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Morgenstern E, Kretz M. The human long non-coding RNA LINC00941 and its modes of action in health and disease. Biol Chem 2023; 404:1025-1036. [PMID: 37418674 DOI: 10.1515/hsz-2023-0183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
Long non-coding RNAs have gained attention in recent years as they were shown to play crucial roles in the regulation of cellular processes, but the understanding of the exact mechanisms is still incomplete in most cases. This is also true for long non-coding RNA LINC00941, which was recently found to be highly upregulated in various types of cancer influencing cell proliferation and metastasis. Initial studies could not elucidate the mode of action to understand the role and real impact of LINC00941 in tissue homeostasis and cancer development. However, recent analyses have demonstrated multiple potential modes of action of LINC00941 influencing the functionality of various cancer cell types. Correspondingly, LINC00941 was proposed to be involved in regulation of mRNA transcription and modulation of protein stability, respectively. In addition, several experimental approaches suggest a function of LINC00941 as competitive endogenous RNA, thus acting in a post-transcriptional regulatory fashion. This review summarizes our recent knowledge about the mechanisms of action of LINC00941 elucidated so far and discusses its putative role in miRNA sequestering processes. In addition, the functional role of LINC00941 in regulating human keratinocytes is discussed to also highlight its role in normal tissue homeostasis tissue aside from its involvement in cancer.
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Affiliation(s)
- Eva Morgenstern
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
| | - Markus Kretz
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
- Institute for Molecular Medicine, MSH Medical School Hamburg, 20457 Hamburg, Germany
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2
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 407] [Impact Index Per Article: 407.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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3
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Pecori R, Chillón I, Lo Giudice C, Arnold A, Wüst S, Binder M, Marcia M, Picardi E, Papavasiliou FN. ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts. Front Cell Dev Biol 2023; 10:1080626. [PMID: 36684421 PMCID: PMC9852825 DOI: 10.3389/fcell.2022.1080626] [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: 10/26/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Despite hundreds of RNA modifications described to date, only RNA editing results in a change in the nucleotide sequence of RNA molecules compared to the genome. In mammals, two kinds of RNA editing have been described so far, adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. Recent improvements in RNA sequencing technologies have led to the discovery of a continuously growing number of editing sites. These methods are powerful but not error-free, making routine validation of newly-described editing sites necessary. During one of these validations on DDX58 mRNA, along with A-to-I RNA editing sites, we encountered putative U-to-C editing. These U-to-C edits were present in several cell lines and appeared regulated in response to specific environmental stimuli. The same findings were also observed for the human long intergenic non-coding RNA p21 (hLincRNA-p21). A more in-depth analysis revealed that putative U-to-C edits result from A-to-I editing on overlapping antisense RNAs that are transcribed from the same loci. Such editing events, occurring on overlapping genes transcribed in opposite directions, have recently been demonstrated to be immunogenic and have been linked with autoimmune and immune-related diseases. Our findings, also confirmed by deep transcriptome data, demonstrate that such loci can be recognized simply through the presence of A-to-I and U-to-C mismatches within the same locus, reflective A-to-I editing both in the sense-oriented transcript and in the cis-natural antisense transcript (cis-NAT), implying that such clusters could be a mark of functionally relevant ADAR1 editing events.
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Affiliation(s)
- Riccardo Pecori
- Division of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, Germany,Helmholtz Institute for Translational Oncology (HI-TRON), Mainz, Germany,*Correspondence: Riccardo Pecori, ; Fotini Nina Papavasiliou,
| | - Isabel Chillón
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Claudio Lo Giudice
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, Italy
| | - Annette Arnold
- Division of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, Germany
| | - Sandra Wüst
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response,” German Cancer Research Centre (DKFZ), Research Program Infection, Inflammation and Cancer, Division Virus Associated Carcinogenesis (F170), Heidelberg, Germany
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response,” German Cancer Research Centre (DKFZ), Research Program Infection, Inflammation and Cancer, Division Virus Associated Carcinogenesis (F170), Heidelberg, Germany
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Ernesto Picardi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, Italy
| | - Fotini Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, Germany,*Correspondence: Riccardo Pecori, ; Fotini Nina Papavasiliou,
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Scharf I, Stoldt M, Libbrecht R, Höpfner AL, Jongepier E, Kever M, Foitzik S. Social isolation causes downregulation of immune and stress response genes and behavioural changes in a social insect. Mol Ecol 2021; 30:2378-2389. [PMID: 33772940 DOI: 10.1111/mec.15902] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 12/27/2022]
Abstract
Humans and other social mammals experience isolation from their group as stressful, triggering behavioural and physiological anomalies that reduce fitness. While social isolation has been intensely studied in social mammals, it is less clear how social insects, which evolved sociality independently, respond to isolation. Here we examined whether the typical mammalian responses to social isolation, e.g., an impaired ability to interact socially and immune suppression are also found in social insects. We studied the consequences of social isolation on behaviour and brain gene expression in the ant Temnothorax nylanderi. Following isolation, workers interacted moderately less with adult nestmates, increased the duration of brood contact, and reduced the time spent self-grooming, an important sanitary behaviour. Our brain transcriptome analysis revealed that only a few behaviour-related genes had altered their expression with isolation time. Rather, many genes linked to immune system functioning and stress response had been downregulated. This probably sensitizes isolated individuals to various stressors, in particular because isolated workers exhibit reduced sanitary behaviour. We provide evidence of the diverse consequences of social isolation in social insects, some of which resemble those found in social mammals, suggesting a general link between social well-being, stress tolerance, and immune competence in social animals.
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Affiliation(s)
- Inon Scharf
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Marah Stoldt
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Romain Libbrecht
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Anna Lena Höpfner
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Evelien Jongepier
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Marion Kever
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Susanne Foitzik
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
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5
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Bergalet J, Patel D, Legendre F, Lapointe C, Benoit Bouvrette LP, Chin A, Blanchette M, Kwon E, Lécuyer E. Inter-dependent Centrosomal Co-localization of the cen and ik2 cis-Natural Antisense mRNAs in Drosophila. Cell Rep 2021; 30:3339-3352.e6. [PMID: 32160541 DOI: 10.1016/j.celrep.2020.02.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 12/24/2019] [Accepted: 02/10/2020] [Indexed: 11/30/2022] Open
Abstract
Overlapping genes are prevalent in most genomes, but the extent to which this organization influences regulatory events operating at the post-transcriptional level remains unclear. Studying the cen and ik2 genes of Drosophila melanogaster, which are convergently transcribed as cis-natural antisense transcripts (cis-NATs) with overlapping 3' UTRs, we found that their encoded mRNAs strikingly co-localize to centrosomes. These transcripts physically interact in a 3' UTR-dependent manner, and the targeting of ik2 requires its 3' UTR sequence and the presence of cen mRNA, which serves as the main driver of centrosomal co-localization. The cen transcript undergoes localized translation in proximity to centrosomes, and its localization is perturbed by polysome-disrupting drugs. By interrogating global fractionation-sequencing datasets generated from Drosophila and human cellular models, we find that RNAs expressed as cis-NATs tend to co-localize to specific subcellular fractions. This work suggests that post-transcriptional interactions between RNAs with complementary sequences can dictate their localization fate in the cytoplasm.
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Affiliation(s)
- Julie Bergalet
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Dhara Patel
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Félix Legendre
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Catherine Lapointe
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Louis Philip Benoit Bouvrette
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Ashley Chin
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | | | - Eunjeong Kwon
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
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6
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Li Y, Li X, Yang J, He Y. Natural antisense transcripts of MIR398 genes suppress microR398 processing and attenuate plant thermotolerance. Nat Commun 2020; 11:5351. [PMID: 33093449 PMCID: PMC7582911 DOI: 10.1038/s41467-020-19186-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) and natural antisense transcripts (NATs) control many biological processes and have been broadly applied for genetic manipulation of eukaryotic gene expression. Still unclear, however, are whether and how NATs regulate miRNA production. Here, we report that the cis-NATs of MIR398 genes repress the processing of their pri-miRNAs. Through genome-wide analysis of RNA sequencing data, we identify cis-NATs of MIRNA genes in Arabidopsis and Brassica. In Arabidopsis, MIR398b and MIR398c are coexpressed in vascular tissues with their antisense genes NAT398b and NAT398c, respectively. Knock down of NAT398b and NAT398c promotes miR398 processing, resulting in stronger plant thermotolerance owing to silencing of miR398-targeted genes; in contrast, their overexpression activates NAT398b and NAT398c, causing poorer thermotolerance due to the upregulation of miR398-targeted genes. Unexpectedly, overexpression of MIR398b and MIR398c activates NAT398b and NAT398c. Taken together, these results suggest that NAT398b/c repress miR398 biogenesis and attenuate plant thermotolerance via a regulatory loop. MiRNAs and natural antisense transcripts can both regulate gene expression and plant development. Here, the authors show that cis-NATs to MIR398 repress processing of pri-miR398 and that cis-NAT expression is downregulated at high temperatures, contributing to miR398 mediated thermotolerance responses.
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Affiliation(s)
- Yajie Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.,University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaorong Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.,University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.
| | - Yuke He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.
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Rosikiewicz W, Suzuki Y, Makalowska I. OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes. Nucleic Acids Res 2019; 46:D186-D193. [PMID: 29069459 PMCID: PMC5753363 DOI: 10.1093/nar/gkx948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/20/2017] [Indexed: 01/24/2023] Open
Abstract
Gene overlap plays various regulatory functions on transcriptional and post-transcriptional levels. Most current studies focus on protein-coding genes overlapping with non-protein-coding counterparts, the so called natural antisense transcripts. Considerably less is known about the role of gene overlap in the case of two protein-coding genes. Here, we provide OverGeneDB, a database of human and mouse 5′ end protein-coding overlapping genes. The database contains 582 human and 113 mouse gene pairs that are transcribed using overlapping promoters in at least one analyzed library. Gene pairs were identified based on the analysis of the transcription start site (TSS) coordinates in 73 human and 10 mouse organs, tissues and cell lines. Beside TSS data, resources for 26 human lung adenocarcinoma cell lines also contain RNA-Seq and ChIP-Seq data for seven histone modifications and RNA Polymerase II activity. The collected data revealed that the overlap region is rarely conserved between the studied species and tissues. In ∼50% of the overlapping genes, transcription started explicitly in the overlap regions. In the remaining half of overlapping genes, transcription was initiated both from overlapping and non-overlapping TSSs. OverGeneDB is accessible at http://overgenedb.amu.edu.pl.
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Affiliation(s)
- Wojciech Rosikiewicz
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-712 Poznan, Poland
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 272-8562, Japan
| | - Izabela Makalowska
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-712 Poznan, Poland
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Qian X, Zhao J, Yeung PY, Zhang QC, Kwok CK. Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches. Trends Biochem Sci 2018; 44:33-52. [PMID: 30459069 DOI: 10.1016/j.tibs.2018.09.012] [Citation(s) in RCA: 290] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 11/28/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as significant players in almost every level of gene function and regulation. Thus, characterizing the structures and interactions of lncRNAs is essential for understanding their mechanistic roles in cells. Through a combination of (bio)chemical approaches and automated capillary and high-throughput sequencing (HTS), the complexity and diversity of RNA structures and interactions has been revealed in the transcriptomes of multiple species. These methods have uncovered important biological insights into the mechanistic and functional roles of lncRNA in gene expression and RNA metabolism, as well as in development and disease. In this review, we summarize the latest sequencing strategies to reveal RNA structure, RNA-RNA, RNA-DNA, and RNA-protein interactions, and highlight the recent applications of these approaches to map functional lncRNAs. We discuss the advantages and limitations of these strategies, and provide recommendations to further advance methodologies capable of mapping RNA structure and interactions in order to discover new biology of lncRNAs and decipher their molecular mechanisms and implication in diseases.
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Affiliation(s)
- Xingyang Qian
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; These authors contributed equally to this work
| | - Jieyu Zhao
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; These authors contributed equally to this work
| | - Pui Yan Yeung
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; These authors contributed equally to this work
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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Jung J, Lee S, Cho HS, Park K, Ryu JW, Jung M, Kim J, Kim H, Kim DS. Bioinformatic analysis of regulation of natural antisense transcripts by transposable elements in human mRNA. Genomics 2018; 111:159-166. [PMID: 29366860 DOI: 10.1016/j.ygeno.2018.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/19/2022]
Abstract
Non-coding RNA is no longer considered to be "junk" DNA, based on evidence uncovered in recent decades. In particular, the important role played by natural antisense transcripts (NATs) in regulating the expression of genes is receiving increasing attention. However, the regulatory mechanisms of NATs remain incompletely understood. It is well-known that the insertion of transposable elements (TEs) can affect gene transcription. Using a bioinformatics approach, we identified NATs using human mRNA sequences from the UCSC Genome Browser Database. Our in silico analysis identified 1079 NATs and 700 sense-antisense gene pairs. We identified 179 NATs that showed evidence of having been affected by TEs during cellular gene expression. These findings may provide an understanding of the complex regulation mechanisms of NATs. If our understanding of NATs as modulators of gene expression is further enhanced, we can develop ways to control gene expression.
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Affiliation(s)
- Jaeeun Jung
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sugi Lee
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyun-Soo Cho
- Department of Stem Cell Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Kunhyang Park
- Department of Core Facility Management Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jea-Woon Ryu
- Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Minah Jung
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jeongkil Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - HyeRan Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Plant Systems Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Dae-Soo Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea.
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Matsui A, Iida K, Tanaka M, Yamaguchi K, Mizuhashi K, Kim JM, Takahashi S, Kobayashi N, Shigenobu S, Shinozaki K, Seki M. Novel Stress-Inducible Antisense RNAs of Protein-Coding Loci Are Synthesized by RNA-Dependent RNA Polymerase. PLANT PHYSIOLOGY 2017; 175:457-472. [PMID: 28710133 PMCID: PMC5580770 DOI: 10.1104/pp.17.00787] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/12/2017] [Indexed: 05/03/2023]
Abstract
Our previous study identified approximately 6,000 abiotic stress-responsive noncoding transcripts existing on the antisense strand of protein-coding genes and implied that a type of antisense RNA was synthesized from a sense RNA template by RNA-dependent RNA polymerase (RDR). Expression analyses revealed that the expression of novel abiotic stress-induced antisense RNA on 1,136 gene loci was reduced in the rdr1/2/6 mutants. RNase protection indicated that the RD29A antisense RNA and other RDR1/2/6-dependent antisense RNAs are involved in the formation of dsRNA. The accumulation of stress-inducible antisense RNA was decreased and increased in dcp5 and xrn4, respectively, but not changed in dcl2/3/4, nrpd1a and nrpd1b RNA-seq analyses revealed that the majority of the RDR1/2/6-dependent antisense RNA loci did not overlap with RDR1/2/6-dependent 20-30 nt RNA loci. Additionally, rdr1/2/6 mutants decreased the degradation rate of the sense RNA and exhibited arrested root growth during the recovery stage following a drought stress, whereas dcl2/3/4 mutants did not. Collectively, these results indicate that RDRs have stress-inducible antisense RNA synthesis activity and a novel biological function that is different from the known endogenous small RNA pathways from protein-coding genes. These data reveal a novel mechanism of RNA regulation during abiotic stress response that involves complex RNA degradation pathways.
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Affiliation(s)
- Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kei Iida
- Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Kayoko Mizuhashi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Satoshi Takahashi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Norio Kobayashi
- Computational Engineering Applications Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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12
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Targeting long non-coding RNA ASBEL with oligonucleotide antagonist for breast cancer therapy. Biochem Biophys Res Commun 2017; 489:386-392. [PMID: 28552529 DOI: 10.1016/j.bbrc.2017.05.136] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/23/2017] [Indexed: 01/03/2023]
Abstract
Long non-coding RNAs (lncRNAs) are defined as a class of RNA transcripts longer than 200 nucleotides encoded by mammalian genomes that lack protein-coding potential. LncRNA ASBEL has been identified as an anti-sense transcript of BTG3 (B cell translocation gene 3) gene, which encodes an anti-proliferation protein. Remarkable down-regulation of BTG3 has been reported in triple-negative breast cancer (TNBC). In the present study, a number of single-stranded modified anti-sense DNA oligonucleotides (antago) were designed, synthesized and screened for specific lncRNA ASBEL knockdown. We showed here that anti-ASBEL antago played a significant tumor suppressive role in TNBC by effective down-regulating lncRNA ASBEL, which in turn led to increased BTG3 expression. The obtained data suggest lncRNA ASBEL as a novel therapeutic target in TNBC.
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Abstract
The recognition of functional roles for transcribed long non-coding RNA (lncRNA) has provided a new dimension to our understanding of cellular physiology and disease pathogenesis. LncRNAs are a large group of structurally complex RNA genes that can interact with DNA, RNA, or protein molecules to modulate gene expression and to exert cellular effects through diverse mechanisms. The emerging knowledge regarding their functional roles and their aberrant expression in disease states emphasizes the potential for lncRNA to serve as targets for therapeutic intervention. In this concise review, we outline the mechanisms of action of lncRNAs, their functional cellular roles, and their involvement in disease. Using liver cancer as an example, we provide an overview of the emerging opportunities and potential approaches to target lncRNA-dependent mechanisms for therapeutic purposes.
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Lin S, Zhang L, Luo W, Zhang X. Characteristics of Antisense Transcript Promoters and the Regulation of Their Activity. Int J Mol Sci 2015; 17:E9. [PMID: 26703594 PMCID: PMC4730256 DOI: 10.3390/ijms17010009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/23/2015] [Accepted: 12/16/2015] [Indexed: 02/07/2023] Open
Abstract
Recently, an increasing number of studies on natural antisense transcripts have been reported, especially regarding their classification, temporal and spatial expression patterns, regulatory functions and mechanisms. It is well established that natural antisense transcripts are produced from the strand opposite to the strand encoding a protein. Despite the pivotal roles of natural antisense transcripts in regulating the expression of target genes, the transcriptional mechanisms initiated by antisense promoters (ASPs) remain unknown. To date, nearly all of the studies conducted on this topic have focused on the ASP of a single gene of interest, whereas no study has systematically analyzed the locations of ASPs in the genome, ASP activity, or factors influencing this activity. This review focuses on elaborating on and summarizing the characteristics of ASPs to extend our knowledge about the mechanisms of antisense transcript initiation.
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Affiliation(s)
- Shudai Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Li Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
- Agricultural College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
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Yu X, Yang J, Li X, Liu X, Sun C, Wu F, He Y. Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa. BMC PLANT BIOLOGY 2013; 13:208. [PMID: 24320882 PMCID: PMC4029752 DOI: 10.1186/1471-2229-13-208] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 12/05/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND Brassica rapa includes several important leaf vegetable crops whose production is often damaged by high temperature. Cis-natural antisense transcripts (cis-NATs) and cis-NATs-derived small interfering RNAs (nat-siRNAs) play important roles in plant development and stress responses. However, genome-wide cis-NATs in B. rapa are not known. The NATs and nat-siRNAs that respond to heat stress have never been well studied in B. rapa. Here, we took advantage of RNA-seq and small RNA (sRNA) deep sequencing technology to identify cis-NATs and heat responsive nat-siRNAs in B. rapa. RESULTS Analyses of four RNA sequencing datasets revealed 1031 cis-NATs B. rapa ssp. chinensis cv Wut and B. rapa ssp. pekinensis cv. Bre. Based on sequence homology between Arabidopsis thaliana and B. rapa, 303 conserved cis-NATs in B. rapa were found to correspond to 280 cis-NATs in Arabidopsis; the remaining 728 novel cis-NATs were identified as Brassica-specific ones. Using six sRNA libraries, 4846 nat-siRNAs derived from 150 cis-NATs were detected. Differential expression analysis revealed that nat-siRNAs derived from 12 cis-NATs were responsive to heat stress, and most of them showed strand bias. Real-time PCR indicated that most of the transcripts generating heat-responsive nat-siRNAs were upregulated under heat stress, while the transcripts from the opposite strands of the same loci were downregulated. CONCLUSIONS Our results provide the first subsets of genome-wide cis-NATs and heat-responsive nat-siRNAs in B. rapa; these sRNAs are potentially useful for the genetic improvement of heat tolerance in B. rapa and other crops.
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Affiliation(s)
- Xiang Yu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Xiaorong Li
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Xuxin Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Chuanbao Sun
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Feijie Wu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Yuke He
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol 2013; 14:699-712. [PMID: 24105322 DOI: 10.1038/nrm3679] [Citation(s) in RCA: 1106] [Impact Index Per Article: 100.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The increased application of transcriptome-wide profiling approaches has led to an explosion in the number of documented long non-coding RNAs (lncRNAs). While these new and enigmatic players in the complex transcriptional milieu are encoded by a significant proportion of the genome, their functions are mostly unknown. Early discoveries support a paradigm in which lncRNAs regulate transcription via chromatin modulation, but new functions are steadily emerging. Given the biochemical versatility of RNA, lncRNAs may be used for various tasks, including post-transcriptional regulation, organization of protein complexes, cell-cell signalling and allosteric regulation of proteins.
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18
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Wood EJ, Chin-Inmanu K, Jia H, Lipovich L. Sense-antisense gene pairs: sequence, transcription, and structure are not conserved between human and mouse. Front Genet 2013; 4:183. [PMID: 24133500 PMCID: PMC3783845 DOI: 10.3389/fgene.2013.00183] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/29/2013] [Indexed: 01/25/2023] Open
Abstract
Previous efforts to characterize conservation between the human and mouse genomes focused largely on sequence comparisons. These studies are inherently limited because they don't account for gene structure differences, which may exist despite genomic sequence conservation. Recent high-throughput transcriptome studies have revealed widespread and extensive overlaps between genes, and transcripts, encoded on both strands of the genomic sequence. This overlapping gene organization, which produces sense-antisense (SAS) gene pairs, is capable of effecting regulatory cascades through established mechanisms. We present an evolutionary conservation assessment of SAS pairs, on three levels: genomic, transcriptomic, and structural. From a genome-wide dataset of human SAS pairs, we first identified orthologous loci in the mouse genome, then assessed their transcription in the mouse, and finally compared the genomic structures of SAS pairs expressed in both species. We found that approximately half of human SAS loci have single orthologous locations in the mouse genome; however, only half of those orthologous locations have SAS transcriptional activity in the mouse. This suggests that high human-mouse gene conservation overlooks widespread distinctions in SAS pair incidence and expression. We compared gene structures at orthologous SAS loci, finding frequent differences in gene structure between human and orthologous mouse SAS pair members. Our categorization of human SAS pairs with respect to mouse conservation of expression as well as structure points to limitations of mouse models. Gene structure differences, including at SAS loci, may account for some of the phenotypic distinctions between primates and rodents. Genes in non-conserved SAS pairs may contribute to evolutionary lineage-specific regulatory outcomes.
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Affiliation(s)
- Emily J Wood
- Center for Molecular Medicine and Genetics, Wayne State University Detroit, MI, USA
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19
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ADAR-mediated RNA editing in non-coding RNA sequences. SCIENCE CHINA-LIFE SCIENCES 2013; 56:944-52. [DOI: 10.1007/s11427-013-4546-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 08/20/2013] [Indexed: 12/22/2022]
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20
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ASBEL, an ANA/BTG3 antisense transcript required for tumorigenicity of ovarian carcinoma. Sci Rep 2013; 3:1305. [PMID: 23419616 PMCID: PMC3575586 DOI: 10.1038/srep01305] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 01/22/2013] [Indexed: 12/18/2022] Open
Abstract
Mammalian genomes encode numerous antisense non-coding RNAs, which are assumed to be involved in the regulation of the sense gene expression. However, the mechanisms of their action and involvement in the development of diseases have not been well elucidated. The ANA/BTG3 protein is an antiproliferative protein whose expression is downregulated in prostate and lung cancers. Here we show that an antisense transcript of the ANA/BTG3 gene, termed ASBEL, negatively regulates the levels of ANA/BTG3 protein, but not of ANA/BTG3 mRNA and is required for proliferation and tumorigenicity of ovarian clear cell carcinoma. We further show that knockdown of ANA/BTG3 rescues growth inhibition caused by ASBEL knockdown. Moreover, we demonstrate that ASBEL forms duplexes with ANA/BTG3 mRNA in the nucleus and suppresses its cytoplasmic transportation. Our findings illustrate a novel function for an antisense transcript that critically promotes tumorigenesis by suppressing translation of the sense gene by inhibiting its cytoplasmic transportation.
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21
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Chen J, Yang JT, Doctor DL, Rawlins BA, Shields BC, Vaughn JC. 5'-UTR mediated translational control of splicing assembly factor RNP-4F expression during development of the Drosophila central nervous system. Gene 2013; 528:154-62. [PMID: 23892091 DOI: 10.1016/j.gene.2013.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 07/17/2013] [Indexed: 11/24/2022]
Abstract
Drosophila RNP-4F is a highly conserved protein from yeast to human and functions as a spliceosome assembly factor during pre-mRNA splicing. Two major developmentally regulated rnp-4f mRNA isoforms have been described during fly development, designated "long" and "short," differing by a 177-nt tract in the 5'-UTR. This region potentially folds into a single long stable stem-loop by pairing of intron 0 and part of exon 2. Since the coding potential for the two isoforms is identical, the interesting question arises as to the functional significance of this evolutionarily-conserved 5'-UTR feature. Here we describe the effects of wild-type and mutated stem-loop on modulation of rnp-4f gene expression in embryos using a GFP reporter assay. In this work, a new GFP expression vector designated pUAS-Neostinger was constructed. The UAS-GAL4 system was utilized to trigger GFP expression using tissue-specific promoter driver fly lines. Fluorescence microscopy visualization, Western blotting and real-time qRT-PÇR were used to study and quantify GFP reporter protein and mRNA levels. A significant increase in GFP reporter protein expression due to presence of the wild-type stem-loop sequence/structure was unexpectedly observed with no concomitant increase in GFP reporter mRNA levels, showing that the 177-nt region enhancement acts posttranscriptionally. The effects of potential cis-acting elements within the stem-loop were evaluated using the reporter assay in two mutant constructs. Results of GFP reporter over-expression show that RNP-4F translational regulation is highly sensitive in the developing fly central nervous system. The potential molecular mechanism behind the observed translational enhancement is discussed.
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Affiliation(s)
- Jing Chen
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
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22
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Ghosh S, Wang Y, Cook JA, Chhiba L, Vaughn JC. A molecular, phylogenetic and functional study of the dADAR mRNA truncated isoform during Drosophila embryonic development reveals an editing-independent function. ACTA ACUST UNITED AC 2013; 3:20-30. [PMID: 25414802 PMCID: PMC4235677 DOI: 10.4236/ojas.2013.34a2003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Adenosine Deaminases Acting on RNA (ADARs) have been studied in many animal phyla, where they have been shown to deaminate specific adenosines into inosines in duplex mRNA regions. In Drosophila, two isoform classes are encoded, designated full-length (contains the editase domain) and truncated (lacks this domain). Much is known about the full-length isoform, which plays a major role in regulating functions of voltage-gated ion channel proteins in the adult brain. In contrast, almost nothing is known about the functional significance of the truncated isoform. In situ hybridization shows that both isoform mRNA classes are maternally derived and transcripts for both localize primarily to the developing central nervous system. Quantitative RT-PCR shows that about 35% of all dADAR mRNA transcripts belong to the truncated class in embryos. 3′-RACE results show that abundance of the truncated isoform class is developmentally regulated, with a longer transcript appearing after the mid-blastula transition. 3′-UTR sequences for the truncated isoform have been determined from diverse Drosophila species and important regulatory regions including stop codons have been mapped. Western analysis shows that both mRNA isoform classes are translated into protein during embryonic development, as full-length variant levels gradually diminish. The truncated protein isoform is present in every Drosophila species studied, extending over a period spanning about 40 × 106 years, implying a conserved function. Previous work has shown that a dADAR protein isoform binds to the evolutionarily conserved rnp-4f pre-mRNA stem-loop located in the 5′-UTR to regulate splicing, while no RNA editing was observed, suggesting the hypothesis that it is the non-catalytic truncated isoform which regulates splicing. To test this hypothesis, we have utilized RNAi technology, the results of which support the hypothesis. These results demonstrate a novel, non-catalytic function for the truncated dADAR protein isoform in Drosophila embryonic development, which is very likely evolutionarily conserved.
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Affiliation(s)
- Sushmita Ghosh
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
| | - Yaqi Wang
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
| | - John A Cook
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
| | - Lea Chhiba
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
| | - Jack C Vaughn
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
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Vaughn JC, Ghosh S, Chen J. A phylogenetic study of Drosophila splicing assembly chaperone RNP-4F associated U4-/U6-snRNA secondary structure. ACTA ACUST UNITED AC 2013; 3:36-48. [PMID: 25419488 PMCID: PMC4237228 DOI: 10.4236/ojas.2013.34a2005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The rnp-4f gene in Drosophila melanogaster encodes nuclear protein RNP-4F. This encoded protein is represented by homologs in other eukaryotic species, where it has been shown to function as an intron splicing assembly factor. Here, RNP-4F is believed to initially bind to a recognition sequence on U6-snRNA, serving as a chaperone to facilitate its association with U4-snRNA by intermolecular hydrogen bonding. RNA conformations are a key factor in spliceosome function, so that elucidation of changing secondary structures for interacting snRNAs is a subject of considerable interest and importance. Among the five snRNAs which participate in removal of spliceosomal introns, there is a growing consensus that U6-snRNA is the most structurally dynamic and may constitute the catalytic core. Previous studies by others have generated potential secondary structures for free U4- and U6-snRNAs, including the Y-shaped U4-/U6-snRNA model. These models were based on study of RNAs from relatively few species, and the popular Y-shaped model remains to be systematically re-examined with reference to the many new sequences generated by recent genomic sequencing projects. We have utilized a comparative phylogenetic approach on 60 diverse eukaryotic species, which resulted in a revised and improved U4-/U6-snRNA secondary structure. This general model is supported by observation of abundant compensatory base mutations in every stem, and incorporates more of the nucleotides into base-paired associations than in previous models, thus being more energetically stable. We have extensively sampled the eukaryotic phylogenetic tree to its deepest roots, but did not find genes potentially encoding either U4- or U6-snRNA in the Giardia and Trichomonas data-bases. Our results support the hypothesis that nuclear introns in these most deeply rooted eukaryotes may represent evolutionary intermediates, sharing characteristics of both group II and spliceosomal introns. An unexpected result of this study was discovery of a potential competitive binding site for Drosophila splicing assembly factor RNP-4F to a 5’-UTR regulatory region within its own premRNA, which may play a role in negative feedback control.
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Affiliation(s)
- Jack C Vaughn
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
| | - Sushmita Ghosh
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
| | - Jing Chen
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
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Abstract
Adenosine to inosine (A-to-I) RNA editing is a post-transcriptional process by which adenosines are selectively converted to inosines in double-stranded RNA (dsRNA) substrates. A highly conserved group of enzymes, the adenosine deaminase acting on RNA (ADAR) family, mediates this reaction. All ADARs share a common domain architecture consisting of a variable number of amino-terminal dsRNA binding domains (dsRBDs) and a carboxy-terminal catalytic deaminase domain. ADAR family members are highly expressed in the metazoan nervous system, where these enzymes predominantly localize to the neuronal nucleus. Once in the nucleus, ADARs participate in the modification of specific adenosines in pre-mRNAs of proteins involved in electrical and chemical neurotransmission, including pre-synaptic release machineries, and voltage- and ligand-gated ion channels. Most RNA editing sites in these nervous system targets result in non-synonymous codon changes in functionally important, usually conserved, residues and RNA editing deficiencies in various model organisms bear out a crucial role for ADARs in nervous system function. Mutation or deletion of ADAR genes results in striking phenotypes, including seizure episodes, extreme uncoordination, and neurodegeneration. Not only does the process of RNA editing alter important nervous system peptides, but ADARs also regulate gene expression through modification of dsRNA substrates that enter the RNA interference (RNAi) pathway and may then act at the chromatin level. Here, we present a review on the current knowledge regarding the ADAR protein family, including evolutionary history, key structural features, localization, function and mechanism.
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25
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Lu T, Zhu C, Lu G, Guo Y, Zhou Y, Zhang Z, Zhao Y, Li W, Lu Y, Tang W, Feng Q, Han B. Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice. BMC Genomics 2012; 13:721. [PMID: 23259405 PMCID: PMC3549290 DOI: 10.1186/1471-2164-13-721] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 12/18/2012] [Indexed: 12/24/2022] Open
Abstract
Background Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRNAs), which participate in important biogenesis mechanisms for transcriptional and post-transcriptional regulation in rice. However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs. Results We applied high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq) to deeply sequence mRNA for assessing sense and antisense transcripts that were derived under salt, drought and cold stresses, and normal conditions, in the model plant rice (Oryza sativa). Combined with RAP-DB genome annotation (the Rice Annotation Project Database build-5 data set), 76,013 transcripts corresponding to 45,844 unique gene loci were assembled, in which 4873 gene loci were newly identified. Of 3819 putative rice cis-NATs, 2292 were detected as expressed and giving rise to small RNAs from their overlapping regions through integrated analysis of ssRNA-seq data and small RNA data. Among them, 503 cis-NATs seemed to be associated with specific conditions. The deep sequence data from isolated epidermal cells of rice seedlings further showed that 54.0% of cis-NATs were expressed simultaneously in a population of homogenous cells. Nearly 9.7% of rice transcripts were involved in one-to-one or many-to-many cis-NATs formation. Furthermore, only 17.4-34.7% of 223 many-to-many cis-NAT groups were all expressed and generated nat-siRNAs, indicating that only some cis-NAT groups may be involved in complex regulatory networks. Conclusions Our study profiles an abundance of cis-NATs and nat-siRNAs in rice. These data are valuable for gaining insight into the complex function of the rice transcriptome.
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Affiliation(s)
- Tingting Lu
- National Center for Gene Research & Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China.
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Chen C, Wei R, Qiao R, Ren J, Yang H, Liu C, Huang L. A genome-wide investigation of expression characteristics of natural antisense transcripts in liver and muscle samples of pigs. PLoS One 2012; 7:e52433. [PMID: 23285040 PMCID: PMC3527515 DOI: 10.1371/journal.pone.0052433] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/16/2012] [Indexed: 11/30/2022] Open
Abstract
Natural antisense transcripts are endogenous transcripts that are complementary to the sense-strand of DNA. These transcripts have been identified in various eukaryotic species and are involved in a broad range of regulatory events and biological processes. However, their general biological functions, expression characteristics and regulatory mechanisms are still unclear. In this study, 497 liver and 586 muscle samples were harvested from a White Duroc×Erhualian F2 resource population. The expression profiles of sense and antisense transcripts were determined by tag-based RNA sequencing. We identified 33.7% and 20.4% of transcripts having both sense and antisense expression, and 12.5% and 6.1% of transcripts only expressing antisense transcripts in liver and muscle, respectively. More than 32.2% of imprinting or predicted imprinting genes in the geneimprint database were detected with both sense and antisense expression. The correlations between sense and antisense expression in sense-antisense pairs were diverse in both liver and muscle, showing positive, negative or absent correlation. Antisense expression increases gene expression variability. More interestingly, compared to eQTL mapping of sense transcripts in which more than one eQTL was mapped for a transcript, only one eQTL was identified for each antisense transcript, and the percentage of cis-eQTL in antisense eQTL was higher than that in sense eQTL. This suggests that the expressions of antisense transcripts tend to be cis-regulated by a single genomic locus. To our knowledge, this study is the first systematical investigation of antisense transcription in pigs. The findings improve our understanding of the complexity of porcine transcriptome.
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Affiliation(s)
- Congying Chen
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Rongxing Wei
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
- Nanchang Working Canine Base, Nanchang, People’s Republic of China
| | - Ruimin Qiao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Hui Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Chenlong Liu
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
- * E-mail:
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Lakshmi GG, Ghosh S, Jones GP, Parikh R, Rawlins BA, Vaughn JC. An RNA electrophoretic mobility shift and mutational analysis of rnp-4f 5'-UTR intron splicing regulatory proteins in Drosophila reveals a novel new role for a dADAR protein isoform. Gene 2012; 511:161-8. [PMID: 23026215 PMCID: PMC4123196 DOI: 10.1016/j.gene.2012.09.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 08/09/2012] [Accepted: 09/12/2012] [Indexed: 01/09/2023]
Abstract
Alternative splicing greatly enhances the diversity of proteins encoded by eukaryotic genomes, and is also important in gene expression control. In contrast to the great depth of knowledge as to molecular mechanisms in the splicing pathway itself, relatively little is known about the regulatory events behind this process. The 5'-UTR and 3'-UTR in pre-mRNAs play a variety of roles in controlling eukaryotic gene expression, including translational modulation, and nearly 4000 of the roughly 14,000 protein coding genes in Drosophila contain introns of unknown functional significance in their 5'-UTR. Here we report the results of an RNA electrophoretic mobility shift analysis of Drosophila rnp-4f 5'-UTR intron 0 splicing regulatory proteins. The pre-mRNA potential regulatory element consists of an evolutionarily-conserved 177-nt stem-loop arising from pairing of intron 0 with part of adjacent exon 2. Incubation of in vitro transcribed probe with embryo protein extract is shown to result in two shifted RNA-protein bands, and protein extract from a dADAR null mutant fly line results in only one shifted band. A mutated stem-loop in which the conserved exon 2 primary sequence is changed but secondary structure maintained by introducing compensatory base changes results in diminished band shifts. To test the hypothesis that dADAR plays a role in intron splicing regulation in vivo, levels of unspliced rnp-4f mRNA in dADAR mutant were compared to wild-type via real-time qRT-PCR. The results show that during embryogenesis unspliced rnp-4f mRNA levels fall by up to 85% in the mutant, in support of the hypothesis. Taken together, these results demonstrate a novel role for dADAR protein in rnp-4f 5'-UTR alternative intron splicing regulation which is consistent with a previously proposed model.
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Affiliation(s)
- G. Girija Lakshmi
- Department of Zoology, Cell Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, United States
| | - Sushmita Ghosh
- Department of Zoology, Cell Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, United States
| | - Gabriel P. Jones
- Department of Zoology, Cell Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, United States
| | - Roshni Parikh
- Department of Zoology, Cell Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, United States
| | - Bridgette A. Rawlins
- Department of Zoology, Cell Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, United States
| | - Jack C. Vaughn
- Department of Zoology, Cell Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, United States
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Ehrensberger KM, Mason C, Corkins ME, Anderson C, Dutrow N, Cairns BR, Dalley B, Milash B, Bird AJ. Zinc-dependent regulation of the Adh1 antisense transcript in fission yeast. J Biol Chem 2012; 288:759-69. [PMID: 23223230 DOI: 10.1074/jbc.m112.406165] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In yeast, Adh1 (alcohol dehydrogenase 1) is an abundant zinc-binding protein that is required for the conversion of acetaldehyde to ethanol. Through transcriptome profiling of the Schizosaccharomyces pombe genome, we identified a natural antisense transcript at the adh1 locus that is induced in response to zinc limitation. This antisense transcript (adh1AS) shows a reciprocal expression pattern to that of the adh1 mRNA partner. In this study, we show that increased expression of the adh1AS transcript in zinc-limited cells is necessary for the repression of adh1 gene expression and that the increased level of the adh1AS transcript in zinc-limited cells is a result of two mechanisms. At the transcriptional level, the adh1AS transcript is expressed at a high level in zinc-limited cells. In addition to this transcriptional control, adh1AS transcripts preferentially accumulate in zinc-limited cells when the adh1AS transcript is expressed from a constitutive promoter. This secondary mechanism requires the simultaneous expression of adh1. Our studies reveal how multiple mechanisms can synergistically control the ratio of sense to antisense transcripts and highlight a novel mechanism by which adh1 gene expression can be controlled by cellular zinc availability.
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Affiliation(s)
- Kate M Ehrensberger
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
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Cui P, Liu W, Zhao Y, Lin Q, Ding F, Xin C, Geng J, Song S, Sun F, Hu S, Yu J. The association between H3K4me3 and antisense transcription. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 10:74-81. [PMID: 22768981 PMCID: PMC5054153 DOI: 10.1016/j.gpb.2012.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 05/13/2012] [Indexed: 11/18/2022]
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) is well known to occur in the promoter region of genes for transcription activation. However, when investigating the H3K4me3 profiles in the mouse cerebrum and testis, we discovered that H3K4me3 also has a significant enrichment at the 3' end of actively transcribed (sense) genes, named as 3'-H3K4me3. 3'-H3K4me3 is associated with ~15% of protein-coding genes in both tissues. In addition, we examined the transcriptional initiation signals including RNA polymerase II (RNAPII) binding sites and 5'-CAGE-tag that marks transcriptional start sites. Interestingly, we found that 3'-H3K4me3 is associated with the initiation of antisense transcription. Furthermore, 3'-H3K4me3 modification levels correlate positively with the antisense expression levels of the associated sense genes, implying that 3'-H3K4me3 is involved in the activation of antisense transcription. Taken together, our findings suggest that H3K4me3 may be involved in the regulation of antisense transcription that initiates from the 3' end of sense genes. In addition, a positive correlation was also observed between the expression of antisense and the associated sense genes with 3'-H3K4me3 modification. More importantly, we observed the 3'-H3K4me3 enrichment among genes in human, fruitfly and Arabidopsis, and found that the sequences of 3'-H3K4me3-marked regions are highly conserved and essentially indistinguishable from known promoters in vertebrate. Therefore, we speculate that these 3'-H3K4me3-marked regions may serve as potential promoters for antisense transcription and 3'-H3K4me3 appear to be a universal epigenetic feature in eukaryotes. Our results provide a novel insight into the epigenetic roles of H3K4me3 and the regulatory mechanism of antisense transcription.
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Affiliation(s)
- Peng Cui
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
| | - Wanfei Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhui Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Lin
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
| | - Feng Ding
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
| | - Chengqi Xin
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianing Geng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
| | - Shuhui Song
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
| | - Fanglin Sun
- Institute of Epigenetics and Cancer Research, School of Medicine, Tsinghua University, Beijing 100080, China
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
- Corresponding authors.
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
- Corresponding authors.
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30
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Keegan LP, McGurk L, Palavicini JP, Brindle J, Paro S, Li X, Rosenthal JJC, O'Connell MA. Functional conservation in human and Drosophila of Metazoan ADAR2 involved in RNA editing: loss of ADAR1 in insects. Nucleic Acids Res 2011; 39:7249-62. [PMID: 21622951 PMCID: PMC3167634 DOI: 10.1093/nar/gkr423] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Flies with mutations in the single Drosophila Adar gene encoding an RNA editing enzyme involved in editing 4% of all transcripts have severe locomotion defects and develop age-dependent neurodegeneration. Vertebrates have two ADAR-editing enzymes that are catalytically active; ADAR1 and ADAR2. We show that human ADAR2 rescues Drosophila Adar mutant phenotypes. Neither the short nuclear ADAR1p110 isoform nor the longer interferon-inducible cytoplasmic ADAR1p150 isoform rescue walking defects efficiently, nor do they correctly edit specific sites in Drosophila transcripts. Surprisingly, human ADAR1p110 does suppress age-dependent neurodegeneration in Drosophila Adar mutants whereas ADAR1p150 does not. The single Drosophila Adar gene was previously assumed to represent an evolutionary ancestor of the multiple vertebrate ADARs. The strong functional similarity of human ADAR2 and Drosophila Adar suggests rather that these are true orthologs. By a combination of direct cloning and searching new invertebrate genome sequences we show that distinct ADAR1 and ADAR2 genes were present very early in the Metazoan lineage, both occurring before the split between the Bilateria and Cnidarians. The ADAR1 gene has been lost several times, including during the evolution of insects and crustacea. These data complement our rescue results, supporting the idea that ADAR1 and ADAR2 have evolved highly conserved, distinct functions.
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Affiliation(s)
- Liam P Keegan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
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Paro S, Li X, O'Connell MA, Keegan LP. Regulation and functions of ADAR in drosophila. Curr Top Microbiol Immunol 2011; 353:221-36. [PMID: 21761288 DOI: 10.1007/82_2011_152] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Drosophila melanogaster has a single Adar gene encoding a protein related to mammalian ADAR2 that edits transcripts encoding glutamate receptor subunits. We describe the structure of the Drosophila Adar locus and use ModENCODE information to supplement published data on Adar gene transcription, and splicing. We discuss the roles of ADAR in Drosophila in terms of the two main types of RNA molecules edited and roles of ADARs as RNA-binding proteins. Site-specific RNA editing events in transcripts encoding ion channel subunits were initially found serendipitously and subsequent directed searches for editing sites and transcriptome sequencing have now led to 972 edited sites being identified in 597 transcripts. Four percent of D. melanogaster transcripts are site-specifically edited and these encode a wide range of largely membrane-associated proteins expressed particularly in CNS. Electrophysiological studies on the effects of specific RNA editing events on ion channel subunits do not suggest that loss of RNA editing events in ion channels consistently produce a particular outcome such as making Adar mutant neurons more excitable. This possibility would have been consistent with neurodegeneration seen in Adar mutant fly brains. A further set of ADAR targets are dsRNA intermediates in siRNA generation, derived from transposons and from structured RNA loci. Transcripts with convergent overlapping 3' ends are also edited and the first discovered instance of RNA editing in Drosophila, in the Rnp4F transcript, is an example. There is no evidence yet to show that Adar antagonizes RNA interference in Drosophila. Evidence has been obtained that catalytically inactive ADAR proteins exert effects on microRNA generation and RNA interference. Whether all effects of inactive ADARs are due to RNA-binding or to even further roles of these proteins remains to be determined.
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Affiliation(s)
- Simona Paro
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
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Jouannet V, Crespi M. Long Nonprotein-Coding RNAs in Plants. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2011; 51:179-200. [PMID: 21287139 DOI: 10.1007/978-3-642-16502-3_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In recent years, nonprotein-coding RNAs (or npcRNAs) have emerged as a major part of the eukaryotic transcriptome. Many new regulatory npcRNAs or riboregulators riboregulators have been discovered and characterized due to the advent of new genomic approaches. This growing number suggests that npcRNAs could play a more important role than previously believed and significantly contribute to the generation of evolutionary complexity in multicellular organisms. Regulatory npcRNAs range from small RNAs (si/miRNAs) to very large transcripts (or long npcRNAs) and play diverse functions in development and/or environmental stress responses. Small RNAs include an expanding number of 20-40 nt RNAs that function in the regulation of gene expression by affecting mRNA decay and translational inhibition or lead to DNA methylation and gene silencing. They generally involve double-stranded RNA or stem loops and imply transcriptional or posttranscriptional gene silencing (PTGS). RNA silencing besides small interfering RNA and microRNA, gene silencing in plants is also mediated by tasiRNAs (trans-acting siRNAs) and nat-siRNAs (natural antisense mediated siRNAs). In contrast to small RNAs, much less is known about the large and diverse population of long npcRNAs, and only a few have been implicated in diverse functions such as abiotic stress responses, nodulation and flower development, and sex chromosome-specific expression. Moreover, many long npcRNAs act as antisense transcripts or are substrates of the small RNA pathways, thus interfering with a variety of RNA-related metabolisms. An emerging hypothesis is that long npcRNAs, as shown for small si/miRNAs, integrate into ribonucleoprotein particles (RNPs) to modulate their function, localization, or stability to act on target mRNAs. As plants show a remarkable developmental plasticity to adapt their growth to changing environmental conditions, understanding how npcRNAs work may reveal novel mechanisms involved in growth control and differentiation and help to design new tools for biotechnological applications.
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Affiliation(s)
- Virginie Jouannet
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, 91198, Gif-sur-Yvette Cedex, France
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Fukui T, Itoh M. RNA editing in P transposable element read-through transcripts in Drosophila melanogaster. Genetica 2010; 138:1119-26. [DOI: 10.1007/s10709-010-9499-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 09/05/2010] [Indexed: 10/19/2022]
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Abstract
One type of RNA editing converts adenosines to inosines (A-->I editing) in double-stranded RNA (dsRNA) substrates. A-->I RNA editing is mediated by adenosine deaminase acting on RNA (ADAR) enzymes. A-->I RNA editing of protein-coding sequences of a limited number of mammalian genes results in recoding and subsequent alterations of their functions. However, A-->I RNA editing most frequently targets repetitive RNA sequences located within introns and 5' and 3' untranslated regions (UTRs). Although the biological significance of noncoding RNA editing remains largely unknown, several possibilities, including its role in the control of endogenous short interfering RNAs (esiRNAs), have been proposed. Furthermore, recent studies have revealed that the biogenesis and functions of certain microRNAs (miRNAs) are regulated by the editing of their precursors. Here, I review the recent findings that indicate new functions for A-->I editing in the regulation of noncoding RNAs and for interactions between RNA editing and RNA interference mechanisms.
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Affiliation(s)
- Kazuko Nishikura
- Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania 19104-4268, USA.
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35
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Carpenter JA, Keegan LP, Wilfert L, O'Connell MA, Jiggins FM. Evidence for ADAR-induced hypermutation of the Drosophila sigma virus (Rhabdoviridae). BMC Genet 2009; 10:75. [PMID: 19941656 PMCID: PMC2790459 DOI: 10.1186/1471-2156-10-75] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 11/26/2009] [Indexed: 12/02/2022] Open
Abstract
Background ADARs are RNA editing enzymes that target double stranded RNA and convert adenosine to inosine, which is read by translation machinery as if it were guanosine. Aside from their role in generating protein diversity in the central nervous system, ADARs have been implicated in the hypermutation of some RNA viruses, although why this hypermutation occurs is not well understood. Results Here we describe the hypermutation of adenosines to guanosines in the genome of the sigma virus--a negative sense RNA virus that infects Drosophila melanogaster. The clustering of these mutations and the context in which they occur indicates that they have been caused by ADARs. However, ADAR-editing of viral RNA is either rare or edited viral RNA are rapidly degraded, as we only detected evidence for editing in two of the 104 viral isolates we studied. Conclusion This is the first evidence for ADARs targeting viruses outside of mammals, and it raises the possibility that ADARs could play a role in the antiviral defences of insects.
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Affiliation(s)
- Jennifer A Carpenter
- Institute of Evolutionary Biology, University of Edinburgh, West Mains Rd, Edinburgh EH9 3JT, UK.
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36
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Jamalkandi SA, Masoudi-Nejad A. Reconstruction of Arabidopsis thaliana fully integrated small RNA pathway. Funct Integr Genomics 2009; 9:419-32. [DOI: 10.1007/s10142-009-0141-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 09/09/2009] [Accepted: 09/11/2009] [Indexed: 11/24/2022]
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Abstract
Adenosine deaminases acting on RNA (ADARs) convert adenosines to inosines in double-stranded RNA in animals. Identification of more ADAR targets and genome sequences of diverse eukaryotes present an opportunity to elucidate the origin and evolution of ADAR-mediated RNA editing. Comparative analysis of the adenosine deaminase family indicates that the first ADAR might have evolved from adenosine deaminases acting on tRNAs after the split of protozoa and metazoa. ADAR1 and ADAR2 arose by gene duplications in early metazoan evolution, approximately 700 million years ago, while ADAR3 and TENR might originate after Urochordata-Vertebrata divergence. More ADAR or ADAR-like genes emerged in some animals (e.g., fish). Considering the constrained structure, ADAR targets are proposed to have evolved from transposable elements and repeats, random selection, and fixation, and intermolecular pairs of sense and antisense RNA. In some degree, increased ADAR-mediated gene regulation should substantially contribute to the emergence and evolution of complex metazoans, particularly the nervous system.
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Affiliation(s)
- Yongfeng Jin
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, People's Republic of China.
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38
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Chen J, Lakshmi GG, Hays DL, McDowell KM, Ma E, Vaughn JC. Spatial and temporal expression of dADAR mRNA and protein isoforms during embryogenesis in Drosophila melanogaster. Differentiation 2009; 78:312-20. [PMID: 19720447 DOI: 10.1016/j.diff.2009.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2009] [Revised: 06/22/2009] [Accepted: 08/04/2009] [Indexed: 11/25/2022]
Abstract
Adenosine Deaminases Acting on RNA (ADARs) function to co-transcriptionally deaminate specific (or non-specific) adenosines to inosines within pre-mRNAs, using double-stranded RNAs as substrate. In both Drosophila and mammals, the best-studied ADAR functions are to catalyze specific nucleotide conversions within mRNAs encoding various ligand- or voltage-gated ion channel proteins within the adult brain. In contrast, ADARs within developing fly embryos have scarcely been studied, in part because they contain little or no editase activity, raising interesting questions as to their functional significance. Quantitative RT-PCR shows that two major developmentally regulated mRNA isoform classes are produced (full-length and truncated), which arise by alternative splicing and also alternative 3'-end formation. In situ localization of specific dADAR mRNA isoforms during embryogenesis reveals that the full-length class is found primarily within the developing germ band and central nervous system, whereas the truncated isoform is mostly located in gut endothelium. Developmental Western immunoblots show that both isoform classes are expressed into protein during embryogenesis. Both the rnp-4f 5'-UTR unspliced isoform and the full-length dADAR mRNA primarily localize in the embryonic germ band and subsequently throughout the developing central nervous system. Previous studies have shown that some rnp-4f pre-mRNAs are extensively edited by dADAR in the adult brain. Computer predictions suggest that intron-exon pairing promotes formation of an evolutionarily conserved secondary structure in the rnp-4f 5'-UTR, forming a 177-nt RNA duplex resembling an editing site complementary sequence, which is shown to be associated with splicing failure and to generate a long isoform. Taken together, these observations led us to explore the possibility that interaction between rnp-4f pre-mRNA and nuclear full-length dADAR protein may occur during embryogenesis. In dADAR null mutants, rnp-4f 5'-UTR alternative splicing is significantly diminished, suggesting a non-catalytic role for dADAR in splicing regulation. A working model is proposed which provides a possible molecular mechanism.
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Affiliation(s)
- Jing Chen
- Department of Zoology, Miami University, Oxford, OH 45056, USA
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39
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Faghihi MA, Wahlestedt C. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 2009; 10:637-43. [PMID: 19638999 DOI: 10.1038/nrm2738] [Citation(s) in RCA: 547] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mammalian genomes encode numerous natural antisense transcripts, but the function of these transcripts is not well understood. Functional validation studies indicate that antisense transcripts are not a uniform group of regulatory RNAs but instead belong to multiple categories with some common features. Recent evidence indicates that antisense transcripts are frequently functional and use diverse transcriptional and post-transcriptional gene regulatory mechanisms to carry out a wide variety of biological roles.
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Affiliation(s)
- Mohammad Ali Faghihi
- Molecular and Integrative Neurosciences Department, The Scripps Research Institute, Jupiter, Florida 33458, USA
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40
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Wang P, Yin S, Zhang Z, Xin D, Hu L, Kong X, Hurst LD. Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes. Genome Biol 2008; 9:R169. [PMID: 19055728 PMCID: PMC2646273 DOI: 10.1186/gb-2008-9-12-r169] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 10/02/2008] [Accepted: 12/02/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is increasing realization that regulation of genes is done partly at the RNA level by sense-antisense binding. Studies typically concentrate on the role of non-coding RNAs in regulating coding RNA. But the majority of transcripts in a cell are likely to be coding. Is it possible that coding RNA might regulate other coding RNA by short perfect sense-antisense binding? Here we compare all well-described human protein coding mRNAs against all others to identify sites 15-25 bp long that could potentially perfectly match sense-antisense. RESULTS From 24,968 protein coding mRNA RefSeq sequences, none failed to find at least one match in the transcriptome. By randomizations generating artificial transcripts matched for G+C content and length, we found that there are more such trans short sense-antisense pairs than expected. Several further features are consistent with functionality of some of the putative matches. First, transcripts with more potential partners have lower expression levels, and the pair density of tissue specific genes is significantly higher than that of housekeeping genes. Further, the single nucleotide polymorphism density is lower in short pairing regions than it is in flanking regions. We found no evidence that the sense-antisense pairing regions are associated with small RNAs derived from the protein coding genes. CONCLUSIONS Our results are consistent with the possibility of common short perfect sense-antisense pairing between transcripts of protein coding genes.
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Affiliation(s)
- Ping Wang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, 225 South Chong Qing Road, Shanghai 200025, PR China.
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Kim DS, Cho CY, Huh JW, Kim HS, Cho HG. EVOG: a database for evolutionary analysis of overlapping genes. Nucleic Acids Res 2008; 37:D698-702. [PMID: 18986995 PMCID: PMC2686455 DOI: 10.1093/nar/gkn813] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Overlapping genes are defined as a pair of genes whose transcripts are overlapped. Recently, many cases of overlapped genes have been investigated in various eukaryotic organisms; however, their origin and transcriptional control mechanism has not yet been clearly determined. In this study, we implemented evolutionary visualizer for overlapping genes (EVOG), a Web-based DB with a novel visualization interface, to investigate the evolutionary relationship between overlapping genes. Using this technique, we collected and analyzed all overlapping genes in human, chimpanzee, orangutan, marmoset, rhesus, cow, dog, mouse, rat, chicken, Xenopus, zebrafish and Drosophila. This integrated database provides a manually curated database that displays the evolutionary features of overlapping genes. The EVOG DB components included a number of overlapping genes (10074 in human, 10,009 in chimpanzee, 67,039 in orangutan, 51,001 in marmoset, 219 in rhesus, 3627 in cow, 209 in dog, 10,700 in mouse, 7987 in rat, 1439 in chicken, 597 in Xenopus, 2457 in zebrafish and 4115 in Drosophila). The EVOG database is very effective and easy to use for the analysis of the evolutionary process of overlapping genes when comparing different species. Therefore, EVOG could potentially be used as the main tool to investigate the evolution of the human genome in relation to disease by comparing the expression profiles of overlapping genes. EVOG is available at http://neobio.cs.pusan.ac.kr/evog/.
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Affiliation(s)
- Dae-Soo Kim
- Korean BioInformation Center, KRIBB, Daejeon 305-806, School of Computer Science and Engineering, College of Engineering, Pusan National University, Busan 609-735, Korea
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The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. Curr Genet 2008; 54:241-69. [PMID: 18813928 DOI: 10.1007/s00294-008-0215-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2008] [Revised: 09/02/2008] [Accepted: 09/03/2008] [Indexed: 12/25/2022]
Abstract
Naturally occurring Antisense Transcripts (NATs) compose an emerging group of regulatory RNAs. These regulatory elements appear in all organisms examined, but little is known about global expression of NATs in fungi. Analysis of currently available EST sequences suggests that 352 cis NATs are present in Aspergillus flavus. An Affymetrix GeneChip microarray containing probes for these cis NATs, as well as all predicted genes in A. flavus, allowed a whole genome expression analysis of these elements in response to two ecologically important temperatures for the fungus. RNA expression analysis showed that 32 NATs and 2,709 genes were differentially expressed between 37 degrees C, the optimum temperature for growth, and 28 degrees C, the conducive temperature for the biosynthesis of aflatoxin (AF) and many other secondary metabolites. These NATs correspond to sense genes with diverse functions including transcription initiation, carbohydrate processing and binding, temperature sensitive morphogenesis, and secondary metabolism. This is the first report of a whole genome transcriptional analysis of NAT expression in a fungus.
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Beltran M, Puig I, Peña C, García JM, Alvarez AB, Peña R, Bonilla F, de Herreros AG. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 2008; 22:756-69. [PMID: 18347095 DOI: 10.1101/gad.455708] [Citation(s) in RCA: 507] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Expression of Snail1 in epithelial cells triggers an epithelial-mesenchymal transition (EMT). Here, we demonstrate that the synthesis of Zeb2, a transcriptional repressor of E-cadherin, is up-regulated after Snail1-induced EMT. Snail1 does not affect the synthesis of Zeb2 mRNA, but prevents the processing of a large intron located in its 5'-untranslated region (UTR). This intron contains an internal ribosome entry site (IRES) necessary for the expression of Zeb2. Maintenance of 5'-UTR Zeb2 intron is dependent on the expression of a natural antisense transcript (NAT) that overlaps the 5' splice site in the intron. Ectopic overexpression of this NAT in epithelial cells prevents splicing of the Zeb2 5'-UTR, increases the levels of Zeb2 protein, and consequently down-regulates E-cadherin mRNA and protein. The relevance of these results is demonstrated by the strong association between NAT presence and conservation of the 5'-UTR intron in cells that have undergone EMT or in human tumors with low E-cadherin expression. Therefore, the results presented in this article reveal the existence of a NAT capable of activating Zeb2 expression, explain the mechanism involved in this activation, and demonstrate that this NAT regulates E-cadherin expression.
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Affiliation(s)
- Manuel Beltran
- Programa de Recerca en Càncer, Institut Municipal d'Investigació Mèdica (IMIM)-Hospital del Mar, Barcelona 08003, Spain
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Soldà G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD. Non-random retention of protein-coding overlapping genes in Metazoa. BMC Genomics 2008; 9:174. [PMID: 18416813 PMCID: PMC2330155 DOI: 10.1186/1471-2164-9-174] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 04/16/2008] [Indexed: 11/26/2022] Open
Abstract
Background Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm). Results For all analyzed species the observed number of overlapping genes is always lower than expected assuming functional neutrality, suggesting that gene overlap is negatively selected. The comparison to the random distribution also shows that retained overlaps do not exhibit random features: antiparallel overlaps are significantly enriched, while overlaps lying on the same strand and those involving coding sequences are highly underrepresented. We confirm that overlap is mostly species-specific and provide evidence that it frequently originates through the acquisition of terminal, non-coding exons. Finally, we show that overlapping genes tend to be significantly co-expressed in a breast cancer cDNA library obtained by 454 deep sequencing, and that different overlap types display different patterns of reciprocal expression. Conclusion Our data suggest that overlap between protein-coding genes is selected against in Metazoa. However, when retained it may be used as a species-specific mechanism for the reciprocal regulation of neighboring genes. The tendency of overlaps to involve non-coding regions of the genes leads to the speculation that the advantages achieved by an overlapping arrangement may be optimized by evolving regulatory non-coding transcripts.
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Affiliation(s)
- Giulia Soldà
- 1Department of Biology and Genetics for Medical Sciences, University of Milan, 20133 Milan, Italy.
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Beltran M, Puig I, Peña C, García JM, Alvarez AB, Peña R, Bonilla F, de Herreros AG. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 2008. [PMID: 18347095 DOI: 10.1101/gad.455708%2010.1101/gad.455708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Expression of Snail1 in epithelial cells triggers an epithelial-mesenchymal transition (EMT). Here, we demonstrate that the synthesis of Zeb2, a transcriptional repressor of E-cadherin, is up-regulated after Snail1-induced EMT. Snail1 does not affect the synthesis of Zeb2 mRNA, but prevents the processing of a large intron located in its 5'-untranslated region (UTR). This intron contains an internal ribosome entry site (IRES) necessary for the expression of Zeb2. Maintenance of 5'-UTR Zeb2 intron is dependent on the expression of a natural antisense transcript (NAT) that overlaps the 5' splice site in the intron. Ectopic overexpression of this NAT in epithelial cells prevents splicing of the Zeb2 5'-UTR, increases the levels of Zeb2 protein, and consequently down-regulates E-cadherin mRNA and protein. The relevance of these results is demonstrated by the strong association between NAT presence and conservation of the 5'-UTR intron in cells that have undergone EMT or in human tumors with low E-cadherin expression. Therefore, the results presented in this article reveal the existence of a NAT capable of activating Zeb2 expression, explain the mechanism involved in this activation, and demonstrate that this NAT regulates E-cadherin expression.
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Affiliation(s)
- Manuel Beltran
- Programa de Recerca en Càncer, Institut Municipal d'Investigació Mèdica (IMIM)-Hospital del Mar, Barcelona 08003, Spain
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Jin H, Vacic V, Girke T, Lonardi S, Zhu JK. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol 2008; 9:6. [PMID: 18194570 PMCID: PMC2262095 DOI: 10.1186/1471-2199-9-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 01/14/2008] [Indexed: 11/23/2022] Open
Abstract
Background In spite of large intergenic spaces in plant and animal genomes, 7% to 30% of genes in the genomes encode overlapping cis-natural antisense transcripts (cis-NATs). The widespread occurrence of cis-NATs suggests an evolutionary advantage for this type of genomic arrangement. Experimental evidence for the regulation of two cis-NAT gene pairs by natural antisense transcripts-generated small interfering RNAs (nat-siRNAs) via the RNA interference (RNAi) pathway has been reported in Arabidopsis. However, the extent of siRNA-mediated regulation of cis-NAT genes is still unclear in any genome. Results The hallmarks of RNAi regulation of NATs are 1) inverse regulation of two genes in a cis-NAT pair by environmental and developmental cues and 2) generation of siRNAs by cis-NAT genes. We examined Arabidopsis transcript profiling data from public microarray databases to identify cis-NAT pairs whose sense and antisense transcripts show opposite expression changes. A subset of the cis-NAT genes displayed negatively correlated expression profiles as well as inverse differential expression changes under at least one of the examined developmental stages or treatment conditions. By searching the Arabidopsis Small RNA Project (ASRP) and Massively Parallel Signature Sequencing (MPSS) small RNA databases as well as our stress-treated small RNA dataset, we found small RNAs that matched at least one gene in 646 pairs out of 1008 (64%) protein-coding cis-NAT pairs, which suggests that siRNAs may regulate the expression of many cis-NAT genes. 209 putative siRNAs have the potential to target more than one gene and half of these small RNAs could target multiple members of a gene family. Furthermore, the majority of the putative siRNAs within the overlapping regions tend to target only one transcript of a given NAT pair, which is consistent with our previous finding on salt- and bacteria-induced nat-siRNAs. In addition, we found that genes encoding plastid- or mitochondrion-targeted proteins are over-represented in the Arabidopsis cis-NATs and that 19% of sense and antisense partner genes of cis-NATs share at least one common Gene Ontology term, which suggests that they encode proteins with possible functional connection. Conclusion The negatively correlated expression patterns of sense and antisense genes as well as the presence of siRNAs in many of the cis-NATs suggest that siRNA regulation of cis-NATs via the RNAi pathway is an important gene regulatory mechanism for at least a subgroup of cis-NATs in Arabidopsis.
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Affiliation(s)
- Hailing Jin
- Department of Plant Pathology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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Abstract
There is a growing evidence, that antisense transcription might have a key role in a range of human diseases. Although predefined sense-antisense pairs were extensively studied, the antisense expression of the known sense genes is rarely investigated. We retrieved and correlated the expression of sense and antisense sequences of 1182 mouse transcripts to assess the prevalence and to find the characteristic pattern of antisense transcription. We contrasted three Affymetrix MGU74A version 1 mouse genome chips to six MGU74A version 2 chips. For these 1182 transcripts, the version 1 chips contain the antisense sequences of the transcripts presented on the version 2 chips. The original data was taken from the GEO database (GDS431 and GDS432). As the Affymetrix data are semiquantitative, the relative expression levels of antisense partners were analysed. We detected antisense transcription, although the average antisense expression is shifted towards smaller expression values (MGU74A version 1, 516; version 2, 1688). An inverse direct correlation between sense and antisense expression values could be observed at high expression values. At a very high relative expression--above 40,000--the Pearson correlation coefficient is getting closer to -1. Transcripts with high inverse expression ratio may be correlated to the investigated gene (major histocompatibility complex class II trans activator). The ratio of sense to antisense transcripts varied among different chromosomes; on chromosomes 14 and 1 the level of antisense expression was higher than that of sense. We conclude that antisense transcription is a common phenomenon in the mouse genome. The hypothesis of regulatory role of antisense transcripts is supported by the inverse antisense gene expression of highly expressed genes.
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Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS). BMC Genomics 2007; 8:207. [PMID: 17601345 PMCID: PMC1929076 DOI: 10.1186/1471-2164-8-207] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 07/02/2007] [Indexed: 11/15/2022] Open
Abstract
Background The liver is the largest human internal organ – it is composed of multiple cell types and plays a vital role in fulfilling the body's metabolic needs and maintaining homeostasis. Of these cell types the hepatocytes, which account for three-quarters of the liver's volume, perform its main functions. To discover the molecular basis of hepatocyte function, we employed Massively Parallel Signature Sequencing (MPSS) to determine the transcriptomic profile of adult human hepatocytes obtained by laser capture microdissection (LCM). Results 10,279 UniGene clusters, representing 7,475 known genes, were detected in human hepatocytes. In addition, 1,819 unique MPSS signatures matching the antisense strand of 1,605 non-redundant UniGene clusters (such as APOC1, APOC2, APOB and APOH) were highly expressed in hepatocytes. Conclusion Apart from a large number of protein-coding genes, some of the antisense transcripts expressed in hepatocytes could play important roles in transcriptional interference via a cis-/trans-regulation mechanism. Our result provided a comprehensively transcriptomic atlas of human hepatocytes using MPSS technique, which could be served as an available resource for an in-depth understanding of human liver biology and diseases.
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Galante PAF, Vidal DO, de Souza JE, Camargo AA, de Souza SJ. Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol 2007; 8:R40. [PMID: 17371592 PMCID: PMC1868933 DOI: 10.1186/gb-2007-8-3-r40] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 09/04/2006] [Accepted: 03/19/2007] [Indexed: 12/25/2022] Open
Abstract
Analysis of a catalog of S-AS pairs in the human and mouse genomes revealed several putative roles for natural antisense transcripts and showed that some are artifacts of cDNA library construction. Background A significant number of genes in mammalian genomes are being found to have natural antisense transcripts (NATs). These sense-antisense (S-AS) pairs are believed to be involved in several cellular phenomena. Results Here, we generated a catalog of S-AS pairs occurring in the human and mouse genomes by analyzing different sources of expressed sequences available in the public domain plus 122 massively parallel signature sequencing (MPSS) libraries from a variety of human and mouse tissues. Using this dataset of almost 20,000 S-AS pairs in both genomes we investigated, in a computational and experimental way, several putative roles that have been assigned to NATs, including gene expression regulation. Furthermore, these global analyses allowed us to better dissect and propose new roles for NATs. Surprisingly, we found that a significant fraction of NATs are artifacts produced by genomic priming during cDNA library construction. Conclusion We propose an evolutionary and functional model in which alternative polyadenylation and retroposition account for the origin of a significant number of functional S-AS pairs in mammalian genomes.
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Affiliation(s)
- Pedro AF Galante
- Ludwig Institute for Cancer Research, São Paulo Branch, Hospital Alemão Oswaldo Cruz, Rua João Juliao 245, 1 andar, São Paulo, SP 01323-903, Brazil
- Department Of Biochemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748 - sala 351, São Paulo, SP 05508-900, Brazil
| | - Daniel O Vidal
- Ludwig Institute for Cancer Research, São Paulo Branch, Hospital Alemão Oswaldo Cruz, Rua João Juliao 245, 1 andar, São Paulo, SP 01323-903, Brazil
| | - Jorge E de Souza
- Ludwig Institute for Cancer Research, São Paulo Branch, Hospital Alemão Oswaldo Cruz, Rua João Juliao 245, 1 andar, São Paulo, SP 01323-903, Brazil
| | - Anamaria A Camargo
- Ludwig Institute for Cancer Research, São Paulo Branch, Hospital Alemão Oswaldo Cruz, Rua João Juliao 245, 1 andar, São Paulo, SP 01323-903, Brazil
| | - Sandro J de Souza
- Ludwig Institute for Cancer Research, São Paulo Branch, Hospital Alemão Oswaldo Cruz, Rua João Juliao 245, 1 andar, São Paulo, SP 01323-903, Brazil
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Chen J, Concel VJ, Bhatla S, Rajeshwaran R, Smith DLH, Varadarajan M, Backscheider KL, Bockrath RA, Petschek JP, Vaughn JC. Alternative splicing of an rnp-4f mRNA isoform retaining an evolutionarily-conserved 5'-UTR intronic element is developmentally regulated and shown via RNAi to be essential for normal central nervous system development in Drosophila melanogaster. Gene 2007; 399:91-104. [PMID: 17582706 DOI: 10.1016/j.gene.2007.04.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 04/25/2007] [Accepted: 04/26/2007] [Indexed: 01/08/2023]
Abstract
Two major mRNA isoforms arise via alternative splicing in the 5'-UTR of Drosophila splicing assembly factor rnp-4f pre-mRNA, designated "long" (unspliced) and "short" (alternatively spliced). The coding potential for the two isoforms is identical, raising interesting questions as to the control mechanism and functional significance of this 5'-UTR intronic splicing decision. Developmental Northerns show that two temporally distinct rnp-4f mRNA degradation episodes occur during embryogenesis. The first occurs at the midblastula transition (MBT) stage and involves degradation of both maternally-derived transcripts, while the second involves only the long mRNA isoform and occurs during late embryo stages. Immunostaining of ovaries and staged embryos combined with results from developmental Westerns shows that maternal RNP-4F protein persists into fertilized eggs at high levels, associated with a burst of long isoform-specific transcription which begins just after the MBT and peaks in mid-embryo stages. These observations are discussed in support of a putative negative feedback control model for modulation of RNP-4F translation. In situ hybridization shows that the long isoform is relatively abundant throughout the developing embryonic germ band and central nervous system (CNS), especially along the dorsal roof of the ventral nerve cord. Long rnp-4f mRNA knockdown via RNAi reveals a variety of CNS abnormalities, which leads us to postulate that this isoform acts upstream of other genes which have been shown to be important for normal CNS development.
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Affiliation(s)
- Jing Chen
- Department of Zoology, Miami University, Oxford, OH 45056, United States
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