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Xin M, Guo Q, Lu Q, Lu J, Wang PS, Dong Y, Li T, Chen Y, Gerhard GS, Yang XF, Autieri M, Yang L. Identification of Gm15441, a Txnip antisense lncRNA, as a critical regulator in liver metabolic homeostasis. Cell Biosci 2021; 11:208. [PMID: 34906243 PMCID: PMC8670210 DOI: 10.1186/s13578-021-00722-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
Background The majority of mammalian genome is composed of non-coding regions, where numerous long non-coding RNAs (lncRNAs) are transcribed. Although lncRNAs have been identified to regulate fundamental biological processes, most of their functions remain unknown, especially in metabolic homeostasis. Analysis of our recent genome-wide screen reveals that Gm15441, a thioredoxin-interacting protein (Txnip) antisense lncRNA, is the most robustly induced lncRNA in the fasting mouse liver. Antisense lncRNAs are known to regulate their sense gene expression. Given that Txnip is a critical metabolic regulator of the liver, we aimed to investigate the role of Gm15441 in the regulation of Txnip and liver metabolism. Methods We examined the response of Gm15441 and Txnip under in vivo metabolic signals such as fasting and refeeding, and in vitro signals such as insulin and key metabolic transcription factors. We investigated the regulation of Txnip expression by Gm15441 and the underlying mechanism in mouse hepatocytes. Using adenovirus-mediated liver-specific overexpression, we determined whether Gm15441 regulates Txnip in the mouse liver and modulates key aspects of liver metabolism. Results We found that the expression levels of Gm15441 and Txnip showed a similar response pattern to metabolic signals in vivo and in vitro, but that their functions were predicted to be opposite. Furthermore, we found that Gm15441 robustly reduced Txnip protein expression in vitro through sequence-specific regulation and translational inhibition. Lastly, we confirmed the Txnip inhibition by Gm15441 in vivo (mice) and found that Gm15441 liver-specific overexpression lowered plasma triglyceride and blood glucose levels and elevated plasma ketone body levels. Conclusions Our data demonstrate that Gm15441 is a potent Txnip inhibitor and a critical metabolic regulator in the liver. This study reveals the therapeutic potential of Gm15441 in treating metabolic diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00722-1.
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Affiliation(s)
- Mingyang Xin
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Qian Guo
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Qingchun Lu
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Juan Lu
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, 130021, China
| | - Po-Shun Wang
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Yun Dong
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Department of Endocrinology, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, 541001, China
| | - Tao Li
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Department of Infectious diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Ye Chen
- Department of Mathematics and Statistics, Northern Arizona University, Flagsta, AZ, 86011, USA
| | - Glenn S Gerhard
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Xiao-Feng Yang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Michael Autieri
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Ling Yang
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.
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Kim J, Kim KM, Noh JH, Yoon JH, Abdelmohsen K, Gorospe M. Long noncoding RNAs in diseases of aging. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:209-21. [PMID: 26141605 DOI: 10.1016/j.bbagrm.2015.06.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/13/2015] [Accepted: 06/24/2015] [Indexed: 12/22/2022]
Abstract
Aging is a process during which progressive deteriorating of cells, tissues, and organs over time lead to loss of function, disease, and death. Towards the goal of extending human health span, there is escalating interest in understanding the mechanisms that govern aging-associated pathologies. Adequate regulation of expression of coding and noncoding genes is critical for maintaining organism homeostasis and preventing disease processes. Long noncoding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression at all levels--transcriptional, post-transcriptional and post-translational. In this review, we discuss our emerging understanding of lncRNAs implicated in aging illnesses. We focus on diseases arising from age-driven impairment in energy metabolism (obesity, diabetes), the declining capacity to respond homeostatically to proliferative and damaging stimuli (cancer, immune dysfunction), and neurodegeneration. We identify the lncRNAs involved in these ailments and discuss the rising interest in lncRNAs as diagnostic and therapeutic targets to ameliorate age-associated pathologies and prolong health. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Jiyoung Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kyoung Mi Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
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3
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Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi AM, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR. Landscape of transcription in human cells. Nature 2012; 489:101-8. [PMID: 22955620 PMCID: PMC3684276 DOI: 10.1038/nature11233] [Citation(s) in RCA: 3783] [Impact Index Per Article: 315.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 05/15/2012] [Indexed: 02/07/2023]
Abstract
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.
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Affiliation(s)
- Sarah Djebali
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Carrie A. Davis
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Angelika Merkel
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Alex Dobin
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Timo Lassmann
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Ali M. Mortazavi
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
- University of California Irvine, Dept of. Developmental and Cell Biology, 2300 Biological Sciences III, Irving, CA USA 92697
| | - Andrea Tanzer
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Wei Lin
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Felix Schlesinger
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Chenghai Xue
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Georgi K. Marinov
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Jainab Khatun
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
| | - Brian A. Williams
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Chris Zaleski
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
| | - Maik Röder
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Felix Kokocinski
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire United Kingdom CB10 1SA
| | - Rehab F. Abdelhamid
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Tyler Alioto
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Igor Antoshechkin
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Michael T. Baer
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Nadav S. Bar
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Philippe Batut
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Kimberly Bell
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Ian Bell
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Sudipto Chakrabortty
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Xian Chen
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Jacqueline Chrast
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Joao Curado
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Thomas Derrien
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Jorg Drenkow
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Erica Dumais
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Jacqueline Dumais
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Radha Duttagupta
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Emilie Falconnet
- University of Geneva Medical School, Department of Genetic Medicine and Development and iGE3 Institute of Genetics and Genomics of Geneva, 1 rue Michel-Servet, Geneva, Switzerland 1015
| | - Meagan Fastuca
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Kata Fejes-Toth
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Pedro Ferreira
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Sylvain Foissac
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Melissa J. Fullwood
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Hui Gao
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - David Gonzalez
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Assaf Gordon
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Harsha Gunawardena
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Cedric Howald
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Sonali Jha
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Rory Johnson
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Philipp Kapranov
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
- St. Laurent Institute, One Kendall Square, Cambridge, MA
| | - Brandon King
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Colin Kingswood
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Oscar J. Luo
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Eddie Park
- University of California Irvine, Dept of. Developmental and Cell Biology, 2300 Biological Sciences III, Irving, CA USA 92697
| | - Kimberly Persaud
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Jonathan B. Preall
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Paolo Ribeca
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Brian Risk
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
| | - Daniel Robyr
- University of Geneva Medical School, Department of Genetic Medicine and Development and iGE3 Institute of Genetics and Genomics of Geneva, 1 rue Michel-Servet, Geneva, Switzerland 1015
| | - Michael Sammeth
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Lorian Schaffer
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Lei-Hoon See
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Atif Shahab
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Jorgen Skancke
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ana Maria Suzuki
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Hazuki Takahashi
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Hagen Tilgner
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Diane Trout
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Nathalie Walters
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Huaien Wang
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - John Wrobel
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
| | - Yanbao Yu
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Xiaoan Ruan
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Yoshihide Hayashizaki
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire United Kingdom CB10 1SA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
- Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
| | - Tim Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire United Kingdom CB10 1SA
| | - Alexandre Reymond
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Stylianos E. Antonarakis
- University of Geneva Medical School, Department of Genetic Medicine and Development and iGE3 Institute of Genetics and Genomics of Geneva, 1 rue Michel-Servet, Geneva, Switzerland 1015
| | - Gregory Hannon
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Morgan C. Giddings
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Yijun Ruan
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Barbara Wold
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Piero Carninci
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Thomas R. Gingeras
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
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Kapranov P, St Laurent G. Dark Matter RNA: Existence, Function, and Controversy. Front Genet 2012; 3:60. [PMID: 22536205 PMCID: PMC3332219 DOI: 10.3389/fgene.2012.00060] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 03/30/2012] [Indexed: 12/11/2022] Open
Abstract
The mysteries surrounding the ∼97–98% of the human genome that does not encode proteins have long captivated imagination of scientists. Does the protein-coding, 2–3% of the genome carry the 97–98% as a mere passenger and neutral “cargo” on the evolutionary path, or does the latter have biological function? On one side of the debate, many commentaries have referred to the non-coding portion of the genome as “selfish” or “junk” DNA (Orgel and Crick, 1980), while on the other side, authors have argued that it contains the real blueprint for organismal development (Penman, 1995; Mattick, 2003), and the mechanisms of developmental complexity. Thus, this question could be referred to without much exaggeration as the most important issue in genetics today.
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Abstract
It is clear that RNA has a diverse set of functions and is more than just a messenger between gene and protein. The mammalian genome is extensively transcribed, giving rise to thousands of non-coding transcripts. Whether all of these transcripts are functional is debated, but it is evident that there are many functional large non-coding RNAs (ncRNAs). Recent studies have begun to explore the functional diversity and mechanistic role of these large ncRNAs. Here we synthesize these studies to provide an emerging model whereby large ncRNAs might achieve regulatory specificity through modularity, assembling diverse combinations of proteins and possibly RNA and DNA interactions.
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Affiliation(s)
- Mitchell Guttman
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
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6
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Abstract
The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serve as the template for protein synthesis. The discovery of extensive transcription of large RNA transcripts that do not code for proteins, termed long noncoding RNAs (lncRNAs), provides an important new perspective on the centrality of RNA in gene regulation. Here, we discuss genome-scale strategies to discover and characterize lncRNAs. An emerging theme from multiple model systems is that lncRNAs form extensive networks of ribonucleoprotein (RNP) complexes with numerous chromatin regulators and then target these enzymatic activities to appropriate locations in the genome. Consistent with this notion, lncRNAs can function as modular scaffolds to specify higher-order organization in RNP complexes and in chromatin states. The importance of these modes of regulation is underscored by the newly recognized roles of long RNAs for proper gene control across all kingdoms of life.
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Affiliation(s)
- John L. Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
| | - Howard Y. Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305
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7
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Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL. Genomewide characterization of non-polyadenylated RNAs. Genome Biol 2011; 12:R16. [PMID: 21324177 PMCID: PMC3188798 DOI: 10.1186/gb-2011-12-2-r16] [Citation(s) in RCA: 313] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/19/2011] [Accepted: 02/16/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNAs can be physically classified into poly(A)+ or poly(A)- transcripts according to the presence or absence of a poly(A) tail at their 3' ends. Current deep sequencing approaches largely depend on the enrichment of transcripts with a poly(A) tail, and therefore offer little insight into the nature and expression of transcripts that lack poly(A) tails. RESULTS We have used deep sequencing to explore the repertoire of both poly(A)+ and poly(A)- RNAs from HeLa cells and H9 human embryonic stem cells (hESCs). Using stringent criteria, we found that while the majority of transcripts are poly(A)+, a significant portion of transcripts are either poly(A)- or bimorphic, being found in both the poly(A)+ and poly(A)- populations. Further analyses revealed that many mRNAs may not contain classical long poly(A) tails and such messages are overrepresented in specific functional categories. In addition, we surprisingly found that a few excised introns accumulate in cells and thus constitute a new class of non-polyadenylated long non-coding RNAs. Finally, we have identified a specific subset of poly(A)- histone mRNAs, including two histone H1 variants, that are expressed in undifferentiated hESCs and are rapidly diminished upon differentiation; further, these same histone genes are induced upon reprogramming of fibroblasts to induced pluripotent stem cells. CONCLUSIONS We offer a rich source of data that allows a deeper exploration of the poly(A)- landscape of the eukaryotic transcriptome. The approach we present here also applies to the analysis of the poly(A)- transcriptomes of other organisms.
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Affiliation(s)
- Li Yang
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT 06030-6403, USA
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8
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Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM. Poly A- transcripts expressed in HeLa cells. PLoS One 2008; 3:e2803. [PMID: 18665230 PMCID: PMC2481391 DOI: 10.1371/journal.pone.0002803] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Accepted: 07/04/2008] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Transcripts expressed in eukaryotes are classified as poly A+ transcripts or poly A- transcripts based on the presence or absence of the 3' poly A tail. Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown. METHODOLOGY/PRINCIPAL FINDINGS We developed the TRD (Total RNA Detection) system for transcript identification. The system detects the transcripts through the following steps: 1) depleting the abundant ribosomal and small-size transcripts; 2) synthesizing cDNA without regard to the status of the 3' poly A tail; 3) applying the 454 sequencing technology for massive 3' EST collection from the cDNA; and 4) determining the genome origins of the detected transcripts by mapping the sequences to the human genome reference sequences. Using this system, we characterized the cytoplasmic transcripts from HeLa cells. Of the 13,467 distinct 3' ESTs analyzed, 24% are poly A-, 36% are poly A+, and 40% are bimorphic with poly A+ features but without the 3' poly A tail. Most of the poly A- 3' ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3' ESTs, and their mapped intergenic regions are evolutionarily conserved. Experiments confirmed the authenticity of the detected poly A- transcripts. CONCLUSION/SIGNIFICANCE Our study provides the first large-scale sequence evidence for the presence of poly A- transcripts in eukaryotes. The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts.
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Affiliation(s)
- Qingfa Wu
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yeong C. Kim
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Jian Lu
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Zhenyu Xuan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jun Chen
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yonglan Zheng
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Tom Zhou
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Michael Q. Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Chung-I Wu
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - San Ming Wang
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
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9
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Smith KP, Byron M, Johnson C, Xing Y, Lawrence JB. Defining early steps in mRNA transport: mutant mRNA in myotonic dystrophy type I is blocked at entry into SC-35 domains. ACTA ACUST UNITED AC 2007; 178:951-64. [PMID: 17846170 PMCID: PMC2064620 DOI: 10.1083/jcb.200706048] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In myotonic dystrophy type 1 (DM1), triplet repeat expansion in the 3' untranslated region of dystrophia myotonica protein kinase (DMPK) causes the nuclear retention of mutant messenger RNA (mRNA). Although the DMPK gene locus positions precisely at the outer edge of a factor-rich SC-35 domain, the normal mRNA consistently accumulates within the domain, and this RNA is depleted upon transcriptional inhibition. In DM1, mutant transcripts detach from the gene but accumulate in granules that abut but do not enter SC-35 domains, suggesting that RNA entry into the domain is blocked. Despite their exclusion from these compartments, mutant transcripts are spliced. MBNL1 (muscleblind-like protein 1) is an alternative splicing factor that becomes highly concentrated with mutant RNA foci. Small interfering RNA-mediated knockdown of MBNL1 promotes the accumulation or entry of newly synthesized mutant transcripts in the SC-35 domain. Collectively, these data suggest that an initial step in the intranuclear path of some mRNAs is passage from the gene into an SC-35 domain and implicate these structures in postsplicing steps before export.
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Affiliation(s)
- Kelly P Smith
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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10
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Abstract
Direct localization of specific genes, RNAs, and proteins has allowed the dissection of individual nuclear speckles in relation to the molecular biology of gene expression. Nuclear speckles (aka SC35 domains) are essentially ubiquitous structures enriched for most pre-mRNA metabolic factors, yet their relationship to gene expression has been poorly understood. Analyses of specific genes and their spliced or mature mRNA strongly support that SC35 domains are hubs of activity, not stores of inert factors detached from gene expression. We propose that SC35 domains are hubs that spatially link expression of specific pre-mRNAs to rapid recycling of copious RNA metabolic complexes, thereby facilitating expression of many highly active genes. In addition to increasing the efficiency of each step, sequential steps in gene expression are structurally integrated at each SC35 domain, consistent with other evidence that the biochemical machineries for transcription, splicing, and mRNA export are coupled. Transcription and splicing are subcompartmentalized at the periphery, with largely spliced mRNA entering the domain prior to export. In addition, new findings presented here begin to illuminate the structural underpinnings of a speckle by defining specific perturbations of phosphorylation that promote disassembly or assembly of an SC35 domain in relation to other components. Results thus far are consistent with the SC35 spliceosome assembly factor as an integral structural component. Conditions that disperse SC35 also disperse poly(A) RNA, whereas the splicing factor ASF/SF2 can be dispersed under conditions in which SC35 or SRm300 remain as intact components of a core domain.
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Affiliation(s)
- Lisa L Hall
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, 01655, USA
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11
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Abstract
The discoveries of RNA interference and RNA-mediated posttranscriptional gene silencing have opened an unanticipated new window on the regulation of gene expression as well as a facile and highly effective tool for knocking down gene expression in many organisms and cells. In addition, RNA interference and RNA silencing may conceivably be exploited for human therapeutics sometime in the future, possibly bringing greater clinical impact than have the so far disappointing antisense endeavors. This essay summarizes recent developments and offers some personalized perspectives, with emphasis on what we do not yet know.
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Affiliation(s)
- Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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12
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Zeng C, Kim E, Warren SL, Berget SM. Dynamic relocation of transcription and splicing factors dependent upon transcriptional activity. EMBO J 1997; 16:1401-12. [PMID: 9135155 PMCID: PMC1169737 DOI: 10.1093/emboj/16.6.1401] [Citation(s) in RCA: 167] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Recent interest in understanding the spatial organization of gene expression has focused attention on nuclear structures known as speckles or interchromatin granule clusters (IGCs) revealed by immunofluorescence or electron microscopy. Staining of nuclear factors involved in pre-mRNA splicing or, more recently, transcription, reveals 20-40 speckles per nucleus, resulting in the intriguing suggestion that speckles are nuclear sites of transcription and processing. In contrast, other investigations have observed transcription in other areas of the nucleus. In this study, we have examined the localization of active transcription as detected by uridine incorporation and recently developed RNA polymerase II antibodies, and compared this pattern with that of known splicing and polyadenylation factors. Our results indicate that in actively transcribing cells, transcription and splicing factors are dispersed throughout the nucleus with abundant sites of preferred localization. In contrast, in poorly transcribing cells, polymerase II and splicing factors localize to speckles. In nuclei inactivated for transcription by drugs or heat shock, the speckle type of co-localization is accentuated. These observations suggest that bulk transcription and splicing occur throughout the nucleus during periods of active transcription; and that factors involved in these two processes re-locate to minimal speckle domains during periods of inactive transcription.
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Affiliation(s)
- C Zeng
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
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13
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Clemson CM, McNeil JA, Willard HF, Lawrence JB. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J Cell Biol 1996; 132:259-75. [PMID: 8636206 PMCID: PMC2120729 DOI: 10.1083/jcb.132.3.259] [Citation(s) in RCA: 592] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The XIST gene is implicated in X chromosome inactivation, yet the RNA contains no apparent open reading frame. An accumulation of XIST RNA is observed near its site of transcription, the inactive X chromosome (Xi). A series of molecular cytogenetic studies comparing properties of XIST RNA to other protein coding RNAs, support a critical distinction for XIST RNA; XIST does not concentrate at Xi simply because it is transcribed and processed there. Most notably, morphometric and 3-D analysis reveals that XIST RNA and Xi are coincident in 2- and 3-D space; hence, the XIST RNA essentially paints Xi. Several results indicate that the XIST RNA accumulation has two components, a minor one associated with transcription and processing, and a spliced major component, which stably associates with Xi. Upon transcriptional inhibition the major spliced component remains in the nucleus and often encircles the extra-prominent heterochromatic Barr body. The continually transcribed XIST gene and its polyadenylated RNA consistently localize to a nuclear region devoid of splicing factor/poly A RNA rich domains. XIST RNA remains with the nuclear matrix fraction after removal of chromosomal DNA. XIST RNA is released from its association with Xi during mitosis, but shows a unique highly particulate distribution. Collective results indicate that XIST RNA may be an architectural element of the interphase chromosome territory, possibly a component of nonchromatin nuclear structure that specifically associates with Xi. XIST RNA is a novel nuclear RNA which potentially provides a specific precedent for RNA involvement in nuclear structure and cis-limited gene regulation via higher-order chromatin packaging.
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Affiliation(s)
- C M Clemson
- Department of Cell Biology, University of Massachusetts Medical Center, Worcester 01655, USA
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14
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Xing Y, Johnson CV, Moen PT, McNeil JA, Lawrence J. Nonrandom gene organization: structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J Cell Biol 1995; 131:1635-47. [PMID: 8557734 PMCID: PMC2120660 DOI: 10.1083/jcb.131.6.1635] [Citation(s) in RCA: 203] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
This work demonstrates a highly nonrandom distribution of specific genes relative to nuclear domains enriched in splicing factors and poly(A)+ RNA, and provides evidence for the direct involvement of these in pre-mRNA metabolism. As investigated in hundreds of diploid fibroblasts, human collagen I alpha 1 and beta-actin DNA/RNA showed a very high degree of spatial association with SC-35 domains, whereas three nontranscribed genes, myosin heavy chain, neurotensin, and albumin, showed no such preferential association. Collagen I alpha 1 RNA accumulates within the more central region of the domain, whereas beta-actin RNA localizes at the periphery. A novel approach revealed that collagen RNA tracks are polarized, with the entire gene at one end, on the edge of the domain, and the RNA extending into the domain. Intron 26 is spliced within the RNA track at the domain periphery. Transcriptional inhibition studies show both the structure of the domain and the gene's relationship to it are not dependent upon the continued presence of accumulated collagen RNA, and that domains remaining after inhibition are not just storage sites. Results support a model reconciling light and electron microscopic observations which proposes that transcription of some specific genes occurs at the border of domains, which may also function in the assembly or distribution of RNA metabolic components. In contrast to the apparently random dispersal of total undefined hnRNA synthesis through interdomain space, transcription and splicing for some genes occurs preferentially at specific sites, and a high degree of individual pre-mRNA metabolism is compartmentalized with discrete SC-35 domains.
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Affiliation(s)
- Y Xing
- School, Worcester 01655, USA
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15
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Wansink DG, Schul W, van der Kraan I, van Steensel B, van Driel R, de Jong L. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J Cell Biol 1993; 122:283-93. [PMID: 8320255 PMCID: PMC2119648 DOI: 10.1083/jcb.122.2.283] [Citation(s) in RCA: 436] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Several nuclear activities and components are concentrated in discrete nuclear compartments. To understand the functional significance of nuclear compartmentalization, knowledge on the spatial distribution of transcriptionally active chromatin is essential. We have examined the distribution of sites of transcription by RNA polymerase II (RPII) by labeling nascent RNA with 5-bromouridine 5'-triphosphate, in vitro and in vivo. Nascent RPII transcripts were found in over 100 defined areas, scattered throughout the nucleoplasm. No preferential localization was observed in either the nuclear interior or the periphery. Each transcription site may represent the activity of a single gene or, considering the number of active pre-mRNA genes in a cell, of a cluster of active genes. The relation between the distribution of nascent RPII transcripts and that of the essential splicing factor SC-35 was investigated in double labeling experiments. Antibodies against SC-35 recognize a number of well-defined, intensely labeled nuclear domains, in addition to labeling of more diffuse areas between these domains (Spector, D. L., X. -D. Fu, and T. Maniatis. 1991. EMBO (Eur. Mol. Biol. Organ.) J. 10:3467-3481). We observe no correlation between intensely labeled SC-35 domains and sites of pre-mRNA synthesis. However, many sites of RPII synthesis colocalize with weakly stained areas. This implies that contranscriptional splicing takes place in these weakly stained areas. These areas may also be sites where splicing is completed posttranscriptionally. Intensely labeled SC-35 domains may function as sites for assembly, storage, or regeneration of splicing components, or as compartments for degradation of introns.
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Affiliation(s)
- D G Wansink
- E.C. Slater Institute, University of Amsterdam, The Netherlands
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16
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Abstract
The nuclear matrix is concealed by a much larger mass of chromatin, which can be removed selectively by digesting nuclei with DNase I followed by elution of chromatin with 0.25 M ammonium sulfate. This mild procedure removes chromatin almost completely and preserves nuclear matrix morphology. The complete nuclear matrix consists of a nuclear lamina with an interior matrix composed of thick, polymorphic fibers and large masses that resemble remnant nucleoli. Further extraction of the nuclear matrices of HeLa or MCF-7 cells with 2 M sodium chloride uncovered a network of core filaments. A few dark masses remained enmeshed in the filament network and may be remnants of the nuclear matrix thick fibers and nucleoli. The highly branched core filaments had diameters of 9 and 13 nm measured relative to the intermediate filaments. They may serve as the core structure around which the matrix is constructed. The core filaments retained 70% of nuclear RNA. This RNA consisted both of ribosomal RNA precursors and of very high molecular weight hnRNA with a modal size of 20 kb. Treatment with RNase A removed the core filaments. When 2 M sodium chloride was used directly to remove chromatin after DNase I digestion without a preceding 0.25 M ammonium sulfate extraction, the core filaments were not revealed. Instead, the nuclear interior was filled with amorphous masses that may cover the filaments. This reflected a requirement for a stepwise increase in ionic strength because gradual addition of sodium chloride to a final concentration of 2 M without an 0.25 M ammonium sulfate extraction uncovered core filaments.
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Affiliation(s)
- D C He
- Department of Biology, Beijing Normal University, Peoples Republic of China
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17
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Transcriptional regulation of two serum-induced RNAs in mouse fibroblasts: equivalence of one species to B2 repetitive elements. Mol Cell Biol 1986. [PMID: 3837843 DOI: 10.1128/mcb.5.11.3280] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We obtained eight cDNA clones that define five genes whose expression (appearance of transcripts in the cytoplasm) is enhanced when quiescent mouse fibroblasts are stimulated with serum to divide. Two of these clones (designated 49C8 and 16C8) correspond to RNA species that are present in the cytoplasm of quiescent cells at very low levels. After serum stimulation, the level of 16C8 mRNA rose more rapidly than that of 49C8 RNA, reaching a maximum around 6 to 12 h. The data suggest that 49C8 and 16C8 RNAs are induced as a result of independent stimuli. Either fibroblast growth factor or 12-tetradecanoylphorbol-13-acetate alone could induce 16C8 expression almost as effectively as serum; in contrast, 49C8 was not efficiently induced by epidermal growth factor, fibroblast growth factor, insulin, or 12-tetradecanoylphorbol-13-acetate. Inhibitors of transcription and translation diminished the induction of 16C8, while 49C8 expression was sensitive to actinomycin D but not cycloheximide or 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole. In vitro transcription experiments with isolated nuclei revealed a peak in transcriptional activity of the 16C8 gene at around 3 h after serum stimulation. Sequence analysis of the 49C8 cDNA clone showed greater than 90% homology of a large portion to a consensus rodent B2 repetitive element.
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18
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Edwards DR, Parfett CL, Denhardt DT. Transcriptional regulation of two serum-induced RNAs in mouse fibroblasts: equivalence of one species to B2 repetitive elements. Mol Cell Biol 1985; 5:3280-8. [PMID: 3837843 PMCID: PMC369145 DOI: 10.1128/mcb.5.11.3280-3288.1985] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We obtained eight cDNA clones that define five genes whose expression (appearance of transcripts in the cytoplasm) is enhanced when quiescent mouse fibroblasts are stimulated with serum to divide. Two of these clones (designated 49C8 and 16C8) correspond to RNA species that are present in the cytoplasm of quiescent cells at very low levels. After serum stimulation, the level of 16C8 mRNA rose more rapidly than that of 49C8 RNA, reaching a maximum around 6 to 12 h. The data suggest that 49C8 and 16C8 RNAs are induced as a result of independent stimuli. Either fibroblast growth factor or 12-tetradecanoylphorbol-13-acetate alone could induce 16C8 expression almost as effectively as serum; in contrast, 49C8 was not efficiently induced by epidermal growth factor, fibroblast growth factor, insulin, or 12-tetradecanoylphorbol-13-acetate. Inhibitors of transcription and translation diminished the induction of 16C8, while 49C8 expression was sensitive to actinomycin D but not cycloheximide or 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole. In vitro transcription experiments with isolated nuclei revealed a peak in transcriptional activity of the 16C8 gene at around 3 h after serum stimulation. Sequence analysis of the 49C8 cDNA clone showed greater than 90% homology of a large portion to a consensus rodent B2 repetitive element.
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19
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Newly formed mRNA lacking polyadenylic acid enters the cytoplasm and the polyribosomes but has a shorter half-life in the absence of polyadenylic acid. Mol Cell Biol 1982. [PMID: 6981059 DOI: 10.1128/mcb.2.5.517] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Labeled adenovirus type 2 nuclear RNA molecules from cells treated with 3'-deoxyadenosine (3'dA) were earlier reported to lack polyadenylic acid [poly(A)], but to be correctly spliced in the nucleus (M. Zeevi et al., Cell 26:39-46, 1981). We have now found that the shortened mRNA molecules, lacking poly(A), can also be found in the cytoplasm of 3'dA-treated cells in association with the polyribosomes. In addition, the accumulation of labeled, nuclear adenovirus-specific RNA complementary to early regions 1a, 1b, and 2 of the adenovirus genome was approximately equal in 3'dA-treated and control cells. At the initial appearance of newly labeled adenovirus type 2 RNA (10 min) in the cytoplasm, there was one-half as much labeled RNA in 3'dA-treated cells as in the control. However, control cells accumulated additional mRNA in the cytoplasm very rapidly in the first 40 min of labeling, whereas the 3'dA-treated cells did not. Therefore, it appears that the correctly spliced, poly(A)- mRNA molecules that are labeled in the presence of 3'dA can be transported from the nucleus with nearly the same frequency and the same exit time as in control cells and can be translated in the cytoplasm but have a much shorter half-life than the poly(A)+ mRNA molecules from control infected cells. From these results it is suggested that the role of poly(A) may be entirely to increase the longevity of cytoplasmic mRNA.
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20
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Zeevi M, Nevins JR, Darnell JE. Newly formed mRNA lacking polyadenylic acid enters the cytoplasm and the polyribosomes but has a shorter half-life in the absence of polyadenylic acid. Mol Cell Biol 1982; 2:517-25. [PMID: 6981059 PMCID: PMC369821 DOI: 10.1128/mcb.2.5.517-525.1982] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Labeled adenovirus type 2 nuclear RNA molecules from cells treated with 3'-deoxyadenosine (3'dA) were earlier reported to lack polyadenylic acid [poly(A)], but to be correctly spliced in the nucleus (M. Zeevi et al., Cell 26:39-46, 1981). We have now found that the shortened mRNA molecules, lacking poly(A), can also be found in the cytoplasm of 3'dA-treated cells in association with the polyribosomes. In addition, the accumulation of labeled, nuclear adenovirus-specific RNA complementary to early regions 1a, 1b, and 2 of the adenovirus genome was approximately equal in 3'dA-treated and control cells. At the initial appearance of newly labeled adenovirus type 2 RNA (10 min) in the cytoplasm, there was one-half as much labeled RNA in 3'dA-treated cells as in the control. However, control cells accumulated additional mRNA in the cytoplasm very rapidly in the first 40 min of labeling, whereas the 3'dA-treated cells did not. Therefore, it appears that the correctly spliced, poly(A)- mRNA molecules that are labeled in the presence of 3'dA can be transported from the nucleus with nearly the same frequency and the same exit time as in control cells and can be translated in the cytoplasm but have a much shorter half-life than the poly(A)+ mRNA molecules from control infected cells. From these results it is suggested that the role of poly(A) may be entirely to increase the longevity of cytoplasmic mRNA.
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