1
|
Andjus S, Szachnowski U, Vogt N, Gioftsidi S, Hatin I, Cornu D, Papadopoulos C, Lopes A, Namy O, Wery M, Morillon A. Pervasive translation of Xrn1-sensitive unstable long noncoding RNAs in yeast. RNA (NEW YORK, N.Y.) 2024; 30:662-679. [PMID: 38443115 PMCID: PMC11098462 DOI: 10.1261/rna.079903.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
Despite being predicted to lack coding potential, cytoplasmic long noncoding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNA translation remain poorly studied. In yeast, cytoplasmic Xrn1-sensitive unstable transcripts (XUTs) are targeted by nonsense-mediated mRNA decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are pervasively translated, which impacts their decay. We show that XUTs globally accumulate upon translation elongation inhibition, but not when initial ribosome loading is impaired. Ribo-seq confirmed ribosomes binding to XUTs and identified ribosome-associated 5'-proximal small ORFs. Mechanistically, the NMD-sensitivity of XUTs mainly depends on the 3'-untranslated region length. Finally, we show that the peptide resulting from the translation of an NMD-sensitive XUT reporter exists in NMD-competent cells. Our work highlights the role of translation in the posttranscriptional metabolism of XUTs. We propose that XUT-derived peptides could be exposed to natural selection, while NMD restricts XUT levels.
Collapse
Affiliation(s)
- Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| | - Ugo Szachnowski
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| | - Nicolas Vogt
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| | - Stamatia Gioftsidi
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| | - Isabelle Hatin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - David Cornu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Chris Papadopoulos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Anne Lopes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Olivier Namy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| |
Collapse
|
2
|
Ma Z, Sharma R, Rogers AN. Physiological Consequences of Nonsense-Mediated Decay and Its Role in Adaptive Responses. Biomedicines 2024; 12:1110. [PMID: 38791071 PMCID: PMC11117581 DOI: 10.3390/biomedicines12051110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The evolutionarily conserved nonsense-mediated mRNA decay (NMD) pathway is a quality control mechanism that degrades aberrant mRNA containing one or more premature termination codons (PTCs). Recent discoveries indicate that NMD also differentially regulates mRNA from wild-type protein-coding genes despite lacking PTCs. Together with studies showing that NMD is involved in development and adaptive responses that influence health and longevity, these findings point to an expanded role of NMD that adds a new layer of complexity in the post-transcriptional regulation of gene expression. However, the extent of its control, whether different types of NMD play different roles, and the resulting physiological outcomes remain unclear and need further elucidation. Here, we review different branches of NMD and what is known of the physiological outcomes associated with this type of regulation. We identify significant gaps in the understanding of this process and the utility of genetic tools in accelerating progress in this area.
Collapse
Affiliation(s)
- Zhengxin Ma
- MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Ratna Sharma
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA;
| | | |
Collapse
|
3
|
Singh AK. Rules and impacts of nonsense-mediated mRNA decay in the degradation of long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1853. [PMID: 38741356 DOI: 10.1002/wrna.1853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality-control process that selectively degrades mRNAs having premature termination codon, upstream open reading frame, or unusually long 3'UTR. NMD detects such mRNAs and rapidly degrades them during initial rounds of translation in the eukaryotic cells. Since NMD is a translation-dependent cytoplasmic mRNA surveillance process, the noncoding RNAs were initially believed to be NMD-resistant. The sequence feature-based analysis has revealed that many putative long noncoding RNAs (lncRNAs) have short open reading frames, most of which have translation potential. Subsequent transcriptome-based molecular studies showed an association of a large set of such putative lncRNAs with translating ribosomes, and some of them produce stable and functionally active micropeptides. The translationally active lncRNAs typically have relatively longer and unprotected 3'UTR, which can induce their NMD-dependent degradation. This review defines the mechanism and regulation of NMD-dependent degradation of lncRNAs and its impact on biological processes related to the functions of lncRNAs or their encoded micropeptides. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Anand Kumar Singh
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
| |
Collapse
|
4
|
Zhu Y, Vvedenskaya IO, Sze SH, Nickels BE, Kaplan CD. Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels. Nat Struct Mol Biol 2024; 31:190-202. [PMID: 38177677 PMCID: PMC10928753 DOI: 10.1038/s41594-023-01171-9] [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: 12/14/2021] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
Transcription start site (TSS) selection is a key step in gene expression and occurs at many promoter positions over a wide range of efficiencies. Here we develop a massively parallel reporter assay to quantitatively dissect contributions of promoter sequence, nucleoside triphosphate substrate levels and RNA polymerase II (Pol II) activity to TSS selection by 'promoter scanning' in Saccharomyces cerevisiae (Pol II MAssively Systematic Transcript End Readout, 'Pol II MASTER'). Using Pol II MASTER, we measure the efficiency of Pol II initiation at 1,000,000 individual TSS sequences in a defined promoter context. Pol II MASTER confirms proposed critical qualities of S. cerevisiae TSS -8, -1 and +1 positions, quantitatively, in a controlled promoter context. Pol II MASTER extends quantitative analysis to surrounding sequences and determines that they tune initiation over a wide range of efficiencies. These results enabled the development of a predictive model for initiation efficiency based on sequence. We show that genetic perturbation of Pol II catalytic activity alters initiation efficiency mostly independently of TSS sequence, but selectively modulates preference for the initiating nucleotide. Intriguingly, we find that Pol II initiation efficiency is directly sensitive to guanosine-5'-triphosphate levels at the first five transcript positions and to cytosine-5'-triphosphate and uridine-5'-triphosphate levels at the second position genome wide. These results suggest individual nucleoside triphosphate levels can have transcript-specific effects on initiation, representing a cryptic layer of potential regulation at the level of Pol II biochemical properties. The results establish Pol II MASTER as a method for quantitative dissection of transcription initiation in eukaryotes.
Collapse
Affiliation(s)
- Yunye Zhu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Irina O Vvedenskaya
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Sing-Hoi Sze
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
5
|
Zavileyskiy LG, Pervouchine DD. Post-transcriptional Regulation of Gene Expression via Unproductive Splicing. Acta Naturae 2024; 16:4-13. [PMID: 38698955 PMCID: PMC11062102 DOI: 10.32607/actanaturae.27337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/01/2024] [Indexed: 05/05/2024] Open
Abstract
Unproductive splicing is a mechanism of post-transcriptional gene expression control in which premature stop codons are inserted into protein-coding transcripts as a result of regulated alternative splicing, leading to their degradation via the nonsense-mediated decay pathway. This mechanism is especially characteristic of RNA-binding proteins, which regulate each other's expression levels and those of other genes in multiple auto- and cross-regulatory loops. Deregulation of unproductive splicing is a cause of serious human diseases, including cancers, and is increasingly being considered as a prominent therapeutic target. This review discusses the types of unproductive splicing events, the mechanisms of auto- and cross-regulation, nonsense-mediated decay escape, and problems in identifying unproductive splice isoforms. It also provides examples of deregulation of unproductive splicing in human diseases and discusses therapeutic strategies for its correction using antisense oligonucleotides and small molecules.
Collapse
Affiliation(s)
- L. G. Zavileyskiy
- Lomonosov Moscow State University, Moscow, 119192 Russian Federation
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
| | - D. D. Pervouchine
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
| |
Collapse
|
6
|
Colón EM, Haddock LA, Lasalde C, Lin Q, Ramírez-Lugo JS, González CI. Characterization of the mIF4G Domains in the RNA Surveillance Protein Upf2p. Curr Issues Mol Biol 2023; 46:244-261. [PMID: 38248319 PMCID: PMC10814901 DOI: 10.3390/cimb46010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Thirty percent of all mutations causing human disease generate mRNAs with premature termination codons (PTCs). Recognition and degradation of these PTC-containing mRNAs is carried out by the mechanism known as nonsense-mediated mRNA decay (NMD). Upf2 is a scaffold protein known to be a central component of the NMD surveillance pathway. It harbors three middle domains of eukaryotic initiation factor 4G (mIF4G-1, mIF4G-2, mIF4G-3) in its N-terminal region that are potentially important in regulating the surveillance pathway. In this study, we defined regions within the mIF4G-1 and mIF4G-2 that are required for proper function of Upf2p in NMD and translation termination in Saccharomyces cerevisiae. In addition, we narrowed down the activity of these regions to an aspartic acid (D59) in mIF4G-1 that is important for NMD activity and translation termination accuracy. Taken together, these studies suggest that inherently charged residues within mIF4G-1 of Upf2p play a role in the regulation of the NMD surveillance mechanism in S. cerevisiae.
Collapse
Affiliation(s)
- Edgardo M. Colón
- Department of Biology, Río Piedras Campus, University of Puerto Rico, San Juan, PR 00931, USA (C.L.); (J.S.R.-L.)
- Molecular Sciences Research Center, University of Puerto Rico, San Juan, PR 00926, USA
| | - Luis A. Haddock
- Department of Biology, Río Piedras Campus, University of Puerto Rico, San Juan, PR 00931, USA (C.L.); (J.S.R.-L.)
- Molecular Sciences Research Center, University of Puerto Rico, San Juan, PR 00926, USA
| | - Clarivel Lasalde
- Department of Biology, Río Piedras Campus, University of Puerto Rico, San Juan, PR 00931, USA (C.L.); (J.S.R.-L.)
| | - Qishan Lin
- Department of Chemistry, University at Albany, Albany, NY 12222, USA;
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - Juan S. Ramírez-Lugo
- Department of Biology, Río Piedras Campus, University of Puerto Rico, San Juan, PR 00931, USA (C.L.); (J.S.R.-L.)
| | - Carlos I. González
- Department of Biology, Río Piedras Campus, University of Puerto Rico, San Juan, PR 00931, USA (C.L.); (J.S.R.-L.)
- Molecular Sciences Research Center, University of Puerto Rico, San Juan, PR 00926, USA
| |
Collapse
|
7
|
Garrido-Godino AI, Gupta I, Pelechano V, Navarro F. RNA Pol II Assembly Affects ncRNA Expression. Int J Mol Sci 2023; 25:507. [PMID: 38203678 PMCID: PMC10778713 DOI: 10.3390/ijms25010507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
RNA pol II assembly occurs in the cytoplasm before translocation of the enzyme to the nucleus. Affecting this assembly influences mRNA transcription in the nucleus and mRNA decay in the cytoplasm. However, very little is known about the consequences on ncRNA synthesis. In this work, we show that impairment of RNA pol II assembly leads to a decrease in cryptic non-coding RNAs (preferentially CUTs and SUTs). This alteration is partially restored upon overcoming the assembly defect. Notably, this drop in ncRNAs is only partially dependent on the nuclear exosome, which suggests a major specific effect of enzyme assembly. Our data also point out a defect in transcription termination, which leads us to propose that CTD phosphatase Rtr1 could be involved in this process.
Collapse
Affiliation(s)
- Ana I. Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain;
| | - Ishaan Gupta
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany;
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain;
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva (INUO), Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| |
Collapse
|
8
|
Nelde A, Schuster H, Heitmann JS, Bauer J, Maringer Y, Zwick M, Volkmer JP, Chen JY, Stanger AMP, Lehmann A, Appiah B, Märklin M, Rücker-Braun E, Salih HR, Roerden M, Schroeder SM, Häring MF, Schlosser A, Schetelig J, Schmitz M, Boerries M, Köhler N, Lengerke C, Majeti R, Weissman IL, Rammensee HG, Walz JS. Immune Surveillance of Acute Myeloid Leukemia Is Mediated by HLA-Presented Antigens on Leukemia Progenitor Cells. Blood Cancer Discov 2023; 4:468-489. [PMID: 37847741 PMCID: PMC10618727 DOI: 10.1158/2643-3230.bcd-23-0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/13/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Therapy-resistant leukemia stem and progenitor cells (LSC) are a main cause of acute myeloid leukemia (AML) relapse. LSC-targeting therapies may thus improve outcome of patients with AML. Here we demonstrate that LSCs present HLA-restricted antigens that induce T-cell responses allowing for immune surveillance of AML. Using a mass spectrometry-based immunopeptidomics approach, we characterized the antigenic landscape of patient LSCs and identified AML- and AML/LSC-associated HLA-presented antigens absent from normal tissues comprising nonmutated peptides, cryptic neoepitopes, and neoepitopes of common AML driver mutations of NPM1 and IDH2. Functional relevance of shared AML/LSC antigens is illustrated by presence of their cognizant memory T cells in patients. Antigen-specific T-cell recognition and HLA class II immunopeptidome diversity correlated with clinical outcome. Together, these antigens shared among AML and LSCs represent prime targets for T cell-based therapies with potential of eliminating residual LSCs in patients with AML. SIGNIFICANCE The elimination of therapy-resistant leukemia stem and progenitor cells (LSC) remains a major challenge in the treatment of AML. This study identifies and functionally validates LSC-associated HLA class I and HLA class II-presented antigens, paving the way to the development of LSC-directed T cell-based immunotherapeutic approaches for patients with AML. See related commentary by Ritz, p. 430 . This article is featured in Selected Articles from This Issue, p. 419.
Collapse
Affiliation(s)
- Annika Nelde
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Heiko Schuster
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jonas S. Heitmann
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Jens Bauer
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Melissa Zwick
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jens-Peter Volkmer
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
| | - James Y. Chen
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
| | - Anna M. Paczulla Stanger
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Ariane Lehmann
- Faculty of Medicine, Medical Center, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Germany
| | - Bismark Appiah
- Faculty of Medicine, Medical Center, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Germany
| | - Melanie Märklin
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Elke Rücker-Braun
- Department of Medicine I, University Hospital of Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Helmut R. Salih
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Malte Roerden
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Sarah M. Schroeder
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Max-Felix Häring
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | | | - Johannes Schetelig
- Department of Medicine I, University Hospital of Dresden, Dresden, Germany
- German Bone Marrow Donor Center (DKMS), Clinical Trials Unit, Dresden, Germany
| | - Marc Schmitz
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Faculty of Medicine, Medical Center, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site, Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Köhler
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Claudia Lengerke
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
- Clinic for Hematology, University of Basel and University Hospital Basel, Basel, Switzerland
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Juliane S. Walz
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| |
Collapse
|
9
|
Wery M, Szachnowski U, Andjus S, de Andres-Pablo A, Morillon A. The RNA helicases Dbp2 and Mtr4 regulate the expression of Xrn1-sensitive long non-coding RNAs in yeast. FRONTIERS IN RNA RESEARCH 2023; 1:1244554. [PMID: 37667796 PMCID: PMC7615016 DOI: 10.3389/frnar.2023.1244554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The expression of yeast long non-coding (lnc)RNAs is restricted by RNA surveillance machineries, including the cytoplasmic 5'-3' exonuclease Xrn1 which targets a conserved family of lncRNAs defined as XUTs, and that are mainly antisense to protein-coding genes. However, the co-factors involved in the degradation of these transcripts and the underlying molecular mechanisms remain largely unknown. Here, we show that two RNA helicases, Dbp2 and Mtr4, act as global regulators of XUTs expression. Using RNA-Seq, we found that most of them accumulate upon Dbp2 inactivation or Mtr4 depletion. Mutants of the cytoplasmic RNA helicases Ecm32, Ski2, Slh1, Dbp1, and Dhh1 did not recapitulate this global stabilization of XUTs, suggesting that XUTs decay is specifically controlled by Dbp2 and Mtr4. Notably, Dbp2 and Mtr4 affect XUTs independently of their configuration relative to their paired-sense mRNAs. Finally, we show that the effect of Dbp2 on XUTs depends on a cytoplasmic localization. Overall, our data indicate that Dbp2 and Mtr4 are global regulators of lncRNAs expression and contribute to shape the non-coding transcriptome together with RNA decay machineries.
Collapse
Affiliation(s)
- Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
| | - Ugo Szachnowski
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
| | - Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL
University, Sorbonne Université, CNRS UMR3244, Paris Cedex, France
| | - Alvaro de Andres-Pablo
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
| |
Collapse
|
10
|
Bedran G, Gasser HC, Weke K, Wang T, Bedran D, Laird A, Battail C, Zanzotto FM, Pesquita C, Axelson H, Rajan A, Harrison DJ, Palkowski A, Pawlik M, Parys M, O'Neill JR, Brennan PM, Symeonides SN, Goodlett DR, Litchfield K, Fahraeus R, Hupp TR, Kote S, Alfaro JA. The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I-Associated Peptides. Cancer Immunol Res 2023; 11:747-762. [PMID: 36961404 PMCID: PMC10236148 DOI: 10.1158/2326-6066.cir-22-0621] [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: 08/01/2022] [Revised: 11/25/2022] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
Tumor antigens can emerge through multiple mechanisms, including translation of noncoding genomic regions. This noncanonical category of tumor antigens has recently gained attention; however, our understanding of how they recur within and between cancer types is still in its infancy. Therefore, we developed a proteogenomic pipeline based on deep learning de novo mass spectrometry (MS) to enable the discovery of noncanonical MHC class I-associated peptides (ncMAP) from noncoding regions. Considering that the emergence of tumor antigens can also involve posttranslational modifications (PTM), we included an open search component in our pipeline. Leveraging the wealth of MS-based immunopeptidomics, we analyzed data from 26 MHC class I immunopeptidomic studies across 11 different cancer types. We validated the de novo identified ncMAPs, along with the most abundant PTMs, using spectral matching and controlled their FDR to 1%. The noncanonical presentation appeared to be 5 times enriched for the A03 HLA supertype, with a projected population coverage of 55%. The data reveal an atlas of 8,601 ncMAPs with varying levels of cancer selectivity and suggest 17 cancer-selective ncMAPs as attractive therapeutic targets according to a stringent cutoff. In summary, the combination of the open-source pipeline and the atlas of ncMAPs reported herein could facilitate the identification and screening of ncMAPs as targets for T-cell therapies or vaccine development.
Collapse
Affiliation(s)
- Georges Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Kenneth Weke
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Tongjie Wang
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Dominika Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Alexander Laird
- Urology Department, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Christophe Battail
- CEA, Grenoble Alpes University, INSERM, IRIG, Biosciences and Bioengineering for Health Laboratory (BGE) - UA13 INSERM-CEA-UGA, Grenoble, France
| | | | - Catia Pesquita
- LASIGE, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Håkan Axelson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ajitha Rajan
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - David J. Harrison
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Aleksander Palkowski
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Maciej Pawlik
- Academic Computer Centre CYFRONET, AGH University of Science and Technology, Cracow, Poland
| | - Maciej Parys
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - J. Robert O'Neill
- Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Stefan N. Symeonides
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - David R. Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
- University of Victoria Genome BC Proteome Centre, Victoria, Canada
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Paris, France
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Javier A. Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| |
Collapse
|
11
|
André KM, Giordanengo Aiach N, Martinez-Fernandez V, Zeitler L, Alberti A, Goldar A, Werner M, Denby Wilkes C, Soutourina J. Functional interplay between Mediator and RSC chromatin remodeling complex controls nucleosome-depleted region maintenance at promoters. Cell Rep 2023; 42:112465. [PMID: 37133993 DOI: 10.1016/j.celrep.2023.112465] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/05/2023] [Accepted: 04/18/2023] [Indexed: 05/04/2023] Open
Abstract
Chromatin organization is crucial for transcriptional regulation in eukaryotes. Mediator is an essential and conserved co-activator thought to act in concert with chromatin regulators. However, it remains largely unknown how their functions are coordinated. Here, we provide evidence in the yeast Saccharomyces cerevisiae that Mediator establishes physical contact with RSC (Remodels the Structure of Chromatin), a conserved and essential chromatin remodeling complex that is crucial for nucleosome-depleted region (NDR) formation. We determine the role of Mediator-RSC interaction in their chromatin binding, nucleosome occupancy, and transcription on a genomic scale. Mediator and RSC co-localize on wide NDRs of promoter regions, and specific Mediator mutations affect nucleosome eviction and TSS-associated +1 nucleosome stability. This work shows that Mediator contributes to RSC remodeling function to shape NDRs and maintain chromatin organization on promoter regions. It will help in our understanding of transcriptional regulation in the chromatin context relevant for severe diseases.
Collapse
Affiliation(s)
- Kévin M André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Nathalie Giordanengo Aiach
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Veronica Martinez-Fernandez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Leo Zeitler
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Adriana Alberti
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Michel Werner
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| |
Collapse
|
12
|
RNA-Mediated Regulation of Meiosis in Budding Yeast. Noncoding RNA 2022; 8:ncrna8060077. [PMID: 36412912 PMCID: PMC9680404 DOI: 10.3390/ncrna8060077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cells change their physiological state in response to environmental cues. In the absence of nutrients, unicellular fungi such as budding yeast exit mitotic proliferation and enter the meiotic cycle, leading to the production of haploid cells that are encased within spore walls. These cell state transitions are orchestrated in a developmentally coordinated manner. Execution of the meiotic cell cycle program in budding yeast, Saccharomyces cerevisiae, is regulated by the key transcription factor, Ime1. Recent developments have uncovered the role of non-coding RNA in the regulation of Ime1 and meiosis. In this review, we summarize the role of ncRNA-mediated and RNA homeostasis-based processes in the regulation of meiosis in Saccharomyces cerevisiae.
Collapse
|
13
|
Wu AC, Vivori C, Patel H, Sideri T, Moretto F, van Werven FJ. RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription. Life Sci Alliance 2022; 5:e202201394. [PMID: 36114005 PMCID: PMC9481977 DOI: 10.26508/lsa.202201394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
The directionality of gene promoters-the ratio of protein-coding over divergent noncoding transcription-is highly variable. How promoter directionality is controlled remains poorly understood. Here, we show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) dictate promoter directionality by attenuating divergent transcription relative to protein-coding transcription. At gene promoters that are highly directional, depletion of RSC leads to a relative increase in divergent noncoding transcription and thus to a decrease in promoter directionality. We find that RSC has a modest effect on nucleosome positioning upstream in promoters at the sites of divergent transcription. These promoters are also enriched for the binding of GRFs such as Reb1 and Abf1. Ectopic targeting of divergent transcription initiation sites with GRFs or the dCas9 DNA-binding protein suppresses divergent transcription. Our data suggest that RSC and GRFs play a pervasive role in limiting divergent transcription relative to coding direction transcription. We propose that any DNA-binding factor, when stably associated with cryptic transcription start sites, forms a barrier which represses divergent transcription, thereby promoting promoter directionality.
Collapse
Affiliation(s)
- Andrew Ck Wu
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Claudia Vivori
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Theodora Sideri
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| |
Collapse
|
14
|
Gopaul D, Denby Wilkes C, Goldar A, Giordanengo Aiach N, Barrault MB, Novikova E, Soutourina J. Genomic analysis of Rad26 and Rad1-Rad10 reveals differences in their dependence on Mediator and RNA polymerase II. Genome Res 2022; 32:gr.276371.121. [PMID: 35738899 PMCID: PMC9435749 DOI: 10.1101/gr.276371.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 06/16/2022] [Indexed: 02/03/2023]
Abstract
Mediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and nucleotide excision repair (NER) via a direct contact with Rad2/ERCC5(XPG) endonuclease. In this work, we analyzed the genome-wide distribution of Rad26/ERCC6(CSB) and Rad1-Rad10/ERCC4(XPF)-ERCC1, addressing the question of a potential link of these proteins with Mediator and Pol II in yeast Saccharomyces cerevisiae Our genomic analyses reveal that Rad1-Rad10 and Rad26 are present on the yeast genome in the absence of genotoxic stress, especially at highly transcribed regions, with Rad26 binding strongly correlating with that of Pol II. Moreover, we show that Rad1-Rad10 and Rad26 colocalize with Mediator at intergenic regions and physically interact with this complex. Using kin28 TFIIH mutant, we found that Mediator stabilization on core promoters leads to an increase in Rad1-Rad10 chromatin binding, whereas Rad26 occupancy follows mainly a decrease in Pol II transcription. Combined with multivariate analyses, our results show the relationships between Rad1-Rad10, Rad26, Mediator, and Pol II, modulated by the changes in binding dynamics of Mediator and Pol II transcription. In conclusion, we extend the Mediator link to Rad1-Rad10 and Rad26 NER proteins and reveal important differences in their dependence on Mediator and Pol II. Rad2 is the most dependent on Mediator, followed by Rad1-Rad10, whereas Rad26 is the most closely related to Pol II. Our work thus contributes to new concepts of the functional interplay between transcription and DNA repair machineries, which are relevant for human diseases including cancer and XP/CS syndromes.
Collapse
Affiliation(s)
- Diyavarshini Gopaul
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Nathalie Giordanengo Aiach
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie-Bénédicte Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Elizaveta Novikova
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| |
Collapse
|
15
|
Villa T, Porrua O. Pervasive transcription: a controlled risk. FEBS J 2022. [PMID: 35587776 DOI: 10.1111/febs.16530] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/26/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
Transcriptome-wide interrogation of eukaryotic genomes has unveiled the pervasive nature of RNA polymerase II transcription. Virtually, any DNA region with an accessible chromatin structure can be transcribed, resulting in a mass production of noncoding RNAs (ncRNAs) with the potential of interfering with gene expression programs. Budding yeast has proved to be a powerful model organism to understand the mechanisms at play to control pervasive transcription and overcome the risks of hazardous disruption of cellular functions. In this review, we focus on the actors and strategies yeasts employ to govern ncRNA production, and we discuss recent findings highlighting the dangers of losing control over pervasive transcription.
Collapse
Affiliation(s)
- Tommaso Villa
- Institut Jacques Monod CNRS, Université de Paris Cité France
| | - Odil Porrua
- Institut Jacques Monod CNRS, Université de Paris Cité France
| |
Collapse
|
16
|
Alalam H, Zepeda-Martínez JA, Sunnerhagen P. Global SLAM-seq for accurate mRNA decay determination and identification of NMD targets. RNA (NEW YORK, N.Y.) 2022; 28:905-915. [PMID: 35296539 PMCID: PMC9074897 DOI: 10.1261/rna.079077.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Gene expression analysis requires accurate measurements of global RNA degradation rates, earlier problematic with methods disruptive to cell physiology. Recently, metabolic RNA labeling emerged as an efficient and minimally invasive technique applied in mammalian cells. Here, we have adapted SH-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) for a global mRNA stability study in yeast using 4-thiouracil pulse-chase labeling. We assign high-confidence half-life estimates for 67.5% of expressed ORFs, and measure a median half-life of 9.4 min. For mRNAs where half-life estimates exist in the literature, their ranking order was in good agreement with previous data, indicating that SLAM-seq efficiently classifies stable and unstable transcripts. We then leveraged our yeast protocol to identify targets of the nonsense-mediated decay (NMD) pathway by measuring the change in RNA half-lives, instead of steady-state RNA level changes. With SLAM-seq, we assign 580 transcripts as putative NMD targets, based on their measured half-lives in wild-type and upf3Δ mutants. We find 225 novel targets, and observe a strong agreement with previous reports of NMD targets, 61.2% of our candidates being identified in previous studies. This indicates that SLAM-seq is a simpler and more economic method for global quantification of mRNA half-lives. Our adaptation for yeast yielded global quantitative measures of the NMD effect on transcript half-lives, high correlation with RNA half-lives measured previously with more technically challenging protocols, and identification of novel NMD regulated transcripts that escaped prior detection.
Collapse
Affiliation(s)
- Hanna Alalam
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, S-405 30 Göteborg, Sweden
| | | | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, S-405 30 Göteborg, Sweden
| |
Collapse
|
17
|
Ha T, DiPrima M, Koparde V, Jailwala P, Ohnuki H, Feng JX, Palangat M, Larson D, Tosato G. Antisense transcription from lentiviral gene targeting linked to an integrated stress response in colorectal cancer cells. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:877-891. [PMID: 35694213 PMCID: PMC9163427 DOI: 10.1016/j.omtn.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/12/2022] [Indexed: 11/10/2022]
Abstract
Advances in gene therapy research have resulted in the successful development of new therapies for clinical use. Here, we explored a gene targeting approach to deplete ephrinB2 from colorectal cancer cells using an inducible lentiviral vector. EphrinB2, a transmembrane ephrin ligand, promotes colorectal cancer cell growth and viability and predicts poor patient survival when expressed at high levels in colorectal cancer tissues. We discovered that lentiviral vector integration and expression in the host DNA frequently drive divergent host gene transcription, generating antisense reads coupled with splicing events and generation of chimeric vector/host transcripts. Antisense transcription of host DNA was linked to development of an integrated stress response and cell death. Despite recent successes, off-target effects remain a concern in genetic medicine. Our results provide evidence that divergent gene transcription is a previously unrecognized off-target effect of lentiviral vector integration with built-in properties for regulation of gene expression.
Collapse
|
18
|
Nikolov VN, Malavia D, Kubota T. SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes. Nat Commun 2022; 13:1968. [PMID: 35413952 PMCID: PMC9005695 DOI: 10.1038/s41467-022-29591-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/23/2022] [Indexed: 12/13/2022] Open
Abstract
The Pleiotropic Drug Resistance (PDR) network is central to the drug response in fungi, and its overactivation is associated with drug resistance. However, gene regulation of the PDR network is not well understood. Here, we show that the histone chaperone Rtt106 and the chromatin remodeller SWI/SNF control expression of the PDR network genes and confer drug resistance. In Saccharomyces cerevisiae, Rtt106 specifically localises to PDR network gene promoters dependent on transcription factor Pdr3, but not Pdr1, and is essential for Pdr3-mediated basal expression of the PDR network genes, while SWI/SNF is essential for both basal and drug-induced expression. Also in the pathogenic fungus Candida glabrata, Rtt106 and SWI/SNF regulate drug-induced PDR gene expression. Consistently, loss of Rtt106 or SWI/SNF sensitises drug-resistant S. cerevisiae mutants and C. glabrata to antifungal drugs. Since they cooperatively drive PDR network gene expression, Rtt106 and SWI/SNF represent potential therapeutic targets to combat antifungal resistance.
Collapse
Affiliation(s)
- Vladislav N Nikolov
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Dhara Malavia
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- MRC Centre for Medical Mycology, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Takashi Kubota
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
| |
Collapse
|
19
|
Gilbert A, Saveanu C. Unusual SMG suspects recruit degradation enzymes in nonsense-mediated mRNA decay. Bioessays 2022; 44:e2100296. [PMID: 35266563 DOI: 10.1002/bies.202100296] [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: 12/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/09/2022]
Abstract
Degradation of eukaryotic RNAs that contain premature termination codons (PTC) during nonsense-mediated mRNA decay (NMD) is initiated by RNA decapping or endonucleolytic cleavage driven by conserved factors. Models for NMD mechanisms, including recognition of PTCs or the timing and role of protein phosphorylation for RNA degradation are challenged by new results. For example, the depletion of the SMG5/7 heterodimer, thought to activate RNA degradation by decapping, leads to a phenotype showing a defect of endonucleolytic activity of NMD complexes. This phenotype is not correlated to a decreased binding of the endonuclease SMG6 with the core NMD factor UPF1, suggesting that it is the result of an imbalance between active (e.g., in polysomes) and inactive (e.g., in RNA-protein condensates) states of NMD complexes. Such imbalance between multiple complexes is not restricted to NMD and should be taken into account when establishing causal links between gene function perturbation and observed phenotypes.
Collapse
Affiliation(s)
- Agathe Gilbert
- Institut Pasteur, Sorbonne Université, CNRS UMR-3525, Paris, F-75015, France
| | - Cosmin Saveanu
- Institut Pasteur, Sorbonne Université, CNRS UMR-3525, Paris, F-75015, France
| |
Collapse
|
20
|
Abstract
Transcription start site (TSS) usage is a critical factor in the regulation of gene expression. A number of methods for global TSS mapping have been developed, but barriers of expense, technical difficulty, time, and/or cost have limited their broader adoption. To address these issues, we developed Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq). Requiring only three enzymatic steps with intervening bead cleanups, a STRIPE-seq library can be prepared from as little as 50 ng total RNA in ~5 h at a cost of ~$12 (US). In addition to profiling TSS usage, STRIPE-seq provides information on transcript levels that can be used for differential expression analysis. Thanks to its simplicity and low cost, we envision that STRIPE-seq could be employed by any molecular biology laboratory interested in profiling transcription initiation.
Collapse
Affiliation(s)
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, IN, USA.
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA.
- eGenesis, Inc., Cambridge, MA, USA.
| |
Collapse
|
21
|
Lu Z, Berry K, Hu Z, Zhan Y, Ahn TH, Lin Z. TSSr: an R package for comprehensive analyses of TSS sequencing data. NAR Genom Bioinform 2021; 3:lqab108. [PMID: 34805991 PMCID: PMC8598296 DOI: 10.1093/nargab/lqab108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/05/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription initiation is regulated in a highly organized fashion to ensure proper cellular functions. Accurate identification of transcription start sites (TSSs) and quantitative characterization of transcription initiation activities are fundamental steps for studies of regulated transcriptions and core promoter structures. Several high-throughput techniques have been developed to sequence the very 5'end of RNA transcripts (TSS sequencing) on the genome scale. Bioinformatics tools are essential for processing, analysis, and visualization of TSS sequencing data. Here, we present TSSr, an R package that provides rich functions for mapping TSS and characterizations of structures and activities of core promoters based on all types of TSS sequencing data. Specifically, TSSr implements several newly developed algorithms for accurately identifying TSSs from mapped sequencing reads and inference of core promoters, which are a prerequisite for subsequent functional analyses of TSS data. Furthermore, TSSr also enables users to export various types of TSS data that can be visualized by genome browser for inspection of promoter activities in association with other genomic features, and to generate publication-ready TSS graphs. These user-friendly features could greatly facilitate studies of transcription initiation based on TSS sequencing data. The source code and detailed documentations of TSSr can be freely accessed at https://github.com/Linlab-slu/TSSr.
Collapse
Affiliation(s)
- Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Keenan Berry
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Zhenbin Hu
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Yu Zhan
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Tae-Hyuk Ahn
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| |
Collapse
|
22
|
Egorov AA, Alexandrov AI, Urakov VN, Makeeva DS, Edakin RO, Kushchenko AS, Gladyshev VN, Kulakovskiy IV, Dmitriev SE. A standard knockout procedure alters expression of adjacent loci at the translational level. Nucleic Acids Res 2021; 49:11134-11144. [PMID: 34606617 PMCID: PMC8565318 DOI: 10.1093/nar/gkab872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/11/2021] [Accepted: 09/15/2021] [Indexed: 12/13/2022] Open
Abstract
The Saccharomyces cerevisiae gene deletion collection is widely used for functional gene annotation and genetic interaction analyses. However, the standard G418-resistance cassette used to produce knockout mutants delivers strong regulatory elements into the target genetic loci. To date, its side effects on the expression of neighboring genes have never been systematically assessed. Here, using ribosome profiling data, RT-qPCR, and reporter expression, we investigated perturbations induced by the KanMX module. Our analysis revealed significant alterations in the transcription efficiency of neighboring genes and, more importantly, severe impairment of their mRNA translation, leading to changes in protein abundance. In the ‘head-to-head’ orientation of the deleted and neighboring genes, knockout often led to a shift of the transcription start site of the latter, introducing new uAUG codon(s) into the expanded 5′ untranslated region (5′ UTR). In the ‘tail-to-tail’ arrangement, knockout led to activation of alternative polyadenylation signals in the neighboring gene, thus altering its 3′ UTR. These events may explain the so-called neighboring gene effect (NGE), i.e. false genetic interactions of the deleted genes. We estimate that in as much as ∼1/5 of knockout strains the expression of neighboring genes may be substantially (>2-fold) deregulated at the level of translation.
Collapse
Affiliation(s)
- Artyom A Egorov
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny 141700, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia
| | - Alexander I Alexandrov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,FRC of Biotechnology of the Russian Academy of Sciences, Bach Institute of Biochemistry, Moscow 119071, Russia
| | - Valery N Urakov
- FRC of Biotechnology of the Russian Academy of Sciences, Bach Institute of Biochemistry, Moscow 119071, Russia
| | - Desislava S Makeeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia
| | - Roman O Edakin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Artem S Kushchenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ivan V Kulakovskiy
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| |
Collapse
|
23
|
Zhao T, Vvedenskaya IO, Lai WKM, Basu S, Pugh BF, Nickels BE, Kaplan CD. Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae. eLife 2021; 10:e71013. [PMID: 34652274 PMCID: PMC8589449 DOI: 10.7554/elife.71013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/14/2021] [Indexed: 12/31/2022] Open
Abstract
In Saccharomyces cerevisiae, RNA polymerase II (Pol II) selects transcription start sites (TSSs) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ~40-120 bp downstream. Several lines of evidence indicate that Ssl2, the yeast homolog of XPB and an essential and conserved subunit of the general transcription factor (GTF) TFIIH, drives scanning through its DNA-dependent ATPase activity, therefore potentially controlling both scanning rate and scanning extent (processivity). To address questions of how Ssl2 functions in promoter scanning and interacts with other initiation activities, we leveraged distinct initiation-sensitive reporters to identify novel ssl2 alleles. These ssl2 alleles, many of which alter residues conserved from yeast to human, confer either upstream or downstream TSS shifts at the model promoter ADH1 and genome-wide. Specifically, tested ssl2 alleles alter TSS selection by increasing or narrowing the distribution of TSSs used at individual promoters. Genetic interactions of ssl2 alleles with other initiation factors are consistent with ssl2 allele classes functioning through increasing or decreasing scanning processivity but not necessarily scanning rate. These alleles underpin a residue interaction network that likely modulates Ssl2 activity and TFIIH function in promoter scanning. We propose that the outcome of promoter scanning is determined by two functional networks, the first being Pol II activity and factors that modulate it to determine initiation efficiency within a scanning window, and the second being Ssl2/TFIIH and factors that modulate scanning processivity to determine the width of the scanning widow.
Collapse
Affiliation(s)
- Tingting Zhao
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Irina O Vvedenskaya
- Department of Genetics and Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - William KM Lai
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Shrabani Basu
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Craig D Kaplan
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| |
Collapse
|
24
|
Abstract
Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is frequently observed in human diseases including cancer. In this review, we discuss the breadth of techniques that have been used to globally profile TSSs and the resulting insights into gene regulation, as well as future prospects in this area of inquiry.
Collapse
Affiliation(s)
| | - Gabriel E. Zentner
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
| |
Collapse
|
25
|
Andjus S, Morillon A, Wery M. From Yeast to Mammals, the Nonsense-Mediated mRNA Decay as a Master Regulator of Long Non-Coding RNAs Functional Trajectory. Noncoding RNA 2021; 7:ncrna7030044. [PMID: 34449682 PMCID: PMC8395947 DOI: 10.3390/ncrna7030044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 12/22/2022] Open
Abstract
The Nonsense-Mediated mRNA Decay (NMD) has been classically viewed as a translation-dependent RNA surveillance pathway degrading aberrant mRNAs containing premature stop codons. However, it is now clear that mRNA quality control represents only one face of the multiple functions of NMD. Indeed, NMD also regulates the physiological expression of normal mRNAs, and more surprisingly, of long non-coding (lnc)RNAs. Here, we review the different mechanisms of NMD activation in yeast and mammals, and we discuss the molecular bases of the NMD sensitivity of lncRNAs, considering the functional roles of NMD and of translation in the metabolism of these transcripts. In this regard, we describe several examples of functional micropeptides produced from lncRNAs. We propose that translation and NMD provide potent means to regulate the expression of lncRNAs, which might be critical for the cell to respond to environmental changes.
Collapse
Affiliation(s)
- Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France;
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France
- Correspondence: (A.M.); (M.W.)
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France
- Correspondence: (A.M.); (M.W.)
| |
Collapse
|
26
|
Policastro RA, McDonald DJ, Brendel VP, Zentner GE. Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR. NAR Genom Bioinform 2021; 3:lqab051. [PMID: 34250478 PMCID: PMC8265037 DOI: 10.1093/nargab/lqab051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/29/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
Heterogeneity in transcription initiation has important consequences for transcript stability and translation, and shifts in transcription start site (TSS) usage are prevalent in various developmental, metabolic, and disease contexts. Accordingly, numerous methods for global TSS profiling have been developed, including most recently Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a method to profile transcription start sites (TSSs) on a genome-wide scale with significant cost and time savings compared to previous methods. In anticipation of more widespread adoption of STRIPE-seq and related methods for construction of promoter atlases and studies of differential gene expression, we built TSRexploreR, an R package for end-to-end analysis of TSS mapping data. TSRexploreR provides functions for TSS and transcription start region (TSR) detection, normalization, correlation, visualization, and differential TSS/TSR analyses. TSRexploreR is highly interoperable, accepting the data structures of TSS and TSR sets generated by several existing tools for processing and alignment of TSS mapping data, such as CAGEr for Cap Analysis of Gene Expression (CAGE) data. Lastly, TSRexploreR implements a novel approach for the detection of shifts in TSS distribution.
Collapse
Affiliation(s)
| | - Daniel J McDonald
- Department of Statistics, Indiana University, Bloomington, IN 47405, USA
| | - Volker P Brendel
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
| |
Collapse
|
27
|
Ivanov M, Sandelin A, Marquardt S. TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes. BMC Bioinformatics 2021; 22:290. [PMID: 34058980 PMCID: PMC8166035 DOI: 10.1186/s12859-021-04208-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The quality of gene annotation determines the interpretation of results obtained in transcriptomic studies. The growing number of genome sequence information calls for experimental and computational pipelines for de novo transcriptome annotation. Ideally, gene and transcript models should be called from a limited set of key experimental data. RESULTS We developed TranscriptomeReconstructoR, an R package which implements a pipeline for automated transcriptome annotation. It relies on integrating features from independent and complementary datasets: (i) full-length RNA-seq for detection of splicing patterns and (ii) high-throughput 5' and 3' tag sequencing data for accurate definition of gene borders. The pipeline can also take a nascent RNA-seq dataset to supplement the called gene model with transient transcripts. We reconstructed de novo the transcriptional landscape of wild type Arabidopsis thaliana seedlings and Saccharomyces cerevisiae cells as a proof-of-principle. A comparison to the existing transcriptome annotations revealed that our gene model is more accurate and comprehensive than the most commonly used community gene models, TAIR10 and Araport11 for A.thaliana and SacCer3 for S.cerevisiae. In particular, we identify multiple transient transcripts missing from the existing annotations. Our new annotations promise to improve the quality of A.thaliana and S.cerevisiae genome research. CONCLUSIONS Our proof-of-concept data suggest a cost-efficient strategy for rapid and accurate annotation of complex eukaryotic transcriptomes. We combine the choice of library preparation methods and sequencing platforms with the dedicated computational pipeline implemented in the TranscriptomeReconstructoR package. The pipeline only requires prior knowledge on the reference genomic DNA sequence, but not the transcriptome. The package seamlessly integrates with Bioconductor packages for downstream analysis.
Collapse
Affiliation(s)
- Maxim Ivanov
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiskberg C, Denmark.
| | - Albin Sandelin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiskberg C, Denmark.
| |
Collapse
|
28
|
Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston F. Essential histone chaperones collaborate to regulate transcription and chromatin integrity. Genes Dev 2021; 35:698-712. [PMID: 33888559 PMCID: PMC8091981 DOI: 10.1101/gad.348431.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/30/2021] [Indexed: 12/15/2022]
Abstract
Histone chaperones are critical for controlling chromatin integrity during transcription, DNA replication, and DNA repair. Three conserved and essential chaperones, Spt6, Spn1/Iws1, and FACT, associate with elongating RNA polymerase II and interact with each other physically and/or functionally; however, there is little understanding of their individual functions or their relationships with each other. In this study, we selected for suppressors of a temperature-sensitive spt6 mutation that disrupts the Spt6-Spn1 physical interaction and that also causes both transcription and chromatin defects. This selection identified novel mutations in FACT. Surprisingly, suppression by FACT did not restore the Spt6-Spn1 interaction, based on coimmunoprecipitation, ChIP, and mass spectrometry experiments. Furthermore, suppression by FACT bypassed the complete loss of Spn1. Interestingly, the FACT suppressor mutations cluster along the FACT-nucleosome interface, suggesting that they alter FACT-nucleosome interactions. In agreement with this observation, we showed that the spt6 mutation that disrupts the Spt6-Spn1 interaction caused an elevated level of FACT association with chromatin, while the FACT suppressors reduced the level of FACT-chromatin association, thereby restoring a normal Spt6-FACT balance on chromatin. Taken together, these studies reveal previously unknown regulation between histone chaperones that is critical for their essential in vivo functions.
Collapse
Affiliation(s)
- Olga Viktorovskaya
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - James Chuang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Natalia I Reim
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Francheska López-Rivera
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Magdalena Murawska
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dan Spatt
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
29
|
Villa T, Barucco M, Martin-Niclos MJ, Jacquier A, Libri D. Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription. Cell Rep 2021; 32:107942. [PMID: 32698007 DOI: 10.1016/j.celrep.2020.107942] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/08/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
A large share of the non-coding transcriptome in yeast is controlled by the Nrd1-Nab3-Sen1 (NNS) complex, which promotes transcription termination of non-coding RNA (ncRNA) genes, and by the nuclear exosome, which limits the steady-state levels of the transcripts produced. How unconstrained ncRNA levels affect RNA metabolism and gene expression are long-standing and important questions. Here, we show that degradation of ncRNAs by the exosome is required for freeing Nrd1 and Nab3 from the released transcript after termination. In exosome mutants, these factors are sequestered by ncRNAs and cannot be efficiently recycled to sites of transcription, inducing termination defects at NNS targets. ncRNA-dependent, genome-wide termination defects can be recapitulated by the expression of a degradation-resistant, circular RNA containing a natural NNS target in exosome-proficient cells. Our results have important implications for the mechanism of termination, the general impact of ncRNAs abundance, and the importance of nuclear ncRNA degradation.
Collapse
Affiliation(s)
- Tommaso Villa
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France.
| | - Mara Barucco
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France
| | | | - Alain Jacquier
- Institut Pasteur, Centre National de la Recherche Scientifique, UMR3525 Paris, France
| | - Domenico Libri
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France.
| |
Collapse
|
30
|
Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression. Mol Cell 2021; 81:2231-2245.e11. [PMID: 33826921 PMCID: PMC8153250 DOI: 10.1016/j.molcel.2021.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/05/2021] [Accepted: 03/09/2021] [Indexed: 12/31/2022]
Abstract
Long undecoded transcript isoforms (LUTIs) represent a class of non-canonical mRNAs that downregulate gene expression through the combined act of transcriptional and translational repression. While single gene studies revealed important aspects of LUTI-based repression, how these features affect gene regulation on a global scale is unknown. Using transcript leader and direct RNA sequencing, here, we identify 74 LUTI candidates that are specifically induced in meiotic prophase. Translational repression of these candidates appears to be ubiquitous and is dependent on upstream open reading frames. However, LUTI-based transcriptional repression is variable. In only 50% of the cases, LUTI transcription causes downregulation of the protein-coding transcript isoform. Higher LUTI expression, enrichment of histone 3 lysine 36 trimethylation, and changes in nucleosome position are the strongest predictors of LUTI-based transcriptional repression. We conclude that LUTIs downregulate gene expression in a manner that integrates translational repression, chromatin state changes, and the magnitude of LUTI expression.
Collapse
|
31
|
Zhang H, Lu Z, Zhan Y, Rodriguez J, Lu C, Xue Y, Lin Z. Distinct roles of nucleosome sliding and histone modifications in controlling the fidelity of transcription initiation. RNA Biol 2021; 18:1642-1652. [PMID: 33280509 DOI: 10.1080/15476286.2020.1860389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Regulation of gene expression starts from the transcription initiation. Regulated transcription initiation is critical for generating correct transcripts with proper abundance. The impact of epigenetic control, such as histone modifications and chromatin remodelling, on gene regulation has been extensively investigated, but their specific role in regulating transcription initiation is far from well understood. Here we aimed to better understand the roles of genes involved in histone H3 methylations and chromatin remodelling on the regulation of transcription initiation at a genome-scale using the budding yeast as a study system. We obtained and compared maps of transcription start site (TSS) at single-nucleotide resolution by nAnT-iCAGE for a strain with depletion of MINC (Mot1-Ino80C-Nc2) by Mot1p and Ino80p anchor-away (Mot1&Ino80AA) and a strain with loss of histone methylation (set1Δset2Δdot1Δ) to their wild-type controls. Our study showed that the depletion of MINC stimulated transcription initiation from many new sites flanking the dominant TSS of genes, while the loss of histone methylation generates more TSSs in the coding region. Moreover, the depletion of MINC led to less confined boundaries of TSS clusters (TCs) and resulted in broader core promoters, and such patterns are not present in the ssdΔ mutant. Our data also exhibits that the MINC has distinctive impacts on TATA-containing and TATA-less promoters. In conclusion, our study shows that MINC is required for accurate identification of bona fide TSSs, particularly in TATA-containing promoters, and histone methylation contributes to the repression of transcription initiation in coding regions.
Collapse
Affiliation(s)
- Huiming Zhang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, Missouri, USA
| | - Yu Zhan
- Department of Biology, Saint Louis University, St. Louis, Missouri, USA
| | - Judith Rodriguez
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, Missouri, USA
| | - Chen Lu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Yong Xue
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, Missouri, USA
| |
Collapse
|
32
|
Moretto F, Wood NE, Chia M, Li C, Luscombe NM, van Werven FJ. Transcription levels of a noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast. Cell Rep 2021; 34:108643. [PMID: 33472063 PMCID: PMC7816125 DOI: 10.1016/j.celrep.2020.108643] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 12/21/2022] Open
Abstract
Transcription through noncoding regions of the genome is pervasive. How these transcription events regulate gene expression remains poorly understood. Here, we report that, in S. cerevisiae, the levels of transcription through a noncoding region, IRT2, located upstream in the promoter of the inducer of meiosis, IME1, regulate opposing chromatin and transcription states. At low levels, the act of IRT2 transcription promotes histone exchange, delivering acetylated histone H3 lysine 56 to chromatin locally. The subsequent open chromatin state directs transcription factor recruitment and induces downstream transcription to repress the IME1 promoter and meiotic entry. Conversely, increasing transcription turns IRT2 into a repressor by promoting transcription-coupled chromatin assembly. The two opposing functions of IRT2 transcription shape a regulatory circuit, which ensures a robust cell-type-specific control of IME1 expression and yeast meiosis. Our data illustrate how intergenic transcription levels are key to controlling local chromatin state, gene expression, and cell fate outcomes.
Collapse
Affiliation(s)
- Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece
| | - N Ezgi Wood
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Minghao Chia
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
| | - Cai Li
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan; UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| |
Collapse
|
33
|
Chia M, Li C, Marques S, Pelechano V, Luscombe NM, van Werven FJ. High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Genome Biol 2021; 22:34. [PMID: 33446241 PMCID: PMC7807719 DOI: 10.1186/s13059-020-02245-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely elusive. We perform an integrative analysis of multiple highly synchronized cell-fate transitions and quantitative genomic techniques in Saccharomyces cerevisiae to identify regulatory functions associated with transcribing alternative isoforms. RESULTS Cell-fate transitions feature widespread elevated expression of alternative TSS and, to a lesser degree, TES usage. These dynamically regulated alternative TSSs are located mostly upstream of canonical TSSs, but also within gene bodies possibly encoding for protein isoforms. Increased upstream alternative TSS usage is linked to various effects on canonical TSS levels, which range from co-activation to repression. We identified two key features linked to these outcomes: an interplay between alternative and canonical promoter strengths, and distance between alternative and canonical TSSs. These two regulatory properties give a plausible explanation of how locally transcribed alternative TSSs control gene transcription. Additionally, we find that specific chromatin modifiers Set2, Set3, and FACT play an important role in mediating gene repression via alternative TSSs, further supporting that the act of upstream transcription drives the local changes in gene transcription. CONCLUSIONS The integrative analysis of multiple cell-fate transitions suggests the presence of a regulatory control system of alternative TSSs that is important for dynamic tuning of gene expression. Our work provides a framework for understanding how TSS heterogeneity governs eukaryotic gene expression, particularly during cell-fate changes.
Collapse
Affiliation(s)
- Minghao Chia
- The Francis Crick Institute, London, UK
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Cai Li
- The Francis Crick Institute, London, UK
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sueli Marques
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Vicente Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, 904-0495, Japan
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | | |
Collapse
|
34
|
Chen SY, Osimiri LC, Chevalier M, Bugaj LJ, Nguyen TH, Greenstein RA, Ng AH, Stewart-Ornstein J, Neves LT, El-Samad H. Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics. Cell Syst 2020; 11:336-353.e24. [PMID: 32898473 PMCID: PMC7648432 DOI: 10.1016/j.cels.2020.08.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/08/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023]
Abstract
Gene expression is thought to be affected not only by the concentration of transcription factors (TFs) but also the dynamics of their nuclear translocation. Testing this hypothesis requires direct control of TF dynamics. Here, we engineer CLASP, an optogenetic tool for rapid and tunable translocation of a TF of interest. Using CLASP fused to Crz1, we observe that, for the same integrated concentration of nuclear TF over time, changing input dynamics changes target gene expression: pulsatile inputs yield higher expression than continuous inputs, or vice versa, depending on the target gene. Computational modeling reveals that a dose-response saturating at low TF input can yield higher gene expression for pulsatile versus continuous input, and that multi-state promoter activation can yield the opposite behavior. Our integrated tool development and modeling approach characterize promoter responses to Crz1 nuclear translocation dynamics, extracting quantitative features that may help explain the differential expression of target genes. CLASP is a modular optogenetic strategy to control the nuclear localization of transcription factors (TFs) and elicit gene expression from their cognate promoters. CLASP control of Crz1 nuclear localization, coupled with computational modeling, revealed how promoters can differentially decode dynamic transcription factor signals. The integrated strategy of CLASP development and modeling presents a generalized approach to causally investigate the transcriptional consequences of dynamic TF nuclear shuttling.
Collapse
Affiliation(s)
- Susan Y Chen
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lindsey C Osimiri
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94143, USA
| | - Michael Chevalier
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Taylor H Nguyen
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - R A Greenstein
- Department of Microbiology and Immunology, George Williams Hooper Foundation, Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrew H Ng
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94143, USA; Cell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacob Stewart-Ornstein
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lauren T Neves
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Cell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
35
|
Kornberg RD, Lorch Y. Primary Role of the Nucleosome. Mol Cell 2020; 79:371-375. [PMID: 32763226 DOI: 10.1016/j.molcel.2020.07.020] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 12/16/2019] [Accepted: 03/10/2020] [Indexed: 11/18/2022]
Abstract
Whereas the core nucleosome is thought to serve as a packaging device for the coiling and contraction in length of genomic DNA, we suggest that it serves primarily in the regulation of transcription. A nucleosome on a promoter prevents the initiation of transcription. The association of nucleosomes with most genomic DNA prevents initiation from cryptic promoters. The nucleosome thus serves not only as a general gene repressor, but also as a repressor of all transcription (genic, intragenic, and intergenic). The core nucleosome performs a fundamental regulatory role, apart from the histone "tails," which modulate gene activity.
Collapse
Affiliation(s)
- Roger D Kornberg
- Department of Structural Biology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Yahli Lorch
- Department of Structural Biology, Stanford School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
36
|
Mohaiminul Islam M, Huang S, Ajwad R, Chi C, Wang Y, Hu P. An integrative deep learning framework for classifying molecular subtypes of breast cancer. Comput Struct Biotechnol J 2020; 18:2185-2199. [PMID: 32952934 PMCID: PMC7473884 DOI: 10.1016/j.csbj.2020.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
Classification of breast cancer subtypes using multi-omics profiles is a difficult problem since the data sets are high-dimensional and highly correlated. Deep neural network (DNN) learning has demonstrated advantages over traditional methods as it does not require any hand-crafted features, but rather automatically extract features from raw data and efficiently analyze high-dimensional and correlated data. We aim to develop an integrative deep learning framework for classifying molecular subtypes of breast cancer. We collect copy number alteration and gene expression data measured on the same breast cancer patients from the Molecular Taxonomy of Breast Cancer International Consortium. We propose a deep learning model to integrate the omics datasets for predicting their molecular subtypes. The performance of our proposed DNN model is compared with some baseline models. Furthermore, we evaluate the misclassification of the subtypes using the learned deep features and explore their usefulness for clustering the breast cancer patients. We demonstrate that our proposed integrative deep learning model is superior to other deep learning and non-deep learning based models. Particularly, we get the best prediction result among the deep learning-based integration models when we integrate the two data sources using the concatenation layer in the models without sharing the weights. Using the learned deep features, we identify 6 breast cancer subgroups and show that Her2-enriched samples can be classified into more than one tumor subtype. Overall, the integrated model show better performance than those trained on individual data sources.
Collapse
Affiliation(s)
- Md. Mohaiminul Islam
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada
| | - Shujun Huang
- College of Pharmacy, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada
| | - Rasif Ajwad
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada
| | - Chen Chi
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada
| | - Yang Wang
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada
- Research Institute in Oncology and Hematology, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada
| |
Collapse
|
37
|
Understanding the proteome encoded by "non-coding RNAs": new insights into human genome. SCIENCE CHINA. LIFE SCIENCES 2020; 63:986-995. [PMID: 32318910 DOI: 10.1007/s11427-019-1677-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/12/2020] [Indexed: 01/19/2023]
Abstract
A great number of non-coding RNAs (ncRNAs) account for the majority of the genome. The translation of these ncRNAs has been noted but seriously underestimated due to both technological and theoretical limitations. Based on the development of ribosome profiling (Ribo-seq), full length translating RNA analysis (RNC-seq) and mass spectrometry technology, more and more ncRNAs are being found to be translated in different organism, and some of them can produce functional peptides. While recently, not only individual new functional proteins, but also a new proteome have been experimentally discovered to be encoded by endogenous lncRNAs and circRNAs. These new proteins are of biological significance, suggesting the connection of the translation of ncRNAs to human physiology and diseases. Therefore, an in-depth and systematic understanding of the coding capabilities of ncRNAs is necessary for basic biology and medicine. In this review, we summarize the advances in the field of discovering this new proteome, i.e. "ncRNA-coded" proteins.
Collapse
|
38
|
Fine Chromatin-Driven Mechanism of Transcription Interference by Antisense Noncoding Transcription. Cell Rep 2020; 31:107612. [DOI: 10.1016/j.celrep.2020.107612] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/12/2020] [Accepted: 04/14/2020] [Indexed: 01/04/2023] Open
|
39
|
Wallace EWJ, Maufrais C, Sales-Lee J, Tuck LR, de Oliveira L, Feuerbach F, Moyrand F, Natarajan P, Madhani HD, Janbon G. Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom. Nucleic Acids Res 2020; 48:2312-2331. [PMID: 32020195 PMCID: PMC7049704 DOI: 10.1093/nar/gkaa060] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5' and 3' ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that quantitatively programs both the expression and the structures of proteins in diverse fungi.
Collapse
Affiliation(s)
- Edward W J Wallace
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, UK
| | - Corinne Maufrais
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
- Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015 Paris, France
| | - Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Laura R Tuck
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, UK
| | - Luciana de Oliveira
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| | - Frank Feuerbach
- Institut Pasteur, Unité Génétique des Interactions Macromoléculaire, Département Génome et Génétique, F-75015 Paris, France
| | - Frédérique Moyrand
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| | - Prashanthi Natarajan
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Guilhem Janbon
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| |
Collapse
|
40
|
Kurosaki T, Popp MW, Maquat LE. Quality and quantity control of gene expression by nonsense-mediated mRNA decay. Nat Rev Mol Cell Biol 2020; 20:406-420. [PMID: 30992545 DOI: 10.1038/s41580-019-0126-2] [Citation(s) in RCA: 417] [Impact Index Per Article: 104.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is one of the best characterized and most evolutionarily conserved cellular quality control mechanisms. Although NMD was first found to target one-third of mutated, disease-causing mRNAs, it is now known to also target ~10% of unmutated mammalian mRNAs to facilitate appropriate cellular responses - adaptation, differentiation or death - to environmental changes. Mutations in NMD genes in humans are associated with intellectual disability and cancer. In this Review, we discuss how NMD serves multiple purposes in human cells by degrading both mutated mRNAs to protect the integrity of the transcriptome and normal mRNAs to control the quantities of unmutated transcripts.
Collapse
Affiliation(s)
- Tatsuaki Kurosaki
- 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
| | - Maximilian W Popp
- 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.
| |
Collapse
|
41
|
Foria S, Copetti D, Eisenmann B, Magris G, Vidotto M, Scalabrin S, Testolin R, Cipriani G, Wiedemann-Merdinoglu S, Bogs J, Di Gaspero G, Morgante M. Gene duplication and transposition of mobile elements drive evolution of the Rpv3 resistance locus in grapevine. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:529-542. [PMID: 31571285 DOI: 10.1111/tpj.14551] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 05/08/2023]
Abstract
A wild grape haplotype (Rpv3-1) confers resistance to Plasmopara viticola. We mapped the causal factor for resistance to an interval containing a TIR-NB-LRR (TNL) gene pair that originated 1.6-2.6 million years ago by a tandem segmental duplication. Transient coexpression of the TNL pair in Vitis vinifera leaves activated pathogen-induced necrosis and reduced sporulation compared with control leaves. Even though transcripts of the TNL pair from the wild haplotype appear to be partially subject to nonsense-mediated mRNA decay, mature mRNA levels in a homozygous resistant genotype were individually higher than the mRNA trace levels observed for the orthologous single-copy TNL in sensitive genotypes. Allelic expression imbalance in a resistant heterozygote confirmed that cis-acting regulatory variation promotes expression in the wild haplotype. The movement of transposable elements had a major impact on the generation of haplotype diversity, altering the DNA context around similar TNL coding sequences and the GC-content in their proximal 5'-intergenic regions. The wild and domesticated haplotypes also diverged in conserved single-copy intergenic DNA, but the highest divergence was observed in intraspecific and not in interspecific comparisons. In this case, introgression breeding did not transgress the genetic boundaries of the domesticated species, because haplotypes present in modern varieties sometimes predate speciation events between wild and cultivated species.
Collapse
Affiliation(s)
- Serena Foria
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle scienze 208, 33100, Udine, Italy
| | - Dario Copetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle scienze 208, 33100, Udine, Italy
- Istituto di Genomica Applicata, via Jacopo Linussio 51, 33100, Udine, Italy
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Birgit Eisenmann
- State Education and Research Center of Viticulture, Horticulture and Rural Development, Breitenweg 71, 67435, Neustadt an der Weinstraße, Germany
- Centre for Organismal Studies Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
| | - Gabriele Magris
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle scienze 208, 33100, Udine, Italy
- Istituto di Genomica Applicata, via Jacopo Linussio 51, 33100, Udine, Italy
| | - Michele Vidotto
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle scienze 208, 33100, Udine, Italy
| | - Simone Scalabrin
- Istituto di Genomica Applicata, via Jacopo Linussio 51, 33100, Udine, Italy
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle scienze 208, 33100, Udine, Italy
| | - Guido Cipriani
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle scienze 208, 33100, Udine, Italy
| | | | - Jochen Bogs
- State Education and Research Center of Viticulture, Horticulture and Rural Development, Breitenweg 71, 67435, Neustadt an der Weinstraße, Germany
- Technische Hochschule Bingen, 55411, Bingen am Rhein, Germany
| | | | - Michele Morgante
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle scienze 208, 33100, Udine, Italy
- Istituto di Genomica Applicata, via Jacopo Linussio 51, 33100, Udine, Italy
| |
Collapse
|
42
|
McMillan J, Lu Z, Rodriguez JS, Ahn TH, Lin Z. YeasTSS: an integrative web database of yeast transcription start sites. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5479513. [PMID: 31032841 PMCID: PMC6484093 DOI: 10.1093/database/baz048] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/04/2019] [Accepted: 03/25/2019] [Indexed: 12/22/2022]
Abstract
The transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants that differ in 5' boundaries due to usages of alternative transcription start sites (TSSs), and the abundance of transcript isoforms are highly variable. Due to a large number and complexity of the TSSs, it is not feasible to depict details of transcript initiation landscape of all genes using text-format genome annotation files. Therefore, it is necessary to provide data visualization of TSSs to represent quantitative TSS maps and the core promoters (CPs). In addition, the selection and activity of TSSs are influenced by various factors, such as transcription factors, chromatin remodeling and histone modifications. Thus, integration and visualization of functional genomic data related to these features could provide a better understanding of the gene promoter architecture and regulatory mechanism of transcription initiation. Yeast species play important roles for the research and human society, yet no database provides visualization and integration of functional genomic data in yeast. Here, we generated quantitative TSS maps for 12 important yeast species, inferred their CPs and built a public database, YeasTSS (www.yeastss.org). YeasTSS was designed as a central portal for visualization and integration of the TSS maps, CPs and functional genomic data related to transcription initiation in yeast. YeasTSS is expected to benefit the research community and public education for improving genome annotation, studies of promoter structure, regulated control of transcription initiation and inferring gene regulatory network.
Collapse
Affiliation(s)
- Jonathan McMillan
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Parks College of Engineering, Aviation and Technology, Program in Computer Engineering, Saint Louis University, St. Louis, MO, USA
| | - Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Judith S Rodriguez
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO, USA
| | - Tae-Hyuk Ahn
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO, USA.,Department of Computer Sciences, Saint Louis University, St. Louis, MO, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO, USA
| |
Collapse
|
43
|
Georges A, Gopaul D, Denby Wilkes C, Giordanengo Aiach N, Novikova E, Barrault MB, Alibert O, Soutourina J. Functional interplay between Mediator and RNA polymerase II in Rad2/XPG loading to the chromatin. Nucleic Acids Res 2019; 47:8988-9004. [PMID: 31299084 PMCID: PMC6753472 DOI: 10.1093/nar/gkz598] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/30/2022] Open
Abstract
Transcription and maintenance of genome integrity are fundamental cellular functions. Deregulation of transcription and defects in DNA repair lead to serious pathologies. The Mediator complex links RNA polymerase (Pol) II transcription and nucleotide excision repair via Rad2/XPG endonuclease. However, the functional interplay between Rad2/XPG, Mediator and Pol II remains to be determined. In this study, we investigated their functional dynamics using genomic and genetic approaches. In a mutant affected in Pol II phosphorylation leading to Mediator stabilization on core promoters, Rad2 genome-wide occupancy shifts towards core promoters following that of Mediator, but decreases on transcribed regions together with Pol II. Specific Mediator mutations increase UV sensitivity, reduce Rad2 recruitment to transcribed regions, lead to uncoupling of Rad2, Mediator and Pol II and to colethality with deletion of Rpb9 Pol II subunit involved in transcription-coupled repair. We provide new insights into the functional interplay between Rad2, Mediator and Pol II and propose that dynamic interactions with Mediator and Pol II are involved in Rad2 loading to the chromatin. Our work contributes to the understanding of the complex link between transcription and DNA repair machineries, dysfunction of which leads to severe diseases.
Collapse
Affiliation(s)
- Adrien Georges
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Diyavarshini Gopaul
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cyril Denby Wilkes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Giordanengo Aiach
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Elizaveta Novikova
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie-Bénédicte Barrault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | | | - Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| |
Collapse
|
44
|
Wei W, Hennig BP, Wang J, Zhang Y, Piazza I, Pareja Sanchez Y, Chabbert CD, Adjalley SH, Steinmetz LM, Pelechano V. Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast. Genome Res 2019; 29:1974-1984. [PMID: 31740578 PMCID: PMC6886497 DOI: 10.1101/gr.243378.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/07/2019] [Indexed: 02/06/2023]
Abstract
Cryptic transcription is widespread and generates a heterogeneous group of RNA molecules of unknown function. To improve our understanding of cryptic transcription, we investigated their transcription start site (TSS) usage, chromatin organization, and posttranscriptional consequences in Saccharomyces cerevisiae We show that TSSs of chromatin-sensitive internal cryptic transcripts retain comparable features of canonical TSSs in terms of DNA sequence, directionality, and chromatin accessibility. We define the 5' and 3' boundaries of cryptic transcripts and show that, contrary to RNA degradation-sensitive ones, they often overlap with the end of the gene, thereby using the canonical polyadenylation site, and associate to polyribosomes. We show that chromatin-sensitive cryptic transcripts can be recognized by ribosomes and may produce truncated polypeptides from downstream, in-frame start codons. Finally, we confirm the presence of the predicted polypeptides by reanalyzing N-terminal proteomic data sets. Our work suggests that a fraction of chromatin-sensitive internal cryptic promoters initiates the transcription of alternative truncated mRNA isoforms. The expression of these chromatin-sensitive isoforms is conserved from yeast to human, expanding the functional consequences of cryptic transcription and proteome complexity.
Collapse
Affiliation(s)
- Wu Wei
- Center for Biomedical Informatics, Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
| | - Bianca P Hennig
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Yujie Zhang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Ilaria Piazza
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Yerma Pareja Sanchez
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Christophe D Chabbert
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | | | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany.,Department of Genetics, School of Medicine, Stanford University, Stanford, California 94305, USA
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| |
Collapse
|
45
|
Aliouat A, Hatin I, Bertin P, François P, Stierlé V, Namy O, Salhi S, Jean-Jean O. Divergent effects of translation termination factor eRF3A and nonsense-mediated mRNA decay factor UPF1 on the expression of uORF carrying mRNAs and ribosome protein genes. RNA Biol 2019; 17:227-239. [PMID: 31619139 PMCID: PMC6973328 DOI: 10.1080/15476286.2019.1674595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In addition to its role in translation termination, eRF3A has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with UPF1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbour upstream open reading frames in their 5ʹ leader sequence. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3A or UPF1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3A and UPF1 and to compare the effect of each of these factors on gene expression. We find that eRF3A and UPF1 have very different impacts on the human transcriptome, less than 250 transcripts being targeted by both factors. We show that eRF3A depletion globally derepresses the expression of mRNAs containing translated uORFs while UPF1 knockdown derepresses only the mRNAs harbouring uORFs with an AUG codon in an optimal context for translation initiation. Finally, we also find that eRF3A and UPF1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation.
Collapse
Affiliation(s)
- Affaf Aliouat
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Isabelle Hatin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pierre Bertin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pauline François
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Vérène Stierlé
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Samia Salhi
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Jean-Jean
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| |
Collapse
|
46
|
Soudet J, Stutz F. Regulation of Gene Expression and Replication Initiation by Non‐Coding Transcription: A Model Based on Reshaping Nucleosome‐Depleted Regions. Bioessays 2019; 41:e1900043. [DOI: 10.1002/bies.201900043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/19/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Julien Soudet
- Department of Cell BiologyUniversity of Geneva 1211 Geneva Switzerland
| | - Françoise Stutz
- Department of Cell BiologyUniversity of Geneva 1211 Geneva Switzerland
| |
Collapse
|
47
|
Soulette CM, Oliverio O, Roy SW. On the Function of Trans-Splicing: No Evidence for Widespread Proteome Diversification in Trypanosomes. Genome Biol Evol 2019; 11:3014-3021. [PMID: 31599940 PMCID: PMC6821157 DOI: 10.1093/gbe/evz217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 11/24/2022] Open
Abstract
A long-standing mystery of genomic/transcriptomic structure involves spliced leader trans-splicing (SLTS), in which short RNA “tags” transcribed from a distinct genomic locus is added near the 5′ end of RNA transcripts by the spliceosome. SLTS has been observed in diverse eukaryotes in a phylogenetic pattern implying recurrent independent evolution. This striking convergence suggests important functions for SLTS, however no general novel function is known. Recent findings of frequent alternative SLTS (ALT-TS) suggest that ALT-TS could impart widespread functionality. Here, we tested the hypothesis that ALT-TS diversifies proteomes by comparing splicing patterns in orthologous genes between two deeply diverged trypanosome parasites. We also tested proteome diversification functions of ALT-TS by utilizing ribosome profiling sequence data. Finally, we investigated ALT-TS as a mechanism to regulate the expression of unproductive transcripts. Although our results indicate the functional importance of some cases of trans-splicing, we find no evidence for the hypothesis that proteome diversification is a general function of trans-splicing.
Collapse
Affiliation(s)
- Cameron M Soulette
- Department of Biology, San Francisco State University.,Molecular, Cellular & Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA
| | | | - Scott W Roy
- Department of Biology, San Francisco State University.,Quantitative Systems Biology, University of California, Merced
| |
Collapse
|
48
|
Kubik S, Bruzzone MJ, Challal D, Dreos R, Mattarocci S, Bucher P, Libri D, Shore D. Opposing chromatin remodelers control transcription initiation frequency and start site selection. Nat Struct Mol Biol 2019; 26:744-754. [PMID: 31384063 DOI: 10.1038/s41594-019-0273-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/28/2019] [Indexed: 12/31/2022]
Abstract
Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome occupancy following rapid remodeler depletion, we investigated the interplay between these enzymes and their impact on transcription in yeast. We show that many promoters are affected by multiple CRs that operate in concert or in opposition to position the key transcription start site (TSS)-associated +1 nucleosome. We also show that nucleosome movement after CR inactivation usually results from the activity of another CR and that in the absence of any remodeling activity, +1 nucleosomes largely maintain their positions. Finally, we present functional assays suggesting that +1 nucleosome positioning often reflects a trade-off between maximizing RNA polymerase recruitment and minimizing transcription initiation at incorrect sites. Our results provide a detailed picture of fundamental mechanisms linking promoter nucleosome architecture to transcription initiation.
Collapse
Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Drice Challal
- Institut Jacques Monod, CNRS-Université Paris Diderot, Paris, France
| | - René Dreos
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stefano Mattarocci
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Philipp Bucher
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Domenico Libri
- Institut Jacques Monod, CNRS-Université Paris Diderot, Paris, France
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland.
| |
Collapse
|
49
|
Nevers A, Doyen A, Malabat C, Néron B, Kergrohen T, Jacquier A, Badis G. Antisense transcriptional interference mediates condition-specific gene repression in budding yeast. Nucleic Acids Res 2019; 46:6009-6025. [PMID: 29788449 PMCID: PMC6158615 DOI: 10.1093/nar/gky342] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/23/2018] [Indexed: 12/20/2022] Open
Abstract
Pervasive transcription generates many unstable non-coding transcripts in budding yeast. The transcription of such noncoding RNAs, in particular antisense RNAs (asRNAs), has been shown in a few examples to repress the expression of the associated mRNAs. Yet, such mechanism is not known to commonly contribute to the regulation of a given class of genes. Using a mutant context that stabilized pervasive transcripts, we observed that the least expressed mRNAs during the exponential phase were associated with high levels of asRNAs. These asRNAs also overlapped their corresponding gene promoters with a much higher frequency than average. Interrupting antisense transcription of a subset of genes corresponding to quiescence-enriched mRNAs restored their expression. The underlying mechanism acts in cis and involves several chromatin modifiers. Our results convey that transcription interference represses up to 30% of the 590 least expressed genes, which includes 163 genes with quiescence-enriched mRNAs. We also found that pervasive transcripts constitute a higher fraction of the transcriptome in quiescence relative to the exponential phase, consistent with gene expression itself playing an important role to suppress pervasive transcription. Accordingly, the HIS1 asRNA, normally only present in quiescence, is expressed in exponential phase upon HIS1 mRNA transcription interruption.
Collapse
Affiliation(s)
- Alicia Nevers
- Unité GIM, Institut Pasteur, Paris, France.,Sorbonne Université Pierre et Marie Curie, Paris, France
| | | | - Christophe Malabat
- Unité GIM, Institut Pasteur, Paris, France.,Bioinformatics and Biostatistics Hub, C3BI, Institut Pasteur, USR 3756 IP CNRS, Paris, France
| | - Bertrand Néron
- Bioinformatics and Biostatistics Hub, C3BI, Institut Pasteur, USR 3756 IP CNRS, Paris, France
| | | | - Alain Jacquier
- Unité GIM, Institut Pasteur, Paris, France.,CNRS UMR3525, Paris, France
| | - Gwenael Badis
- Unité GIM, Institut Pasteur, Paris, France.,CNRS UMR3525, Paris, France
| |
Collapse
|
50
|
Wu AC, Van Werven FJ. Transcribe this way: Rap1 confers promoter directionality by repressing divergent transcription. Transcription 2019; 10:164-170. [PMID: 31057041 PMCID: PMC6602560 DOI: 10.1080/21541264.2019.1608716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/11/2019] [Accepted: 04/13/2019] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, divergent transcription is a major source of noncoding RNAs. Recent studies have uncovered that in yeast, the transcription factor Rap1 restricts transcription in the divergent direction and thereby controls promoter directionality. Here, we summarize these findings, propose regulatory principles, and discuss the implications for eukaryotic gene regulation.
Collapse
Affiliation(s)
- Andrew C.K. Wu
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | | |
Collapse
|