Samira Acajjaoui
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), CS 40220, 38043, Grenoble, France
| | - Montserrat Soler-López
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), CS 40220, 38043, Grenoble, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9, 38042, France
| | - Cameron D Mackereth
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Institut Européen de Chimie et Biologie, 33607, Pessac, France.
| | - André Verdel
- Institut for Advanced Biosciences, UMR Inserm U1209/CNRS 5309/University Grenoble Alpes, La Tronche, France.
| | - Jan Kadlec
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.
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26
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Jia R, Lin J, You J, Li S, Shan G, Huang C. The DEAD-box helicase Hlc regulates basal transcription and chromatin opening of stress-responsive genes. Nucleic Acids Res 2022; 50:9175-9189. [PMID: 35950495 PMCID: PMC9458421 DOI: 10.1093/nar/gkac684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/17/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
Stress-responsive genes are lowly transcribed under normal conditions and robustly induced in response to stress. The significant difference between basal and induced transcription indicates that the general transcriptional machinery requires a mechanism to distinguish each transcription state. However, what factors specifically function in basal transcription remains poorly understood. Using a classic model stress-responsive gene (Drosophila MtnA), we found that knockdown of the DEAD-box helicase Hlc resulted in a significant transcription attenuation of MtnA under normal, but not stressed, conditions. Mechanistically, Hlc directly binds to the MtnA locus to maintain the accessibility of chromatin near the transcriptional start site, which allows the recruitment of RNA polymerase II and subsequent MtnA transcription. Using RNA-seq, we then identified plenty of additional stress-responsive genes whose basal transcription was reduced upon knockdown of Hlc. Taken together, these data suggest that Hlc-mediated basal transcription regulation is an essential and widespread mechanism for precise control of stress-responsive genes.
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Affiliation(s)
| | | | | | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- To whom correspondence should be addressed. Tel: +86 19956025374;
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27
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Wu M, Schmid M, Jensen T, Sandelin A. Computational identification of signals predictive for nuclear RNA exosome degradation pathway targeting. NAR Genom Bioinform 2022; 4:lqac071. [PMID: 36128426 PMCID: PMC9477074 DOI: 10.1093/nargab/lqac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 08/05/2022] [Accepted: 09/01/2022] [Indexed: 11/15/2022] Open
Abstract
The RNA exosome degrades transcripts in the nucleoplasm of mammalian cells. Its substrate specificity is mediated by two adaptors: the ‘nuclear exosome targeting (NEXT)’ complex and the ‘poly(A) exosome targeting (PAXT)’ connection. Previous studies have revealed some DNA/RNA elements that differ between the two pathways, but how informative these features are for distinguishing pathway targeting, or whether additional genomic features that are informative for such classifications exist, is unknown. Here, we leverage the wealth of available genomic data and develop machine learning models that predict exosome targets and subsequently rank the features the models use by their predictive power. As expected, features around transcript end sites were most predictive; specifically, the lack of canonical 3′ end processing was highly predictive of NEXT targets. Other associated features, such as promoter-proximal G/C content and 5′ splice sites, were informative, but only for distinguishing NEXT and not PAXT targets. Finally, we discovered predictive features not previously associated with exosome targeting, in particular RNA helicase DDX3X binding sites. Overall, our results demonstrate that nucleoplasmic exosome targeting is to a large degree predictable, and our approach can assess the predictive power of previously known and new features in an unbiased way.
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Affiliation(s)
- Mengjun Wu
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen , Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , 171 65 Solna , Sweden
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University , Universitetsbyen 81, Aarhus , DK-8000, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University , Universitetsbyen 81, Aarhus , DK-8000, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen , Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
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28
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Vahlensieck C, Thiel CS, Pöschl D, Bradley T, Krammer S, Lauber B, Polzer J, Ullrich O. Post-Transcriptional Dynamics is Involved in Rapid Adaptation to Hypergravity in Jurkat T Cells. Front Cell Dev Biol 2022; 10:933984. [PMID: 35859900 PMCID: PMC9289288 DOI: 10.3389/fcell.2022.933984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 06/10/2022] [Indexed: 12/12/2022] Open
Abstract
The transcriptome of human immune cells rapidly reacts to altered gravity in a highly dynamic way. We could show in previous experiments that transcriptional patterns show profound adaption after seconds to minutes of altered gravity. To gain further insight into these transcriptional alteration and adaption dynamics, we conducted a highly standardized RNA-Seq experiment with human Jurkat T cells exposed to 9xg hypergravity for 3 and 15 min, respectively. We investigated the frequency with which individual exons were used during transcription and discovered that differential exon usage broadly appeared after 3 min and became less pronounced after 15 min. Additionally, we observed a shift in the transcript pool from coding towards non-coding transcripts. Thus, adaption of gravity-sensitive differentially expressed genes followed a dynamic transcriptional rebound effect. The general dynamics were compatible with previous studies on the transcriptional effects of short hypergravity on human immune cells and suggest that initial up-regulatory changes mostly result from increased elongation rates. The shift correlated with a general downregulation of the affected genes. All chromosome bands carried homogenous numbers of gravity-sensitive genes but showed a specific tendency towards up- or downregulation. Altered gravity affected transcriptional regulation throughout the entire genome, whereby the direction of differential expression was strongly dependent on the structural location in the genome. A correlation analysis with potential mediators of the early transcriptional response identified a link between initially upregulated genes with certain transcription factors. Based on these findings, we have been able to further develop our model of the transcriptional response to altered gravity.
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Affiliation(s)
- Christian Vahlensieck
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Dübendorf, Switzerland
| | - Cora S. Thiel
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Dübendorf, Switzerland
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center (KSC), Merritt Island, FL, United States
- Space Biotechnology, Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- *Correspondence: Cora S. Thiel, ; Oliver Ullrich,
| | - Daniel Pöschl
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Timothy Bradley
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Sonja Krammer
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Dübendorf, Switzerland
| | - Beatrice Lauber
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Jennifer Polzer
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Oliver Ullrich
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Dübendorf, Switzerland
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center (KSC), Merritt Island, FL, United States
- Space Biotechnology, Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Space Medicine, Ernst-Abbe-Hochschule (EAH) Jena, Department of Industrial Engineering, Jena, Germany
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
- *Correspondence: Cora S. Thiel, ; Oliver Ullrich,
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29
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Pérez-Ortín JE, Chávez S. Nucleo-cytoplasmic shuttling of RNA-binding factors: mRNA buffering and beyond. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194849. [PMID: 35907432 DOI: 10.1016/j.bbagrm.2022.194849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/18/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Gene expression is a highly regulated process that adapts RNAs and proteins content to the cellular context. Under steady-state conditions, mRNA homeostasis is robustly maintained by tight controls that act on both nuclear transcription and cytoplasmic mRNA stability. In recent years, it has been revealed that several RNA-binding proteins (RBPs) that perform functions in mRNA decay can move to the nucleus and regulate transcription. The RBPs involved in transcription can also travel to the cytoplasm and regulate mRNA degradation and/or translation. The multifaceted functions of these shuttling nucleo-cytoplasm RBPs have raised the possibility that they can act as mRNA metabolism coordinators. In addition, this indicates the existence of crosstalk mechanisms between the enzymatic machineries that drive the different mRNA life-cycle phases. The buffering of the mRNA concentration is the best known consequence of a transcription-degradation crosstalk counteraction, but alternative ways of RBP action can also imply enhanced gene regulation.
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Affiliation(s)
- José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València. C/Dr. Moliner 50, E46100 Burjassot, Spain.
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain; Dirección de Evaluación y Acreditación, Agencia Andaluza del Conocimiento, Doña Berenguela s/n, planta 3ª C.P., 14006 Córdoba, Spain
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30
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Chappleboim A, Joseph-Strauss D, Gershon O, Friedman N. Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown. Nucleic Acids Res 2022; 50:5864-5880. [PMID: 35640599 PMCID: PMC9177992 DOI: 10.1093/nar/gkac411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 01/02/2023] Open
Abstract
In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells' total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1-the main 5'-3' mRNA exonuclease-which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5'-3' degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5'-3' exonucleolytic pathway rather than its outputs.
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Affiliation(s)
- Alon Chappleboim
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daphna Joseph-Strauss
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Omer Gershon
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Friedman
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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31
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Berry S, Müller M, Rai A, Pelkmans L. Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells. Cell Syst 2022; 13:454-470.e15. [PMID: 35613616 DOI: 10.1016/j.cels.2022.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/13/2021] [Accepted: 04/21/2022] [Indexed: 12/18/2022]
Abstract
RNA concentration homeostasis involves coordinating RNA abundance and synthesis rates with cell size. Here, we study this in human cells by combining genome-wide perturbations with quantitative single-cell measurements. Despite relative ease in perturbing RNA synthesis, we find that RNA concentrations generally remain highly constant. Perturbations that would be expected to increase nuclear mRNA levels, including those targeting nuclear mRNA degradation or export, result in downregulation of RNA synthesis. This is associated with reduced abundance of transcription-associated proteins and protein states that are normally coordinated with RNA production in single cells, including RNA polymerase II (RNA Pol II) itself. Acute perturbations, elevation of nuclear mRNA levels, and mathematical modeling indicate that mammalian cells achieve robust mRNA concentration homeostasis by the mRNA-based negative feedback on transcriptional activity in the nucleus. This ultimately acts to coordinate RNA Pol II abundance with nuclear mRNA degradation and export rates and may underpin the scaling of mRNA abundance with cell size.
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Affiliation(s)
- Scott Berry
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.
| | - Micha Müller
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Arpan Rai
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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32
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Gerlach P, Garland W, Lingaraju M, Salerno-Kochan A, Bonneau F, Basquin J, Jensen TH, Conti E. Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome. Mol Cell 2022; 82:2505-2518.e7. [PMID: 35688157 PMCID: PMC9278407 DOI: 10.1016/j.molcel.2022.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/07/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting (NEXT) complex plays a central role in directing non-functional transcripts to exosome-mediated degradation, but the structural and molecular mechanisms remain enigmatic. Here, we elucidated the architecture of the human NEXT complex, showing that it exists as a dimer of MTR4-ZCCHC8-RBM7 heterotrimers. Dimerization preconfigures the major MTR4-binding region of ZCCHC8 and arranges the two MTR4 helicases opposite to each other, with each protomer able to function on many types of RNAs. In the inactive state of the complex, the 3′ end of an RNA substrate is enclosed in the MTR4 helicase channel by a ZCCHC8 C-terminal gatekeeping domain. The architecture of a NEXT-exosome assembly points to the molecular and regulatory mechanisms with which the NEXT complex guides RNA substrates to the exosome. NEXT homodimerizes through two intertwined ZCCHC8 subunits ZCCHC8 binds MTR4 with both constitutive and regulatory interactions Stable MTR4 arch interactions orient the two helicases in opposite directions Regulatory interactions at the MTR4 helicase domain guide RNA to the exosome
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Affiliation(s)
- Piotr Gerlach
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany.
| | - William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mahesh Lingaraju
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Anna Salerno-Kochan
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany.
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33
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Hemagirri M, Sasidharan S. Biology of aging: Oxidative stress and RNA oxidation. Mol Biol Rep 2022; 49:5089-5105. [PMID: 35449319 DOI: 10.1007/s11033-022-07219-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 01/10/2023]
Abstract
The prevalence of aged people has increased rapidly in recent years and brings profound demographic changes worldwide. The multi-level progression of aging occurs at diverse stages of complexity, from cell to organ systems and eventually to the human as a whole. The cellular and molecular damages are usually regulated by the cells; repair or degrade mechanisms. However, these mechanisms are not entirely functional; their effectiveness decreases with age due to influence from endogenous sources like oxidative stress, which all contribute to the aging process. The hunt for novel strategies to increase the man's longevity since ancient times needs better understandings of the biology of aging, oxidative stress, and their roles in RNA oxidation. The critical goal in developing new strategies to increase the man's longevity is to compile the novel developed knowledge on human aging into a single picture, preferably able to understand the biology of aging and the contributing factors. This review discusses the biology of aging, oxidative stress, and their roles in RNA oxidation, leading to aging in humans.
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Affiliation(s)
- Manisekaran Hemagirri
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Sreenivasan Sasidharan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia.
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34
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Vijayakumar A, Park A, Steitz JA. Modulation of mRNA 3'-End Processing and Transcription Termination in Virus-Infected Cells. Front Immunol 2022; 13:828665. [PMID: 35222412 PMCID: PMC8866245 DOI: 10.3389/fimmu.2022.828665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/24/2022] [Indexed: 11/21/2022] Open
Abstract
Eukaryotic mRNA 3´-end processing is a multi-step process beginning with pre-mRNA transcript cleavage followed by poly(A) tail addition. Closely coupled to transcription termination, 3´-end processing is a critical step in the regulation of gene expression, and disruption of 3´-end processing is known to affect mature mRNA levels. Various viral proteins interfere with the 3´-end processing machinery, causing read-through transcription and altered levels of mature transcripts through inhibition of cleavage and polyadenylation. Thus, disruption of 3´-end processing contributes to widespread host shutoff, including suppression of the antiviral response. Additionally, observed features of read-through transcripts such as decreased polyadenylation, nuclear retention, and decreased translation suggest that viruses may utilize these mechanisms to modulate host protein production and dominate cellular machinery. The degree to which the effects of read-through transcript production are harnessed by viruses and host cells remains unclear, but existing research highlights the importance of host 3´-end processing modulation during viral infection.
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Affiliation(s)
- Aarthi Vijayakumar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Annsea Park
- Department of Immunobiology, Yale University, New Haven, CT, United States
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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35
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Vidya E, Duchaine TF. Eukaryotic mRNA Decapping Activation. Front Genet 2022; 13:832547. [PMID: 35401681 PMCID: PMC8984151 DOI: 10.3389/fgene.2022.832547] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
The 5′-terminal cap is a fundamental determinant of eukaryotic gene expression which facilitates cap-dependent translation and protects mRNAs from exonucleolytic degradation. Enzyme-directed hydrolysis of the cap (decapping) decisively affects mRNA expression and turnover, and is a heavily regulated event. Following the identification of the decapping holoenzyme (Dcp1/2) over two decades ago, numerous studies revealed the complexity of decapping regulation across species and cell types. A conserved set of Dcp1/2-associated proteins, implicated in decapping activation and molecular scaffolding, were identified through genetic and molecular interaction studies, and yet their exact mechanisms of action are only emerging. In this review, we discuss the prevailing models on the roles and assembly of decapping co-factors, with considerations of conservation across species and comparison across physiological contexts. We next discuss the functional convergences of decapping machineries with other RNA-protein complexes in cytoplasmic P bodies and compare current views on their impact on mRNA stability and translation. Lastly, we review the current models of decapping activation and highlight important gaps in our current understanding.
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Affiliation(s)
- Elva Vidya
- Goodman Cancer Institute, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Thomas F. Duchaine
- Goodman Cancer Institute, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- *Correspondence: Thomas F. Duchaine,
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36
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Garland W, Müller I, Wu M, Schmid M, Imamura K, Rib L, Sandelin A, Helin K, Jensen TH. Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression. Mol Cell 2022; 82:1691-1707.e8. [PMID: 35349793 PMCID: PMC9433625 DOI: 10.1016/j.molcel.2022.03.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) are widespread genetic parasites known to be kept under tight transcriptional control. Here, we describe a functional connection between the mouse-orthologous “nuclear exosome targeting” (NEXT) and “human silencing hub” (HUSH) complexes, involved in nuclear RNA decay and the epigenetic silencing of TEs, respectively. Knocking out the NEXT component ZCCHC8 in embryonic stem cells results in elevated TE RNA levels. We identify a physical interaction between ZCCHC8 and the MPP8 protein of HUSH and establish that HUSH recruits NEXT to chromatin at MPP8-bound TE loci. However, while NEXT and HUSH both dampen TE RNA expression, their activities predominantly affect shorter non-polyadenylated and full-length polyadenylated transcripts, respectively. Indeed, our data suggest that the repressive action of HUSH promotes a condition favoring NEXT RNA decay activity. In this way, transcriptional and post-transcriptional machineries synergize to suppress the genotoxic potential of TE RNAs. Garland et al. report a physical and functional connection between the NEXT complex, involved in RNA decay, and the HUSH complex, involved in chromatin regulation. Together, NEXT and HUSH cooperate to control transposable element (TE) RNA expression in embryonic stem cells, suppressing pA− and pA+ transcripts, respectively.
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Affiliation(s)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iris Müller
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mengjun Wu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Leonor Rib
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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37
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Liu X, Guo Z, Han J, Peng B, Zhang B, Li H, Hu X, David CJ, Chen M. The PAF1 complex promotes 3' processing of pervasive transcripts. Cell Rep 2022; 38:110519. [PMID: 35294889 DOI: 10.1016/j.celrep.2022.110519] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/06/2022] [Accepted: 02/18/2022] [Indexed: 11/03/2022] Open
Abstract
The PAF1 complex (PAF1C) functions in multiple transcriptional processes involving RNA polymerase II (RNA Pol II). Enhancer RNAs (eRNAs) and promoter upstream transcripts (PROMPTs) are pervasive transcripts transcribed by RNA Pol II and degraded rapidly by the nuclear exosome complex after 3' endonucleolytic cleavage by the Integrator complex (Integrator). Here we show that PAF1C has a role in termination of eRNAs and PROMPTs that are cleaved 1-3 kb downstream of the transcription start site. Mechanistically, PAF1C facilitates recruitment of Integrator to sites of pervasive transcript cleavage, promoting timely cleavage and transcription termination. We also show that PAF1C recruits Integrator to coding genes, where PAF1C then dissociates from Integrator upon entry into processive elongation. Our results demonstrate a function of PAF1C in limiting the length and accumulation of pervasive transcripts that result from non-productive transcription.
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Affiliation(s)
- Xinhong Liu
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Ziwei Guo
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Jing Han
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Bo Peng
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Bin Zhang
- Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China; Institute for Immunology, Tsinghua University School of Medicine, Beijing 100084, China
| | - Haitao Li
- Tsinghua University School of Medicine, Beijing 100084, China; Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China; MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Xiaoyu Hu
- Tsinghua University School of Medicine, Beijing 100084, China; Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China; Institute for Immunology, Tsinghua University School of Medicine, Beijing 100084, China
| | - Charles J David
- Tsinghua University School of Medicine, Beijing 100084, China; Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China
| | - Mo Chen
- Tsinghua University School of Medicine, Beijing 100084, China.
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38
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Lange H, Gagliardi D. Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes. THE PLANT CELL 2022; 34:967-988. [PMID: 34954803 PMCID: PMC8894942 DOI: 10.1093/plcell/koab310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/16/2021] [Indexed: 05/08/2023]
Abstract
RNA exosome complexes provide the main 3'-5'-exoribonuclease activities in eukaryotic cells and contribute to the maturation and degradation of virtually all types of RNA. RNA exosomes consist of a conserved core complex that associates with exoribonucleases and with multimeric cofactors that recruit the enzyme to its RNA targets. Despite an overall high level of structural and functional conservation, the enzymatic activities and compositions of exosome complexes and their cofactor modules differ among eukaryotes. This review highlights unique features of plant exosome complexes, such as the phosphorolytic activity of the core complex, and discusses the exosome cofactors that operate in plants and are dedicated to the maturation of ribosomal RNA, the elimination of spurious, misprocessed, and superfluous transcripts, or the removal of mRNAs cleaved by the RNA-induced silencing complex and other mRNAs prone to undergo silencing.
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Affiliation(s)
- Heike Lange
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
- Author for correspondence:
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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39
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Gockert M, Schmid M, Jakobsen L, Jens M, Andersen JS, Jensen TH. Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation. Nucleic Acids Res 2022; 50:1583-1600. [PMID: 35048984 PMCID: PMC8860595 DOI: 10.1093/nar/gkac001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/13/2021] [Accepted: 01/05/2022] [Indexed: 12/15/2022] Open
Abstract
Turnover of nucleoplasmic transcripts by the mammalian multi-subunit RNA exosome is mediated by two adaptors: the Nuclear EXosome Targeting (NEXT) complex and the Poly(A) tail eXosome Targeting (PAXT) connection. Functional analyses of NEXT and PAXT have largely utilized long-term factor depletion strategies, facilitating the appearance of indirect phenotypes. Here, we rapidly deplete NEXT, PAXT and core exosome components, uncovering the direct consequences of their acute losses. Generally, proteome changes are sparse and largely dominated by co-depletion of other exosome and adaptor subunits, reflecting possible subcomplex compositions. While parallel high-resolution 3′ end sequencing of newly synthesized RNA confirms previously established factor specificities, it concomitantly demonstrates an inflation of long-term depletion datasets by secondary effects. Most strikingly, a general intron degradation phenotype, observed in long-term NEXT depletion samples, is undetectable upon short-term depletion, which instead emphasizes NEXT targeting of snoRNA-hosting introns. Further analysis of these introns uncovers an unusual mode of core exosome-independent RNA decay. Our study highlights the accumulation of RNAs as an indirect result of long-term decay factor depletion, which we speculate is, at least partly, due to the exhaustion of alternative RNA decay pathways.
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Affiliation(s)
- Maria Gockert
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Marvin Jens
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, 68-271A, Cambridge, MA 02139-4307, USA
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
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40
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Taniue K, Tanu T, Shimoura Y, Mitsutomi S, Han H, Kakisaka R, Ono Y, Tamamura N, Takahashi K, Wada Y, Mizukami Y, Akimitsu N. RNA Exosome Component EXOSC4 Amplified in Multiple Cancer Types Is Required for the Cancer Cell Survival. Int J Mol Sci 2022; 23:496. [PMID: 35008922 PMCID: PMC8745236 DOI: 10.3390/ijms23010496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 12/04/2022] Open
Abstract
The RNA exosome is a multi-subunit ribonuclease complex that is evolutionally conserved and the major cellular machinery for the surveillance, processing, degradation, and turnover of diverse RNAs essential for cell viability. Here we performed integrated genomic and clinicopathological analyses of 27 RNA exosome components across 32 tumor types using The Cancer Genome Atlas PanCancer Atlas Studies' datasets. We discovered that the EXOSC4 gene, which encodes a barrel component of the RNA exosome, was amplified across multiple cancer types. We further found that EXOSC4 alteration is associated with a poor prognosis of pancreatic cancer patients. Moreover, we demonstrated that EXOSC4 is required for the survival of pancreatic cancer cells. EXOSC4 also repressed BIK expression and destabilized SESN2 mRNA by promoting its degradation. Furthermore, knockdown of BIK and SESN2 could partially rescue pancreatic cells from the reduction in cell viability caused by EXOSC4 knockdown. Our study provides evidence for EXOSC4-mediated regulation of BIK and SESN2 mRNA in the survival of pancreatic tumor cells.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Tanzina Tanu
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Yuki Shimoura
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Shuhei Mitsutomi
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Han Han
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Rika Kakisaka
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo 065-0033, Japan; (R.K.); (Y.O.)
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo 065-0033, Japan; (R.K.); (Y.O.)
| | - Nobue Tamamura
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Kenji Takahashi
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Yusuke Mizukami
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
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41
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Ogami K, Suzuki HI. Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function. Int J Mol Sci 2021; 22:13401. [PMID: 34948199 PMCID: PMC8707817 DOI: 10.3390/ijms222413401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023] Open
Abstract
The genome is pervasively transcribed across various species, yielding numerous non-coding RNAs. As a counterbalance for pervasive transcription, various organisms have a nuclear RNA exosome complex, whose structure is well conserved between yeast and mammalian cells. The RNA exosome not only regulates the processing of stable RNA species, such as rRNAs, tRNAs, small nucleolar RNAs, and small nuclear RNAs, but also plays a central role in RNA surveillance by degrading many unstable RNAs and misprocessed pre-mRNAs. In addition, associated cofactors of RNA exosome direct the exosome to distinct classes of RNA substrates, suggesting divergent and/or multi-layer control of RNA quality in the cell. While the RNA exosome is essential for cell viability and influences various cellular processes, mutations and alterations in the RNA exosome components are linked to the collection of rare diseases and various diseases including cancer, respectively. The present review summarizes the relationships between pervasive transcription and RNA exosome, including evolutionary crosstalk, mechanisms of RNA exosome-mediated RNA surveillance, and physiopathological effects of perturbation of RNA exosome.
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Affiliation(s)
- Koichi Ogami
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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42
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Chitrakar A, Solorio-Kirpichyan K, Prangley E, Rath S, Du J, Korennykh A. Introns encode dsRNAs undetected by RIG-I/MDA5/interferons and sensed via RNase L. Proc Natl Acad Sci U S A 2021; 118:e2102134118. [PMID: 34772806 PMCID: PMC8609619 DOI: 10.1073/pnas.2102134118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2021] [Indexed: 12/24/2022] Open
Abstract
Double-stranded RNA (dsRNA), a hallmark viral material that activates antiviral interferon (IFN) responses, can appear in human cells also in the absence of viruses. We identify phosphorothioate DNAs (PS DNAs) as triggers of such endogenous dsRNA (endo-dsRNA). PS DNAs inhibit decay of nuclear RNAs and induce endo-dsRNA via accumulation of high levels of intronic and intergenic inverted retroelements (IIIR). IIIRs activate endo-dsRNA responses distinct from antiviral defense programs. IIIRs do not turn on transcriptional RIG-I/MDA5/IFN signaling, but they trigger the dsRNA-sensing pathways of OAS3/RNase L and PKR. Thus, nuclear RNA decay and nuclear-cytosolic RNA sorting actively protect from these innate immune responses to self. Our data suggest that the OAS3/RNase L and PKR arms of innate immunity diverge from antiviral IFN responses and monitor nuclear RNA decay by sensing cytosolic escape of IIIRs. OAS3 provides a receptor for IIIRs, whereas RNase L cleaves IIIR-carrying introns and intergenic RNAs.
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Affiliation(s)
- Alisha Chitrakar
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | | | - Eliza Prangley
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Sneha Rath
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Jin Du
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Alexei Korennykh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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43
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Lu YY, Krebber H. Nuclear mRNA Quality Control and Cytoplasmic NMD Are Linked by the Guard Proteins Gbp2 and Hrb1. Int J Mol Sci 2021; 22:ijms222011275. [PMID: 34681934 PMCID: PMC8541090 DOI: 10.3390/ijms222011275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/13/2021] [Accepted: 10/17/2021] [Indexed: 12/23/2022] Open
Abstract
Pre-mRNA splicing is critical for cells, as defects in this process can lead to altered open reading frames and defective proteins, potentially causing neurodegenerative diseases and cancer. Introns are removed in the nucleus and splicing is documented by the addition of exon-junction-complexes (EJCs) at exon-exon boundaries. This “memory” of splicing events is important for the ribosome, which translates the RNAs in the cytoplasm. In case a stop codon was detected before an EJC, translation is blocked and the RNA is eliminated by the nonsense-mediated decay (NMD). In the model organism Saccharomyces cerevisiae, two guard proteins, Gbp2 and Hrb1, have been identified as nuclear quality control factors for splicing. In their absence, intron-containing mRNAs leak into the cytoplasm. Their presence retains transcripts until the process is completed and they release the mRNAs by recruitment of the export factor Mex67. On transcripts that experience splicing problems, these guard proteins recruit the nuclear RNA degradation machinery. Interestingly, they continue their quality control function on exported transcripts. They support NMD by inhibiting translation and recruiting the cytoplasmic degradation factors. In this way, they link the nuclear and cytoplasmic quality control systems. These discoveries are also intriguing for humans, as homologues of these guard proteins are present also in multicellular organisms. Here, we provide an overview of the quality control mechanisms of pre-mRNA splicing, and present Gbp2 and Hrb1, as well as their human counterparts, as important players in these pathways.
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44
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García-Martínez J, Medina DA, Bellvís P, Sun M, Cramer P, Chávez S, Pérez-Ortín JE. The total mRNA concentration buffering system in yeast is global rather than gene-specific. RNA (NEW YORK, N.Y.) 2021; 27:1281-1290. [PMID: 34272303 PMCID: PMC8456998 DOI: 10.1261/rna.078774.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Gene expression in eukaryotes does not follow a linear process from transcription to translation and mRNA degradation. Instead it follows a circular process in which cytoplasmic mRNA decay crosstalks with nuclear transcription. In many instances, this crosstalk contributes to buffer mRNA at a roughly constant concentration. Whether the mRNA buffering concept operates on the total mRNA concentration or at the gene-specific level, and if the mechanism to do so is a global or a specific one, remain unknown. Here we assessed changes in mRNA concentrations and their synthesis rates along the transcriptome of aneuploid strains of the yeast Saccharomyces cerevisiae We also assessed mRNA concentrations and their synthesis rates in nonsense-mediated decay (NMD) targets in euploid strains. We found that the altered synthesis rates in the genes from the aneuploid chromosome and the changes in their mRNA stabilities were not counterbalanced. In addition, the stability of NMD targets was not specifically compensated by the changes in synthesis rate. We conclude that there is no genetic compensation of NMD mRNA targets in yeast, and total mRNA buffering uses mostly a global system rather than a gene-specific one.
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Affiliation(s)
- José García-Martínez
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, E46100 Burjassot, Spain
| | - Daniel A Medina
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, E46100 Burjassot, Spain
| | - Pablo Bellvís
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
| | - Mai Sun
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, 37077 Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, 37077 Göttingen, Germany
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
- Dirección de Evaluación y Acreditación, Agencia Andaluza del Conocimiento, planta 3ª C.P. 14006 Córdoba, Spain
| | - José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, E46100 Burjassot, Spain
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45
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Tanu T, Taniue K, Imamura K, Onoguchi-Mizutani R, Han H, Jensen TH, Akimitsu N. hnRNPH1-MTR4 complex-mediated regulation of NEAT1v2 stability is critical for IL8 expression. RNA Biol 2021; 18:537-547. [PMID: 34470577 DOI: 10.1080/15476286.2021.1971439] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many long noncoding RNAs (lncRNAs) are localized in the nucleus and play important roles in various biological processes, including cell proliferation, differentiation and antiviral response. Yet, it remains unclear how some nuclear lncRNAs are turned over. Here we show that the heterogeneous nuclear ribonucleoprotein H1 (hnRNPH1) controls expression levels of NEAT1v2, a lncRNA involved in the formation of nuclear paraspeckles. hnRNPH1 associates, in an RNA-independent manner, with the RNA helicase MTR4/MTREX, an essential co-factor of the nuclear ribonucleolytic RNA exosome. hnRNPH1 localizes in nuclear speckles and depletion of hnRNPH1 enhances NEAT1v2-mediated expression of the IL8 mRNA, encoding a cytokine involved in the innate immune response. Taken together, our results indicate that the hnRNPH1-MTR4 linkage regulates IL8 expression through the degradation of NEAT1v2 RNA.
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Affiliation(s)
- Tanzina Tanu
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Kenzui Taniue
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Han Han
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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46
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Dendooven T, Paris G, Shkumatov AV, Islam MS, Burt A, Kubańska MA, Yang TY, Hardwick SW, Luisi BF. Multi-scale ensemble properties of the Escherichia coli RNA degradosome. Mol Microbiol 2021; 117:102-120. [PMID: 34415624 PMCID: PMC7613265 DOI: 10.1111/mmi.14800] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022]
Abstract
In organisms from all domains of life, multi-enzyme assemblies play central roles in defining transcript lifetimes and facilitating RNA-mediated regulation of gene expression. An assembly dedicated to such roles, known as the RNA degradosome, is found amongst bacteria from highly diverse lineages. About a fifth of the assembly mass of the degradosome of Escherichia coli and related species is predicted to be intrinsically disordered - a property that has been sustained for over a billion years of bacterial molecular history and stands in marked contrast to the high degree of sequence variation of that same region. Here, we characterize the conformational dynamics of the degradosome using a hybrid structural biology approach that combines solution scattering with ad hoc ensemble modelling, cryo-electron microscopy, and other biophysical methods. The E. coli degradosome can form punctate bodies in vivo that may facilitate its functional activities, and based on our results, we propose an electrostatic switch model to account for the propensity of the degradosome to undergo programmable puncta formation.
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Affiliation(s)
- Tom Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giulia Paris
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Alexander V Shkumatov
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Md Saiful Islam
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Alister Burt
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Marta A Kubańska
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tai Yuchen Yang
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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47
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An introduction to the themed issue on RNA biology in China. Essays Biochem 2021; 64:863-866. [PMID: 33284952 DOI: 10.1042/ebc20200031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/25/2020] [Accepted: 11/02/2020] [Indexed: 11/17/2022]
Abstract
The year 2019 marked the fortieth anniversary of the Chinese Society of Biochemistry and Molecular Biology (CSBMB), whose mission is to promote biomolecular research and education in China. The last 40 years have witnessed tremendous growth and achievements in biomolecular research by Chinese scientists and Essays in Biochemistry is delighted to publish this themed issue that focuses on exciting areas within RNA biology, with each review contributed by key experts from China.
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48
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Reimegård J, Tarbier M, Danielsson M, Schuster J, Baskaran S, Panagiotou S, Dahl N, Friedländer MR, Gallant CJ. A combined approach for single-cell mRNA and intracellular protein expression analysis. Commun Biol 2021; 4:624. [PMID: 34035432 PMCID: PMC8149646 DOI: 10.1038/s42003-021-02142-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/30/2021] [Indexed: 01/28/2023] Open
Abstract
Combined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation. Here, the authors present SPARC, a scalable approach for simultaneously measuring mRNA expression levels and targeted intracellular protein levels in single cells. They use SPARC to measure dynamic expression changes in human cells during neuronal differentiation and show that mRNA levels are poor predictors of protein abundances and activity in individual cells, indicating that the measurements are complementary.
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Affiliation(s)
- Johan Reimegård
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marcus Danielsson
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jens Schuster
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sathishkumar Baskaran
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Styliani Panagiotou
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Caroline J Gallant
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden. .,10x Genomics, Stockholm, Sweden.
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49
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Li Y, Wang M, Yang M, Xiao Y, Jian Y, Shi D, Chen X, Ouyang Y, Kong L, Huang X, Bai J, Hu Y, Lin C, Song L. Nicotine-Induced ILF2 Facilitates Nuclear mRNA Export of Pluripotency Factors to Promote Stemness and Chemoresistance in Human Esophageal Cancer. Cancer Res 2021; 81:3525-3538. [PMID: 33975879 DOI: 10.1158/0008-5472.can-20-4160] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/05/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022]
Abstract
Balancing mRNA nuclear export kinetics with its nuclear decay is critical for mRNA homeostasis control. How this equilibrium is aberrantly disrupted in esophageal cancer to acquire cancer stem cell properties remains unclear. Here we find that the RNA-binding protein interleukin enhancer binding factor 2 (ILF2) is robustly upregulated by nicotine, a major chemical component of tobacco smoke, via activation of JAK2/STAT3 signaling and significantly correlates with poor prognosis in heavy-smoking patients with esophageal cancer. ILF2 bound the THO complex protein THOC4 as a regulatory cofactor to induce selective interactions with pluripotency transcription factor mRNAs to promote their assembly into export-competent messenger ribonucleoprotein complexes. ILF2 facilitated nuclear mRNA export and inhibited hMTR4-mediated exosomal degradation to promote stabilization and expression of SOX2, NANOG, and SALL4, resulting in enhanced stemness and tumor-initiating capacity of esophageal cancer cells. Importantly, inducible depletion of ILF2 significantly increased the therapeutic efficiency of cisplatin and abrogated nicotine-induced chemoresistance in vitro and in vivo. These findings reveal a novel role of ILF2 in nuclear mRNA export and maintenance of cancer stem cells and open new avenues to overcome smoking-mediated chemoresistance in esophageal cancer. SIGNIFICANCE: This study defines a previously uncharacterized role of nicotine-regulated ILF2 in facilitating nuclear mRNA export to promote cancer stemness, suggesting a potential therapeutic strategy against nicotine-induced chemoresistance in esophageal cancer.
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Affiliation(s)
- Yue Li
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Meng Wang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Muwen Yang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yunyun Xiao
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yunting Jian
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongni Shi
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiangfu Chen
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Ouyang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lingzhi Kong
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xinjian Huang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jiewen Bai
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yameng Hu
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chuyong Lin
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. .,Guangdong Esophageal Cancer Institute, Guangzhou, China
| | - Libing Song
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. .,Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences; Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
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50
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Bensidoun P, Zenklusen D, Oeffinger M. Choosing the right exit: How functional plasticity of the nuclear pore drives selective and efficient mRNA export. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1660. [PMID: 33938148 DOI: 10.1002/wrna.1660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/30/2021] [Accepted: 04/04/2021] [Indexed: 12/17/2022]
Abstract
The nuclear pore complex (NPC) serves as a central gate for mRNAs to transit from the nucleus to the cytoplasm. The ability for mRNAs to get exported is linked to various upstream nuclear processes including co-transcriptional RNP assembly and processing, and only export competent mRNPs are thought to get access to the NPC. While the nuclear pore is generally viewed as a monolithic structure that serves as a mediator of transport driven by transport receptors, more recent evidence suggests that the NPC might be more heterogenous than previously believed, both in its composition or in the selective treatment of cargo that seek access to the pore, providing functional plasticity to mRNA export. In this review, we consider the interconnected processes of nuclear mRNA metabolism that contribute and mediate export competence. Furthermore, we examine different aspects of NPC heterogeneity, including the role of the nuclear basket and its associated complexes in regulating selective and/or efficient binding to and transport through the pore. This article is categorized under: RNA Export and Localization > Nuclear Export/Import RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Pierre Bensidoun
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Marlene Oeffinger
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada
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