451
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Zhang L, Yang Z, Trottier J, Barbier O, Wang L. Long noncoding RNA MEG3 induces cholestatic liver injury by interaction with PTBP1 to facilitate shp mRNA decay. Hepatology 2017; 65:604-615. [PMID: 27770549 PMCID: PMC5258819 DOI: 10.1002/hep.28882] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
UNLABELLED Bile acids (BAs) play critical physiological functions in cholesterol homeostasis, and deregulation of BA metabolism causes cholestatic liver injury. The long noncoding RNA maternally expressed gene 3 (MEG3) was recently shown as a potential tumor suppressor; however, its basic hepatic function remains elusive. Using RNA pull-down with biotin-labeled sense or anti-sense MEG 3RNA followed by mass spectrometry, we identified RNA-binding protein polypyrimidine tract-binding protein 1 (PTBP1) as a MEG3 interacting protein and validated their interaction by RNA immunoprecipitation (RIP). Bioinformatics analysis revealed putative binding sites for PTBP1 within the coding region (CDS) of small heterodimer partner (SHP), a key repressor of BA biosynthesis. Forced expression of MEG3 in hepatocellular carcinoma cells guided and facilitated PTBP1 binding to the Shp CDS, resulting in Shp mRNA decay. Transient overexpression of MEG3 RNA in vivo in mouse liver caused rapid Shp mRNA degradation and cholestatic liver injury, which was accompanied by the disruption of BA homeostasis, elevation of liver enzymes, as well as dysregulation of BA synthetic enzymes and metabolic genes. Interestingly, RNA sequencing coupled with quantitative PCR (qPCR) revealed a drastic induction of MEG3 RNA in Shp-/- liver. SHP inhibited MEG3 gene transcription by repressing cAMP response element-binding protein (CREB) transactivation of the MEG3 promoter. In addition, the expression of MEG3 and PTBP1 was activated in human fibrotic and cirrhotic livers. CONCLUSION MEG3 causes cholestasis by serving as a guide RNA scaffold to recruit PTBP1 to destabilize Shp mRNA. SHP in turn represses CREB-mediated activation of MEG3 expression in a feedback-regulatory fashion. (Hepatology 2017;65:604-615).
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Affiliation(s)
- Li Zhang
- Department of Physiology and Neurobiology, and The Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
| | - Zhihong Yang
- Department of Physiology and Neurobiology, and The Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269,Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516
| | - Jocelyn Trottier
- Laboratory of Molecular Pharmacology, CHU-Québec Research Centre and Faculty of Pharmacy, Laval University, Québec, QC, Canada
| | - Olivier Barbier
- Laboratory of Molecular Pharmacology, CHU-Québec Research Centre and Faculty of Pharmacy, Laval University, Québec, QC, Canada
| | - Li Wang
- Department of Physiology and Neurobiology, and The Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269,Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516,Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, CT 06520,School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,Address reprint requests to: Li Wang, Ph.D., 75 North Eagleville Rd., U3156, Storrs, CT 06269. ; Tel: 860-486-0857; Fax: 860-486-3303
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452
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Sridhar B, Rivas-Astroza M, Nguyen TC, Chen W, Yan Z, Cao X, Hebert L, Zhong S. Systematic Mapping of RNA-Chromatin Interactions In Vivo. Curr Biol 2017; 27:602-609. [PMID: 28132817 DOI: 10.1016/j.cub.2017.01.011] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 12/22/2016] [Accepted: 01/06/2017] [Indexed: 12/15/2022]
Abstract
RNA molecules can attach to chromatin. It remains difficult to know what RNAs are associated with chromatin and where the genomic target loci of these RNAs are. Here, we present MARGI (mapping RNA-genome interactions), a technology to massively reveal native RNA-chromatin interactions from unperturbed cells. The gist of this technology is to ligate chromatin-associated RNAs (caRNAs) with their target genomic sequences by proximity ligation, forming RNA-DNA chimeric sequences, which are converted to a sequencing library for paired-end sequencing. Using MARGI, we produced RNA-genome interaction maps for human embryonic stem cells (ESCs) and human embryonic kidney (HEK) cells. MARGI revealed hundreds of caRNAs, including previously known XIST, SNHG1, NEAT1, and MALAT1, as well as each caRNA's genomic interaction loci. Using a cross-species experiment, we estimated that approximately 2.2% of MARGI-identified interactions were false positives. In ESCs and HEK cells, the RNA ends of more than 5% of MARGI read pairs were mapped to distal or inter-chromosomal locations as compared to the locations of their corresponding DNA ends. The majority of transcription start sites are associated with distal or inter-chromosomal caRNAs. Chromatin-immunoprecipitation-sequencing (ChIP-seq)-reported H3K27ac and H3K4me3 levels are positively correlated, while H3K9me3 is negatively correlated, with MARGI-reported RNA attachment levels. The MARGI technology should facilitate revealing novel RNA functions and their genomic target regions.
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Affiliation(s)
- Bharat Sridhar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Marcelo Rivas-Astroza
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tri C Nguyen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Weizhong Chen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhangming Yan
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiaoyi Cao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lucie Hebert
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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453
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Mao X, Su Z, Mookhtiar AK. Long non-coding RNA: a versatile regulator of the nuclear factor-κB signalling circuit. Immunology 2017; 150:379-388. [PMID: 27936492 DOI: 10.1111/imm.12698] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/27/2016] [Accepted: 12/01/2016] [Indexed: 12/16/2022] Open
Abstract
The nuclear factor-κB (NF-κB) family of transcription factors play an essential role for the regulation of inflammatory responses, immune function and malignant transformation. Aberrant activity of this signalling pathway may lead to inflammation, autoimmune diseases and oncogenesis. Over the last two decades great progress has been made in the understanding of NF-κB activation and how the response is counteracted for maintaining tissue homeostasis. Therapeutic targeting of this pathway has largely remained ineffective due to the widespread role of this vital pathway and the lack of specificity of the therapies currently available. Besides regulatory proteins and microRNAs, long non-coding RNA (lncRNA) is emerging as another critical layer of the intricate modulatory architecture for the control of the NF-κB signalling circuit. In this paper we focus on recent progress concerning lncRNA-mediated modulation of the NF-κB pathway, and evaluate the potential therapeutic uses and challenges of using lncRNAs that regulate NF-κB activity.
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Affiliation(s)
- Xiaohua Mao
- Department of Biochemistry, Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Zhenyi Su
- Department of Biochemistry, Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, School of Medicine, Southeast University, Nanjing, Jiangsu, China
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454
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Brock M, Schuoler C, Leuenberger C, Bühlmann C, Haider TJ, Vogel J, Ulrich S, Gassmann M, Kohler M, Huber LC. Analysis of hypoxia-induced noncoding RNAs reveals metastasis-associated lung adenocarcinoma transcript 1 as an important regulator of vascular smooth muscle cell proliferation. Exp Biol Med (Maywood) 2017; 242:487-496. [PMID: 28056547 DOI: 10.1177/1535370216685434] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Vascular remodeling, a pathogenic hallmark in pulmonary hypertension, is mainly driven by a dysbalance between proliferation and apoptosis of human pulmonary artery smooth muscle cells. It has previously been shown that microRNAs are involved in the pathogenesis of pulmonary hypertension. However, the role of long noncoding RNAs has not been evaluated. long noncoding RNA expression was quantified in human pulmonary artery smooth muscle cells using PCR arrays and quantitative PCR. Knockdown of genes was performed by transfection of siRNA or GapmeR. Proliferation and migration were measured using BrdU incorporation and wound healing assays. The mouse model of hypoxia-induced PH was used to determine the physiological meaning of identified long noncoding RNAs. The expression of 84 selected long noncoding RNAs was assessed in hypoxic human pulmonary artery smooth muscle cells and the levels of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) were significantly increased. Depletion of hypoxia-inducible factor 1α abolished the hypoxia-induced upregulation of metastasis-associated lung adenocarcinoma transcript 1 expression. Silencing of MALAT1 significantly decreased proliferation and migration of human pulmonary artery smooth muscle cells. In vivo, MALAT1 expression was significantly increased in lungs of hypoxic mice. Of note, targeting of MALAT1 by GapmeR ameliorated heart hypertrophy in mice with pulmonary hypertension. This is the first report on functional characterization of MALAT1 in the pulmonary vasculature. Our data provide evidence that MALAT1 expression is significantly increased by hypoxia, probably by hypoxia-inducible factor 1α. Intervention experiments confirmed that MALAT1 regulates the proliferative phenotype of smooth muscle cells and silencing of MALAT1 reduced heart hypertrophy in mice with pulmonary hypertension. These data indicate a potential role of MALAT1 in the pathogenesis of pulmonary hypertension. Impact statement Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long noncoding RNA that mediates several biological processes. In the context of vascular biology, MALAT1 has been shown to be inducible by hypoxia and to control cell proliferation. These processes are of major importance for the pathophysiology of hypoxia-induced pulmonary hypertension (PH). Until now, the physiological role of MALAT1 in PH remains unclear. By using smooth muscle cells and by employing an established PH mouse model, we provide evidence that hypoxia induces MALAT1 expression. Moreover, depletion of MALAT1 inhibited migration and proliferation of smooth muscle cells, probably by the induction of cyclin-dependent kinase inhibitors. Of note, MALAT1 was significantly increased in mice exposed to hypoxia and silencing of MALAT1 ameliorated heart hypertrophy in mice with hypoxia-induced PH. Since vascular remodeling and right heart failure as a consequence of pulmonary pressure overload is a major problem in PH, these data have implications for our pathogenetic understanding.
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Affiliation(s)
- Matthias Brock
- 1 Division of Pulmonology, University Hospital Zurich, University of Zurich, Zurich CH-8091, Switzerland
| | - Claudio Schuoler
- 1 Division of Pulmonology, University Hospital Zurich, University of Zurich, Zurich CH-8091, Switzerland.,2 Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich CH-8057, Switzerland
| | - Caroline Leuenberger
- 1 Division of Pulmonology, University Hospital Zurich, University of Zurich, Zurich CH-8091, Switzerland
| | - Carlo Bühlmann
- 1 Division of Pulmonology, University Hospital Zurich, University of Zurich, Zurich CH-8091, Switzerland
| | - Thomas J Haider
- 2 Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich CH-8057, Switzerland.,3 Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich CH-8057, Switzerland
| | - Johannes Vogel
- 2 Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich CH-8057, Switzerland.,3 Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich CH-8057, Switzerland
| | - Silvia Ulrich
- 1 Division of Pulmonology, University Hospital Zurich, University of Zurich, Zurich CH-8091, Switzerland
| | - Max Gassmann
- 2 Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich CH-8057, Switzerland.,3 Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich CH-8057, Switzerland
| | - Malcolm Kohler
- 1 Division of Pulmonology, University Hospital Zurich, University of Zurich, Zurich CH-8091, Switzerland
| | - Lars C Huber
- 1 Division of Pulmonology, University Hospital Zurich, University of Zurich, Zurich CH-8091, Switzerland
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455
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El Bassit G, Patel RS, Carter G, Shibu V, Patel AA, Song S, Murr M, Cooper DR, Bickford PC, Patel NA. MALAT1 in Human Adipose Stem Cells Modulates Survival and Alternative Splicing of PKCδII in HT22 Cells. Endocrinology 2017; 158:183-195. [PMID: 27841943 PMCID: PMC5412980 DOI: 10.1210/en.2016-1819] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 11/04/2016] [Indexed: 01/15/2023]
Abstract
Brain injury may be caused by trauma or may occur in stroke and neurodegenerative diseases. Because the central nervous system is unable to regenerate efficiently, there is utmost interest in the use of stem cells to promote neuronal survival. Of interest here are human adipose-derived stem cells (hASCs), which secrete factors that enhance regeneration and survival of neurons in sites of injury. We evaluated the effect of hASC secretome on immortalized mouse hippocampal cell line (HT22) after injury. Protein kinase C δ (PKCδ) activates survival and proliferation in neurons and is implicated in memory. We previously showed that alternatively spliced PKCδII enhances neuronal survival via B-cell lymphoma 2 Bcl2 in HT22 neuronal cells. Our results demonstrate that following injury, treatment with exosomes from the hASC secretome increases expression of PKCδII in HT22 cells and increases neuronal survival and proliferation. Specifically, we demonstrate that metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long noncoding RNA contained in the hASC exosomes mediates PKCδII splicing, thereby increasing neuronal survival. Using antisense oligonucleotides for MALAT1 and RNA immunoprecipitation assays, we demonstrate that MALAT1 recruits splice factor serine-arginine-rich splice factor 2 (SRSF2) to promote alternative splicing of PKCδII. Finally, we evaluated the role of insulin in enhancing hASC-mediated neuronal survival and demonstrated that insulin treatment dramatically increases the association of MALAT1 and SRSF2 and substantially increases survival and proliferation after injury in HT22 cells. In conclusion, we demonstrate the mechanism of action of hASC exosomes in increasing neuronal survival. This effect of hASC exosomes to promote wound healing can be further enhanced by insulin treatment in HT22 cells.
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Affiliation(s)
| | | | - Gay Carter
- James A. Haley Veterans Hospital, Tampa, Florida 33612; and
| | | | | | - Shijie Song
- James A. Haley Veterans Hospital, Tampa, Florida 33612; and
| | | | - Denise R. Cooper
- James A. Haley Veterans Hospital, Tampa, Florida 33612; and
- Molecular Medicine,
| | - Paula C. Bickford
- James A. Haley Veterans Hospital, Tampa, Florida 33612; and
- Neurosurgery and Brain Survival, University of South Florida, Tampa, Florida 33612
| | - Niketa A. Patel
- James A. Haley Veterans Hospital, Tampa, Florida 33612; and
- Molecular Medicine,
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456
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Peng W, Wang Z, Fan H. LncRNA NEAT1 Impacts Cell Proliferation and Apoptosis of Colorectal Cancer via Regulation of Akt Signaling. Pathol Oncol Res 2016; 23:651-656. [PMID: 28013491 DOI: 10.1007/s12253-016-0172-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/16/2016] [Indexed: 10/20/2022]
Abstract
Long noncoding RNA (lncRNA) have been reported to modulate oncogenesis and be used to be target for tumor. The role of lncRNA NEAT1 (nuclear paraspeckle assembly transcript 1, Gene ID: 283131) in colorectal cancer (CRC) keeps unknown. This work was to investigate the pattern of lncRNA NEAT1 (NEAT1) expression in CRC and its functional value and biological significance. NEAT1 expression was analyzed in 56 cancer tissues and cell lines in CRC cases. Results showed that NEAT1 was significantly overexpressed in CRC cells and tissues. Clinicpathologic detection verified that high NEAT1 expression associated with bulk in CRC. The serum contents of NEAT1 were observably elevated comparing with healthy cases (P < 0.05). The levels of NEAT1 were elevated in distinguishing CRC from normal (ROCAUC = 0.9471; P < 0.01). Moreover, Kaplan-Meier analysis found that NEAT1 elevation led to adverse survival (P < 0.05). Further experiments illustrated that of NEAT1 knockdown signally inhibited growth and facilitated apoptosis. Importantly, we confirmed that Akt signaling pathway was inactivated after loss of NEAT1 in CRC. Taken together, this work support the first evidence that NEAT1 can be used to be a promising biomarker and target for novel treatment for human CRC.
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Affiliation(s)
- Wei Peng
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, No. 42 Baiziting Road, Nanjing, 210009, China.
| | - Zhuo Wang
- Laboratory of Cancer Research, Jiangsu Cancer Hospital, Nanjing Medical University, No. 42 Baiziting Road, Nanjing, 210009, China
| | - Hong Fan
- Department of Gastroenterology, First People's Hospital of Yunnan Province, No. 175 Jinbi Road, Kunming, 650032, China
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457
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Aiello A, Bacci L, Re A, Ripoli C, Pierconti F, Pinto F, Masetti R, Grassi C, Gaetano C, Bassi PF, Pontecorvi A, Nanni S, Farsetti A. MALAT1 and HOTAIR Long Non-Coding RNAs Play Opposite Role in Estrogen-Mediated Transcriptional Regulation in Prostate Cancer Cells. Sci Rep 2016; 6:38414. [PMID: 27922078 PMCID: PMC5138831 DOI: 10.1038/srep38414] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/07/2016] [Indexed: 12/15/2022] Open
Abstract
In the complex network of nuclear hormone receptors, the long non-coding RNAs (lncRNAs) are emerging as critical determinants of hormone action. Here we investigated the involvement of selected cancer-associated lncRNAs in Estrogen Receptor (ER) signaling. Prior studies by Chromatin Immunoprecipitation (ChIP) Sequencing showed that in prostate cancer cells ERs form a complex with the endothelial nitric oxide synthase (eNOS) and that in turn these complexes associate with chromatin in an estrogen-dependent fashion. Among these associations (peaks) we focused our attention on those proximal to the regulatory region of HOTAIR and MALAT1. These transcripts appeared regulated by estrogens and able to control ERs function by interacting with ERα/ERβ as indicated by RNA-ChIP. Further studies performed by ChIRP revealed that in unstimulated condition, HOTAIR and MALAT1 were present on pS2, hTERT and HOTAIR promoters at the ERE/eNOS peaks. Interestingly, upon treatment with17β-estradiol HOTAIR recruitment to chromatin increased significantly while that of MALAT1 was reduced, suggesting an opposite regulation and function for these lncRNAs. Similar results were obtained in cells and in an ex vivo prostate organotypic slice cultures. Overall, our data provide evidence of a crosstalk between lncRNAs, estrogens and estrogen receptors in prostate cancer with important consequences on gene expression regulation.
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Affiliation(s)
- Aurora Aiello
- National Research Council, Institute of Cell Biology and Neurobiology, Rome, 00143, Italy.,Università Cattolica, Institute of Medical Pathology, Rome, 00168, Italy
| | - Lorenza Bacci
- Università Cattolica, Institute of Medical Pathology, Rome, 00168, Italy
| | - Agnese Re
- National Research Council, Institute of Cell Biology and Neurobiology, Rome, 00143, Italy
| | - Cristian Ripoli
- Università Cattolica, Institute of Human Physiology, Rome, 00168, Italy
| | | | - Francesco Pinto
- Università Cattolica, Fondazione Policlinico 'A. Gemelli', Urological Clinic, Rome, 00168, Italy
| | - Riccardo Masetti
- Università Cattolica, Multidisciplinary Breast Center, Fondazione Policlinico 'A. Gemelli', Rome, 00168, Italy
| | - Claudio Grassi
- Università Cattolica, Institute of Human Physiology, Rome, 00168, Italy.,San Raffaele Pisana Scientific Institute for Research, Hospitalization and Health Care, 00163 Rome, Italy
| | - Carlo Gaetano
- Goethe University Frankfurt, Division of Cardiovascular Epigenetics, Department of Cardiology, Internal Medicine Clinic III, Frankfurt am Main, 60590, Germany
| | - Pier Francesco Bassi
- Università Cattolica, Fondazione Policlinico 'A. Gemelli', Urological Clinic, Rome, 00168, Italy
| | - Alfredo Pontecorvi
- Università Cattolica, Institute of Medical Pathology, Rome, 00168, Italy
| | - Simona Nanni
- Università Cattolica, Institute of Medical Pathology, Rome, 00168, Italy
| | - Antonella Farsetti
- National Research Council, Institute of Cell Biology and Neurobiology, Rome, 00143, Italy.,Goethe University Frankfurt, Internal Medicine Clinic III, Frankfurt am Main, 60590, Germany
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458
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Lo PK, Wolfson B, Zhou Q. Cellular, physiological and pathological aspects of the long non-coding RNA NEAT1. FRONTIERS IN BIOLOGY 2016; 11:413-426. [PMID: 29033980 PMCID: PMC5637405 DOI: 10.1007/s11515-016-1433-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The majority of mammalian genomes have been found to be transcribed into non-coding RNAs. One category of non-coding RNAs is classified as long non-coding RNAs (lncRNAs) based on their transcript sizes larger than 200 nucleotides. Growing evidence has shown that lncRNAs are not junk transcripts and play regulatory roles in multiple aspects of biological processes. Dysregulation of lncRNA expression has also been linked to diseases, in particular cancer. Therefore, studies of lncRNAs have attracted significant interest in the field of medical research. Nuclear enriched abundant transcript 1 (NEAT1), a nuclear lncRNA, has recently emerged as a key regulator involved in various cellular processes, physiological responses, developmental processes, and disease development and progression. OBJECTIVE This review will summarize and discuss the most recent findings with regard to the roles of NEAT1 in the function of the nuclear paraspeckle, cellular pathways, and physiological responses and processes. Particularly, the most recently reported studies regarding the pathological roles of deregulated NEAT1 in cancer are highlighted in this review. METHODS We performed a systematic literature search using the Pubmed search engine. Studies published over the last 8 years (between January 2009 and August 2016) were the sources of literature review. The following keywords were used: "Nuclear enriched abundant transcript 1", "NEAT1", and "paraspeckles". RESULTS The Pubmed search identified 34 articles related to the topic of the review. Among the identified literature, thirteen articles report findings related to cellular functions of NEAT1 and eight articles are the investigations of physiological functions of NEAT1. The remaining thirteen articles are studies of the roles of NEAT1 in cancers. CONCLUSION Recent advances in NEAT1 studies reveal the multifunctional roles of NEAT1 in various biological processes, which are beyond its role in nuclear paraspeckles. Recent studies also indicate that dysregulation of NEAT1 function contributes to the development and progression of various cancers. More investigations will be needed to address the detailed mechanisms regarding how NEAT1 executes its cellular and physiological functions and how NEAT1 dysregulation results in tumorigenesis, and to explore the potential of NEAT1 as a target in cancer diagnosis, prognosis and therapy.
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Affiliation(s)
- Pang-Kuo Lo
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Benjamin Wolfson
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Qun Zhou
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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459
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The increasing diversity of functions attributed to the SAFB family of RNA-/DNA-binding proteins. Biochem J 2016; 473:4271-4288. [DOI: 10.1042/bcj20160649] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/28/2016] [Accepted: 09/02/2016] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins play a central role in cellular metabolism by orchestrating the complex interactions of coding, structural and regulatory RNA species. The SAFB (scaffold attachment factor B) proteins (SAFB1, SAFB2 and SAFB-like transcriptional modulator, SLTM), which are highly conserved evolutionarily, were first identified on the basis of their ability to bind scaffold attachment region DNA elements, but attention has subsequently shifted to their RNA-binding and protein–protein interactions. Initial studies identified the involvement of these proteins in the cellular stress response and other aspects of gene regulation. More recently, the multifunctional capabilities of SAFB proteins have shown that they play crucial roles in DNA repair, processing of mRNA and regulatory RNA, as well as in interaction with chromatin-modifying complexes. With the advent of new techniques for identifying RNA-binding sites, enumeration of individual RNA targets has now begun. This review aims to summarise what is currently known about the functions of SAFB proteins.
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460
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Cai L, Chang H, Fang Y, Li G. A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions. Sci Rep 2016; 6:36572. [PMID: 27824113 PMCID: PMC5099911 DOI: 10.1038/srep36572] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 10/18/2016] [Indexed: 11/13/2022] Open
Abstract
LincRNAs are emerging as important regulators with various cellular functions. However, the mechanisms behind their role in transcriptional regulation have not yet been fully explored. In this report, we proposed to characterize the diverse functions of lincRNAs in transcription regulation through an examination of their long-range chromatin interactions. We found that the promoter regions of lincRNAs displayed two distinct patterns of chromatin states, promoter-like and enhancer-like, indicating different regulatory functions for lincRNAs. Notably, the chromatin interactions between lincRNA genes and other genes suggested a potential mechanism for lincRNAs in the regulation of other genes at the RNA level because the transcribed lincRNAs could function at local spaces on other genes that interact with the lincRNAs at the DNA level. These results represent a novel way to predict the functions of lincRNAs. The GWAS-identification of SNPs within the lincRNAs revealed that some lincRNAs were disease-associated, and the chromatin interactions with those lincRNAs suggested that they were potential target genes of these lincRNA-associated SNPs. Our study provides new insights into the roles that lincRNAs play in transcription regulation.
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Affiliation(s)
- Liuyang Cai
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Huidan Chang
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yaping Fang
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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461
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Chillón I, Pyle AM. Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function. Nucleic Acids Res 2016; 44:9462-9471. [PMID: 27378782 PMCID: PMC5100600 DOI: 10.1093/nar/gkw599] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/01/2016] [Accepted: 06/22/2016] [Indexed: 12/18/2022] Open
Abstract
LincRNA-p21 is a long intergenic non-coding RNA (lincRNA) involved in the p53-mediated stress response. We sequenced the human lincRNA-p21 (hLincRNA-p21) and found that it has a single exon that includes inverted repeat Alu elements (IRAlus). Sense and antisense Alu elements fold independently of one another into a secondary structure that is conserved in lincRNA-p21 among primates. Moreover, the structures formed by IRAlus are involved in the localization of hLincRNA-p21 in the nucleus, where hLincRNA-p21 colocalizes with paraspeckles. Our results underscore the importance of IRAlus structures for the function of hLincRNA-p21 during the stress response.
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Affiliation(s)
- Isabel Chillón
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Anna M Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
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462
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Marchese D, de Groot NS, Lorenzo Gotor N, Livi CM, Tartaglia GG. Advances in the characterization of RNA-binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:793-810. [PMID: 27503141 PMCID: PMC5113702 DOI: 10.1002/wrna.1378] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/14/2016] [Accepted: 06/23/2016] [Indexed: 12/14/2022]
Abstract
From transcription, to transport, storage, and translation, RNA depends on association with different RNA-binding proteins (RBPs). Methods based on next-generation sequencing and protein mass-spectrometry have started to unveil genome-wide interactions of RBPs but many aspects still remain out of sight. How many of the binding sites identified in high-throughput screenings are functional? A number of computational methods have been developed to analyze experimental data and to obtain insights into the specificity of protein-RNA interactions. How can theoretical models be exploited to identify RBPs? In addition to oligomeric complexes, protein and RNA molecules can associate into granular assemblies whose physical properties are still poorly understood. What protein features promote granule formation and what effects do these assemblies have on cell function? Here, we describe the newest in silico, in vitro, and in vivo advances in the field of protein-RNA interactions. We also present the challenges that experimental and computational approaches will have to face in future studies. WIREs RNA 2016, 7:793-810. doi: 10.1002/wrna.1378 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Domenica Marchese
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Natalia Sanchez de Groot
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Nieves Lorenzo Gotor
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmen Maria Livi
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- IFOM Foundation, FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Gian G Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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463
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Leucci E, Coe EA, Marine JC, Vance KW. The emerging role of long non-coding RNAs in cutaneous melanoma. Pigment Cell Melanoma Res 2016; 29:619-626. [PMID: 27606977 DOI: 10.1111/pcmr.12537] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/09/2016] [Indexed: 12/21/2022]
Abstract
Malignant melanoma is a highly aggressive form of skin cancer, the incidence of which is rising rapidly. Although MAPK-targeting therapies and immune checkpoint blockade are emerging as attractive therapeutic approaches, their utility is limited to only a subset of patients who often acquire resistance. A better understanding of the aetiologies and genetic underpinnings of melanoma is therefore critical for the development of adjuvant or alternative therapeutic strategies aimed at increasing the proportion of responders and improving treatment efficacy. A key step in identifying novel therapeutic targets may be the shift in focus from the protein-coding components to the non-coding portion of the genome. The latter, representing about 98% of the genome, serves as a template for the transcription of many thousands of long non-coding RNAs (lncRNAs). Intriguingly, lncRNA loci are frequently mutated or altered in a variety of cancers, including melanoma, and there is growing evidence that lncRNAs can function as cancer-causing oncogenes or tumour suppressors. In this review, we summarize recent data highlighting the importance of lncRNAs in the biology of melanoma and their potential utility as biomarkers and therapeutic targets.
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Affiliation(s)
- Eleonora Leucci
- Laboratory for Molecular Cancer Biology, Center for the Biology of Disease, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Center of Human Genetics, Leuven, Belgium
| | - Elizabeth A Coe
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for the Biology of Disease, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Center of Human Genetics, Leuven, Belgium
| | - Keith W Vance
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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464
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Atianand MK, Hu W, Satpathy AT, Shen Y, Ricci EP, Alvarez-Dominguez JR, Bhatta A, Schattgen SA, McGowan JD, Blin J, Braun JE, Gandhi P, Moore MJ, Chang HY, Lodish HF, Caffrey DR, Fitzgerald KA. A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. Cell 2016; 165:1672-1685. [PMID: 27315481 DOI: 10.1016/j.cell.2016.05.075] [Citation(s) in RCA: 360] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/19/2016] [Accepted: 05/25/2016] [Indexed: 12/19/2022]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are important regulators of gene expression. Although lincRNAs are expressed in immune cells, their functions in immunity are largely unexplored. Here, we identify an immunoregulatory lincRNA, lincRNA-EPS, that is precisely regulated in macrophages to control the expression of immune response genes (IRGs). Transcriptome analysis of macrophages from lincRNA-EPS-deficient mice, combined with gain-of-function and rescue experiments, revealed a specific role for this lincRNA in restraining IRG expression. Consistently, lincRNA-EPS-deficient mice manifest enhanced inflammation and lethality following endotoxin challenge in vivo. lincRNA-EPS localizes at regulatory regions of IRGs to control nucleosome positioning and repress transcription. Further, lincRNA-EPS mediates these effects by interacting with heterogeneous nuclear ribonucleoprotein L via a CANACA motif located in its 3' end. Together, these findings identify lincRNA-EPS as a repressor of inflammatory responses, highlighting the importance of lincRNAs in the immune system.
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Affiliation(s)
- Maninjay K Atianand
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Wenqian Hu
- Whitehead Institute, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ying Shen
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emiliano P Ricci
- Howard Hughes Medical Institute and Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - Ankit Bhatta
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Stefan A Schattgen
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jason D McGowan
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Juliana Blin
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Joerg E Braun
- Howard Hughes Medical Institute and Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Pallavi Gandhi
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Melissa J Moore
- Howard Hughes Medical Institute and Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Harvey F Lodish
- Whitehead Institute, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA
| | - Daniel R Caffrey
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA 01605, USA; Centre for Molecular Inflammation Research, Department of Cancer Research and Molecular Medicine, NTNU, 7491 Trondheim, Norway.
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465
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HULC cooperates with MALAT1 to aggravate liver cancer stem cells growth through telomere repeat-binding factor 2. Sci Rep 2016; 6:36045. [PMID: 27782152 PMCID: PMC5080550 DOI: 10.1038/srep36045] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/26/2016] [Indexed: 12/29/2022] Open
Abstract
The dysregulation of lncRNAs has increasingly been linked to many human diseases, especially in cancers. Our results demonstrate HULC, MALAT1 and TRF2 are highly expressed in human hepatocellular carcinoma tissues, and HULC plus MALAT1 overexpression drastically promotes the growth of liver cancer stem cells. Mechanistically, both HULC and MALAT1 overexpression enhanced RNA polII, P300, CREPT to load on the promoter region of telomere repeat-binding factor 2(TRF2), triggering the overexpression, phosphorylation and SUMOylation of TRF2. Strikingly, the excessive TRF2 interacts with HULC or MALAT1 to form the complex that loads on the telomeric region, replacing the CST/AAF and recruiting POT1, pPOT1, ExoI, SNM1B, HP1 α. Accordingly, the telomere is greatly protected and enlonged. Furthermore, the excessive HULC plus MALAT1 reduced the methylation of the TERC promoter dependent on TRF2, increasing the TERC expression that causes the increase of interplay between TRET and TERC. Ultimately, the interaction between RFC and PCNA or between CDK2 and CyclinE, the telomerase activity and the microsatellite instability (MSI) are significantly increased in the liver cancer stem cells. Our demonstrations suggest that haploinsufficiency of HULC/MALAT1 plays an important role in malignant growth of liver cancer stem cell.
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466
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Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol 2016; 17:756-770. [DOI: 10.1038/nrm.2016.126] [Citation(s) in RCA: 420] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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467
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Nascent Connections: R-Loops and Chromatin Patterning. Trends Genet 2016; 32:828-838. [PMID: 27793359 DOI: 10.1016/j.tig.2016.10.002] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/03/2016] [Accepted: 10/06/2016] [Indexed: 11/22/2022]
Abstract
RNA molecules, such as long noncoding RNAs (lncRNAs), have critical roles in regulating gene expression, chromosome architecture, and the modification states of chromatin. Recent developments suggest that RNA also influences gene expression and chromatin patterns through the interaction of nascent transcripts with their DNA template via the formation of co-transcriptional R-loop structures. R-loop formation over specific, conserved, hotspots occurs at thousands of genes in mammalian genomes and represents an important and dynamic feature of mammalian chromatin. Here, focusing primarily on mammalian systems, I describe the accumulating connections and possible mechanisms linking R-loop formation and chromatin patterning. The possible contribution of aberrant R-loops to pathological conditions is also discussed.
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468
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Wang Z, Fan P, Zhao Y, Zhang S, Lu J, Xie W, Jiang Y, Lei F, Xu N, Zhang Y. NEAT1 modulates herpes simplex virus-1 replication by regulating viral gene transcription. Cell Mol Life Sci 2016; 74:1117-1131. [PMID: 27783096 PMCID: PMC5309293 DOI: 10.1007/s00018-016-2398-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/10/2016] [Accepted: 10/11/2016] [Indexed: 12/31/2022]
Abstract
Nuclear paraspeckle assembly transcript 1 (NEAT1) is the crucial structural platform of paraspeckles, which is one type of nuclear bodies. As a stress-induced lncRNA, the expression of NEAT1 increases in response to viral infection, but little is known about the role of NEAT1 or paraspeckles in the replication of herpes simplex virus-1 (HSV-1). Here, we demonstrate that HSV-1 infection increases NEAT1 expression and paraspeckle formation in a STAT3-dependent manner. NEAT1 and other paraspeckle protein components, P54nrb and PSPC1, can associate with HSV-1 genomic DNA. By binding with STAT3, PSPC1 is required for the recruitment of STAT3 to paraspeckles and facilitates the interaction between STAT3 and viral gene promoters, finally increasing viral gene expression and viral replication. Furthermore, thermosensitive gel containing NEAT1 siRNA or STAT3 siRNA effectively healed the skin lesions caused by HSV-1 infection in mice. Our results provide insight into the roles of lncRNAs in the epigenetic control of viral genes and into the function of paraspeckles.
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Affiliation(s)
- Ziqiang Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, People's Republic of China.,Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Ping Fan
- School of Life Sciences, Tsinghua University, Beijing, 100084, People's Republic of China.,Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Yiwan Zhao
- School of Life Sciences, Tsinghua University, Beijing, 100084, People's Republic of China.,Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Shikuan Zhang
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Jinhua Lu
- Shenzhen South China Pharmaceutical Co., Ltd, Shenzhen, 518055, People's Republic of China
| | - Weidong Xie
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Yuyang Jiang
- The State Key Laboratory Breeding Base-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Fan Lei
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Naihan Xu
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, People's Republic of China. .,Open FIESTA Center, Tsinghua University, Shenzhen, 518055, People's Republic of China.
| | - Yaou Zhang
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, People's Republic of China. .,Open FIESTA Center, Tsinghua University, Shenzhen, 518055, People's Republic of China.
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469
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West JA, Mito M, Kurosaka S, Takumi T, Tanegashima C, Chujo T, Yanaka K, Kingston RE, Hirose T, Bond C, Fox A, Nakagawa S. Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization. J Cell Biol 2016; 214:817-30. [PMID: 27646274 PMCID: PMC5037409 DOI: 10.1083/jcb.201601071] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022] Open
Abstract
Paraspeckles are nuclear bodies built on the long noncoding RNA Neat1, which regulates a variety of physiological processes including cancer progression and corpus luteum formation. To obtain further insight into the molecular basis of the function of paraspeckles, we performed fine structural analyses of these nuclear bodies using structural illumination microscopy. Notably, paraspeckle proteins are found within different layers along the radially arranged bundles of Neat1 transcripts, forming a characteristic core-shell spheroidal structure. In cells lacking the RNA binding protein Fus, paraspeckle spheroids are disassembled into smaller particles containing Neat1, which are diffusely distributed in the nucleoplasm. Sequencing analysis of RNAs purified from paraspeckles revealed that AG-rich transcripts associate with Neat1, which are distributed along the shell of the paraspeckle spheroids. We propose that paraspeckles sequester core components inside the spheroids, whereas the outer surface associates with other components in the nucleoplasm to fulfill their function.
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Affiliation(s)
- Jason A West
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114 Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Mari Mito
- RNA Biology Laboratory, RIKEN, Wako 351-0198, Japan
| | | | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Chiharu Tanegashima
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takeshi Chujo
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Kaori Yanaka
- RNA Biology Laboratory, RIKEN, Wako 351-0198, Japan
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114 Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Charles Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Archa Fox
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN, Wako 351-0198, Japan RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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470
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Bouckenheimer J, Assou S, Riquier S, Hou C, Philippe N, Sansac C, Lavabre-Bertrand T, Commes T, Lemaître JM, Boureux A, De Vos J. Long non-coding RNAs in human early embryonic development and their potential in ART. Hum Reprod Update 2016; 23:19-40. [PMID: 27655590 DOI: 10.1093/humupd/dmw035] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 07/20/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human long non-coding RNAs (lncRNAs) are an emerging category of transcripts with increasingly documented functional roles during development. LncRNAs and roles during human early embryo development have recently begun to be unravelled. OBJECTIVE AND RATIONALE This review summarizes the most recent knowledge on lncRNAs and focuses on their expression patterns and role during early human embryo development and in pluripotent stem cells (PSCs). Public mRNA sequencing (mRNA-seq) data were used to illustrate these expression signatures. SEARCH METHODS The PubMed and EMBASE databases were first interrogated using specific terms, such as 'lncRNAs', to get an extensive overview on lncRNAs up to February 2016, and then using 'human lncRNAs' and 'embryo', 'development', or 'PSCs' to focus on lncRNAs involved in human embryo development or in PSC.Recently published RNA-seq data from human oocytes and pre-implantation embryos (including single-cell data), PSC and a panel of normal and malignant adult tissues were used to describe the specific expression patterns of some lncRNAs in early human embryos. OUTCOMES The existence and the crucial role of lncRNAs in many important biological phenomena in each branch of the life tree are now well documented. The number of identified lncRNAs is rapidly increasing and has already outnumbered that of protein-coding genes. Unlike small non-coding RNAs, a variety of mechanisms of action have been proposed for lncRNAs. The functional role of lncRNAs has been demonstrated in many biological and developmental processes, including cell pluripotency induction, X-inactivation or gene imprinting. Analysis of RNA-seq data highlights that lncRNA abundance changes significantly during human early embryonic development. This suggests that lncRNAs could represent candidate biomarkers for developing non-invasive tests for oocyte or embryo quality. Finally, some of these lncRNAs are also expressed in human cancer tissues, suggesting that reactivation of an embryonic lncRNA program may contribute to human malignancies. WIDER IMPLICATIONS LncRNAs are emerging potential key players in gene expression regulation. Analysis of RNA-seq data from human pre-implantation embryos identified lncRNA signatures that are specific to this critical step. We anticipate that further studies will show that these new transcripts are major regulators of embryo development. These findings might also be used to develop new tests/treatments for improving the pregnancy success rate in IVF procedures or for regenerative medicine applications involving PSC.
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Affiliation(s)
- Julien Bouckenheimer
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Said Assou
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Sébastien Riquier
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Cyrielle Hou
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Nicolas Philippe
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France.,Coretec, Montpellier, France
| | - Caroline Sansac
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | | | - Thérèse Commes
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France.,Institut de Biologie Computationnelle, Montpellier F 34000, France
| | - Jean-Marc Lemaître
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France .,INSERM, U1183, Montpellier F 34000, France.,Stem Cell Core Facility SAFE-iPSC, INGESTEM, Saint-Eloi Hospital, Montpellier F 34000, France
| | - Anthony Boureux
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - John De Vos
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France .,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France.,Institut de Biologie Computationnelle, Montpellier F 34000, France.,Stem Cell Core Facility SAFE-iPSC, INGESTEM, Saint-Eloi Hospital, Montpellier F 34000, France.,Department of Cell and Tissue Engineering, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France
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471
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Xiao H, Tang K, Liu P, Chen K, Hu J, Zeng J, Xiao W, Yu G, Yao W, Zhou H, Li H, Pan Y, Li A, Ye Z, Wang J, Xu H, Huang Q. LncRNA MALAT1 functions as a competing endogenous RNA to regulate ZEB2 expression by sponging miR-200s in clear cell kidney carcinoma. Oncotarget 2016; 6:38005-15. [PMID: 26461224 PMCID: PMC4741980 DOI: 10.18632/oncotarget.5357] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/25/2015] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA (lncRNAs) play a critical role in the development of cancers. LncRNA metastasis-associated lung adenocarcinoma transcript 1(MALAT1) has recently been identified to be involved in tumorigenesis of several cancers such as lung cancer, bladder cancer and so on. Here, we found that MALAT1 exist a higher fold change (Tumor/Normal) in clear cell kidney carcinoma (KIRC) from The Cancer Genome Atlas (TCGA) Data Portal and a negative correlation with miR-200s family. We further demonstrated MALAT1 promote KIRC proliferation and metastasis through sponging miR-200s in vitro and in vivo. In addition, miR-200c can partly reverse the MALAT1's stimulation on proliferation and metastasis in KIRC. In summary we unveil a branch of the MALAT1/miR-200s/ZEB2 pathway that regulates the progression of KIRC. The inhibition of MALAT1 expression may be a promising strategy for KIRC therapy.
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Affiliation(s)
- Haibing Xiao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kun Tang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Peijun Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Junhui Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jin Zeng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Xiao
- Translational Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Gan Yu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weiming Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hui Zhou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Heng Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yingtian Pan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Anping Li
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ji Wang
- Department of Cell Death and Cancer Genetics, The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qihong Huang
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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472
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Hu SB, Yao RW, Chen LL. Shedding light on paraspeckle structure by super-resolution microscopy. J Cell Biol 2016; 214:789-91. [PMID: 27646270 PMCID: PMC5037413 DOI: 10.1083/jcb.201609008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 09/01/2016] [Indexed: 12/03/2022] Open
Abstract
The nuclear body paraspeckle is built on the lncRNA Neat1 and plays important roles in gene regulation. In this issue, West et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201601071) use super-resolution structured illumination microscopy to show that paraspeckles are organized in a core-shell spheroidal structure composed of Neat1 and seven proteins.
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Affiliation(s)
- Shi-Bin Hu
- State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Run-Wen Yao
- State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China University of Chinese Academy of Sciences, Beijing 100049, China School of Life Science, ShanghaiTech University, Shanghai 200031, China
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473
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Fang Z, Zhang S, Wang Y, Shen S, Wang F, Hao Y, Li Y, Zhang B, Zhou Y, Yang H. Long non-coding RNA MALAT-1 modulates metastatic potential of tongue squamous cell carcinomas partially through the regulation of small proline rich proteins. BMC Cancer 2016; 16:706. [PMID: 27586393 PMCID: PMC5009554 DOI: 10.1186/s12885-016-2735-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/05/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND We previously described several abnormally expressed long non-coding RNA (lncRNA) in tong squamous cell carcinomas (TSCCs) that might be associated with tumor progression. In the present study, we aimed to investigate the role of abnormally expressed metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1) lncRNA in the metastatic potential of TSCC cells and its molecular mechanisms. METHODS Expression levels of MALAT-1 lncRNA were examined via quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) in 127 TSCC samples as well as paired adjacent normal tissues and lymph node metastases (if exist). Lentiviral vectors expressing short hairpin RNA (shRNA) were used to knock down the expression of MALAT1 gene in two TSCC cell lines (CAL27 and SCC-25) with relatively higher MALAT-1 expression. Proliferational ability of the TSCC cells was analyzed using water soluble tetrazolium-1 (WST-1) assay. Metastatic abilities of TSCC cells were estimated in-vitro and in-vivo. We also performed a microarray-based screen to identify the genes influenced by MALAT-1 alteration, which were validated by real-time PCR analysis. RESULTS Expression of MALAT-1 lncRNA was enhanced in TSCCs, especially in those with lymph node metastasis (LNM). Knockdown (KD) of MALAT-1 lncRNA in TSCC cells led to impaired migration and proliferation ability in-vitro and fewer metastases in-vivo. DNA microarray analysis showed that several members of small proline rich proteins (SPRR) were up-regulated by KD of MALAT-1 lncRNA in TSCC cells. SPRR2A over-expression could impair distant metastasis of TSCC cells in-vivo. CONCLUSION Enhanced expression of MALAT-1 is associated with the growth and metastatic potential of TSCCs. Knock down of MALAT-1 in TSCCs leads to the up-regulation of certain SPRR proteins, which influenced the distant metastasis of TSCC cells.
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Affiliation(s)
- Zhengyu Fang
- Biomedical Research Institute, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong province, China.,Department of Oral and Maxillofacial, Shenzhen Hospital, Peking University, Shenzhen, Guangdong Province, People's Republic of China
| | - Shanshan Zhang
- Department of Oral and Maxillofacial, Shenzhen Hospital, Peking University, Shenzhen, Guangdong Province, People's Republic of China
| | - Yufan Wang
- Department of Oral and Maxillofacial, Shenzhen Hospital, Peking University, Shenzhen, Guangdong Province, People's Republic of China
| | - Shiyue Shen
- Department of Oral and Maxillofacial, Shenzhen Hospital, Peking University, Shenzhen, Guangdong Province, People's Republic of China
| | - Feng Wang
- Department of Oral and Maxillofacial, Shenzhen Hospital, Peking University, Shenzhen, Guangdong Province, People's Republic of China
| | - Yinghua Hao
- Biomedical Research Institute, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong province, China
| | - Yuxia Li
- Biomedical Research Institute, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong province, China
| | - Bingyue Zhang
- Biomedical Research Institute, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong province, China
| | - You Zhou
- Biomedical Research Institute, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong province, China
| | - Hongyu Yang
- Department of Oral and Maxillofacial, Shenzhen Hospital, Peking University, Shenzhen, Guangdong Province, People's Republic of China.
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474
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Cornelis G, Souquere S, Vernochet C, Heidmann T, Pierron G. Functional conservation of the lncRNA NEAT1 in the ancestrally diverged marsupial lineage: Evidence for NEAT1 expression and associated paraspeckle assembly during late gestation in the opossum Monodelphis domestica. RNA Biol 2016; 13:826-36. [PMID: 27315396 PMCID: PMC5014006 DOI: 10.1080/15476286.2016.1197482] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 01/15/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are widely expressed and play various roles in cell homeostasis. However, because of their low conservation at the sequence level, recapitulating lncRNA evolutionary history is often challenging. While performing an ultrastructural analysis of viral particles present in uterine glands of gestating opossum females, we serendipitously noticed the presence of numerous structures similar to paraspeckles, nuclear bodies which in human and mouse cells are assembled around an architectural NEAT1/MENϵ/β lncRNA. Here, using an opossum kidney (OK) cell line, we confirmed by immuno-electron microscopy the presence of paraspeckles in marsupials. We then identified the orthologous opossum NEAT1 gene which, although poorly conserved at the sequence level, displays NEAT1 characteristic features such as short and long isoforms expressed from a unique promoter and for the latter an RNase P cleavage site at its 3'-end. Combining tissue-specific qRT-PCR, in situ hybridization at the optical and electron microscopic levels, we show that (i) NEAT1 is paraspeckle-associated in opossum (ii) NEAT1 expression is strongly induced in late gestation in uterine/placental extracts (iii) NEAT1 induction occurs in the uterine gland nuclei in which paraspeckles were detected. Finally, treatment of OK cells with proteasome inhibitors induces paraspeckle assembly, as previously observed in human cells. Altogether, these results demonstrate that paraspeckles are tissue-specific, stress-responding nuclear bodies in marsupials, illustrating their structural and functional continuity over 200 My of evolution throughout the mammalian lineage. In contrast, the rapid evolution of the NEAT1 transcripts highlights the relaxed constraint that, despite functional conservation, is exerted on this lncRNA.
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Affiliation(s)
| | - Sylvie Souquere
- CNRS-UMR-9196, Institut Gustave Roussy,94805 Villejuif, France
| | | | | | - Gérard Pierron
- CNRS-UMR-9196, Institut Gustave Roussy,94805 Villejuif, France
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475
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Zhao G, Su Z, Song D, Mao Y, Mao X. The long noncoding RNA MALAT1 regulates the lipopolysaccharide-induced inflammatory response through its interaction with NF-κB. FEBS Lett 2016; 590:2884-95. [PMID: 27434861 DOI: 10.1002/1873-3468.12315] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/28/2016] [Accepted: 07/11/2016] [Indexed: 12/14/2022]
Abstract
MALAT1 is a conserved long noncoding RNA whose expression correlates with many human cancers. However, its significance in immunity remains largely unknown. Here, we observe that MALAT1 is upregulated in lipopolysaccharide (LPS)-activated macrophages. Knockdown of MALAT1 increases LPS-induced expression of TNFα and IL-6. Mechanistically, MALAT1 was found to interact with NF-κB in the nucleus, thus inhibiting its DNA binding activity and consequently decreasing the production of inflammatory cytokines. Additionally, abnormal expression of MALAT1 was found to be NF-κB-dependent. These findings suggest that MALAT1 may function as an autonegative feedback regulator of NF-κB to help fine-tune innate immune responses.
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Affiliation(s)
- Gui Zhao
- Department of Biochemistry, School of Medicine & Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, Southeast University, Nanjing, China
| | - Zhenyi Su
- Department of Biochemistry, School of Medicine & Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, Southeast University, Nanjing, China
| | - Dan Song
- Department of Biochemistry, School of Medicine & Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, Southeast University, Nanjing, China
| | - Yimin Mao
- Department of Biochemistry, School of Medicine & Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, Southeast University, Nanjing, China.,School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Xiaohua Mao
- Department of Biochemistry, School of Medicine & Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, Southeast University, Nanjing, China
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476
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Chen LL. Linking Long Noncoding RNA Localization and Function. Trends Biochem Sci 2016; 41:761-772. [PMID: 27499234 DOI: 10.1016/j.tibs.2016.07.003] [Citation(s) in RCA: 774] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/23/2016] [Accepted: 07/01/2016] [Indexed: 02/06/2023]
Abstract
Recent studies have revealed the regulatory potential of many long noncoding RNAs (lncRNAs). Most lncRNAs, like mRNAs, are transcribed by RNA polymerase II and are capped, polyadenylated, and spliced. However, the subcellular fates of lncRNAs are distinct and the mechanisms of action are diverse. Investigating the mechanisms that determine the subcellular fate of lncRNAs has the potential to provide new insights into their biogenesis and specialized functions.
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Affiliation(s)
- Ling-Ling Chen
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai, China.
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477
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Foulds CE, Panigrahi AK, Coarfa C, Lanz RB, O'Malley BW. Long Noncoding RNAs as Targets and Regulators of Nuclear Receptors. Curr Top Microbiol Immunol 2016; 394:143-76. [PMID: 26362934 DOI: 10.1007/82_2015_465] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Intensive research has been directed at the discovery, biogenesis, and expression patterns of long noncoding RNAs , yet their biochemical functions have remained elusive for the most part. Nuclear receptors that interpret signaling mediated by small molecule hormones play a role in regulating the expression of some long noncoding RNAs. More importantly, these RNAs have also been shown to effect hormone-affected gene transcription regulated by the nuclear receptors. In this chapter, we summarize the current knowledge that has been acquired on hormonal signaling inducing expression of long noncoding RNAs and how they then may act in trans or in cis to modulate gene transcription. We highlight a few of these noncoding RNA molecules in terms of how they may impact hormone-driven cancers. Future directions critical for moving this field forward are presented, with a clear emphasis on the need for better biochemical approaches to address the mechanism of action of these exciting RNAs.
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Affiliation(s)
- Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Anil K Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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478
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Torres M, Becquet D, Blanchard MP, Guillen S, Boyer B, Moreno M, Franc JL, François-Bellan AM. Circadian RNA expression elicited by 3'-UTR IRAlu-paraspeckle associated elements. eLife 2016; 5. [PMID: 27441387 PMCID: PMC4987140 DOI: 10.7554/elife.14837] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/20/2016] [Indexed: 12/31/2022] Open
Abstract
Paraspeckles are nuclear bodies form around the long non-coding RNA, Neat1, and RNA-binding proteins. While their role is not fully understood, they are believed to control gene expression at a post-transcriptional level by means of the nuclear retention of mRNA containing in their 3’-UTR inverted repeats of Alu sequences (IRAlu). In this study, we found that, in pituitary cells, all components of paraspeckles including four major proteins and Neat1 displayed a circadian expression pattern. Furthermore the insertion of IRAlu at the 3’-UTR of the EGFP cDNA led to a rhythmic circadian nuclear retention of the egfp mRNA that was lost when paraspeckles were disrupted whereas insertion of a single antisense Alu had only a weak effect. Using real-time video-microscopy, these IRAlu were further shown to drive a circadian expression of EGFP protein. This study shows that paraspeckles, thanks to their circadian expression, control circadian gene expression at a post-transcriptional level. DOI:http://dx.doi.org/10.7554/eLife.14837.001 Many biological features of animals, including body temperature and hormone levels, follow daily rhythms that repeat every 24 hours. These so-called circadian rhythms are driven by an internal body clock and are essential for the organism to adapt to the daily cycle of light and dark. Circadian rhythms also take place inside individual cells – for example, the amount of a given protein in a cell often rises and falls over each 24-hour period. To generate these daily fluctuations, the processes used to make proteins based on the instructions encoded within a gene must be carefully controlled. Genes are first copied or ‘transcribed' into intermediate molecules called messenger RNAs (mRNAs). These mRNA molecules must then travel out of the cell’s nucleus before they can be de-coded to produce proteins. This means that daily fluctuations in mRNA and protein levels could occur because the rate at which the DNA is transcribed fluctuates or because controlling the steps that occur after transcription. However it is not clear how much these post-transcriptional steps contribute to circadian rhythms inside cells. Recently, structures called paraspeckles were seen inside the nucleus. These structures are made from a long RNA molecule that does not code for a protein, and a number of proteins that can bind mRNA molecules. Paraspeckles are thought to prevent certain mRNAs from leaving the nucleus and therefore stop them from being decoded to make proteins. Torres et al. have now investigated whether paraspeckles may play a role in circadian rhythms. Torres et al. looked at the long non-coding RNA and several proteins that are known to be components of paraspeckles in cells taken from the pituitary glands of rats using a variety of techniques. These cells were chosen because they were known to have a working circadian clock. The analysis showed that the levels of these components, as well as the number of paraspeckles within the nucleus, changed over the course of a daily cycle. Torres et al. then confirmed that mRNAs containing a sequence that is known to recruit mRNAs to paraspeckes (the IRAlu sequence) could be also retained in the nucleus or released with a circadian rhythm. This pattern was lost when the paraspeckles were disrupted. These findings suggest that daily fluctuations in protein levels can be post-transcriptionally controlled by paraspeckles rhythmically retaining mRNAs in the nucleus. Future studies could explore whether it may be possible to control circadian rhythms by targeting the paraspeckles, which could help to improve conditions where the internal body clock goes wrong. DOI:http://dx.doi.org/10.7554/eLife.14837.002
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Affiliation(s)
- Manon Torres
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Denis Becquet
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Marie-Pierre Blanchard
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Séverine Guillen
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Bénédicte Boyer
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Mathias Moreno
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Jean-Louis Franc
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
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479
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Hedegaard J, Lamy P, Nordentoft I, Algaba F, Høyer S, Ulhøi BP, Vang S, Reinert T, Hermann GG, Mogensen K, Thomsen MBH, Nielsen MM, Marquez M, Segersten U, Aine M, Höglund M, Birkenkamp-Demtröder K, Fristrup N, Borre M, Hartmann A, Stöhr R, Wach S, Keck B, Seitz AK, Nawroth R, Maurer T, Tulic C, Simic T, Junker K, Horstmann M, Harving N, Petersen AC, Calle ML, Steyerberg EW, Beukers W, van Kessel KEM, Jensen JB, Pedersen JS, Malmström PU, Malats N, Real FX, Zwarthoff EC, Ørntoft TF, Dyrskjøt L. Comprehensive Transcriptional Analysis of Early-Stage Urothelial Carcinoma. Cancer Cell 2016; 30:27-42. [PMID: 27321955 DOI: 10.1016/j.ccell.2016.05.004] [Citation(s) in RCA: 458] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/18/2016] [Accepted: 05/13/2016] [Indexed: 01/01/2023]
Abstract
Non-muscle-invasive bladder cancer (NMIBC) is a heterogeneous disease with widely different outcomes. We performed a comprehensive transcriptional analysis of 460 early-stage urothelial carcinomas and showed that NMIBC can be subgrouped into three major classes with basal- and luminal-like characteristics and different clinical outcomes. Large differences in biological processes such as the cell cycle, epithelial-mesenchymal transition, and differentiation were observed. Analysis of transcript variants revealed frequent mutations in genes encoding proteins involved in chromatin organization and cytoskeletal functions. Furthermore, mutations in well-known cancer driver genes (e.g., TP53 and ERBB2) were primarily found in high-risk tumors, together with APOBEC-related mutational signatures. The identification of subclasses in NMIBC may offer better prognostication and treatment selection based on subclass assignment.
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Affiliation(s)
- Jakob Hedegaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Ferran Algaba
- Section of Pathology, Fundació Puigvert, University Autonoma de Barcelona, Barcelona 08025, Spain
| | - Søren Høyer
- Department of Pathology, Aarhus University Hospital, Aarhus 8000, Denmark
| | | | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Gregers G Hermann
- Department of Urology, Frederiksberg Hospital, Frederiksberg 2000, Denmark
| | - Karin Mogensen
- Department of Urology, Frederiksberg Hospital, Frederiksberg 2000, Denmark
| | | | | | - Mirari Marquez
- Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Ulrika Segersten
- Department of Surgical Sciences, Uppsala University, Uppsala 75185, Sweden
| | - Mattias Aine
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund 22100, Sweden
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund 22100, Sweden
| | | | - Niels Fristrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Robert Stöhr
- Institute of Pathology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Sven Wach
- Department of Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Bastian Keck
- Department of Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Anna Katharina Seitz
- Department of Urology, Klinikum rechts der Isar der Technischen Universität München, Munich 81675, Germany
| | - Roman Nawroth
- Department of Urology, Klinikum rechts der Isar der Technischen Universität München, Munich 81675, Germany
| | - Tobias Maurer
- Department of Urology, Klinikum rechts der Isar der Technischen Universität München, Munich 81675, Germany
| | - Cane Tulic
- Faculty of Medicine, Clinic of Urology, Clinical Centre of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | - Tatjana Simic
- Faculty of Medicine, Institute of Medical and Clinical Biochemistry, University of Belgrade, 11000 Belgrade, Serbia
| | - Kerstin Junker
- Department of Urology, Saarland University, Homburg 66421, Germany
| | - Marcus Horstmann
- Department of Urology, Friedrich-Schiller-University Jena, Jena 07737, Germany
| | - Niels Harving
- Department of Urology, Aalborg University Hospital, Aalborg 9000, Denmark
| | | | - M Luz Calle
- Systems Biology Department, University of Vic, Vic, Barcelona 08500, Spain
| | - Ewout W Steyerberg
- Department of Public Health, Erasmus Medical Centre, 3015 CE Rotterdam, the Netherlands
| | - Willemien Beukers
- Department of Pathology, Erasmus Medical Centre, 3015 CE Rotterdam, the Netherlands
| | - Kim E M van Kessel
- Department of Pathology, Erasmus Medical Centre, 3015 CE Rotterdam, the Netherlands
| | | | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Per-Uno Malmström
- Department of Surgical Sciences, Uppsala University, Uppsala 75185, Sweden
| | - Núria Malats
- Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Francisco X Real
- Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus Medical Centre, 3015 CE Rotterdam, the Netherlands
| | - Torben Falck Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark.
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480
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Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GKJ, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O’Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van’t Veer L, Tutt A, Knappskog S, Tan BKT, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 2016; 534:47-54. [PMID: 27135926 PMCID: PMC4910866 DOI: 10.1038/nature17676] [Citation(s) in RCA: 1574] [Impact Index Per Article: 174.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 03/17/2016] [Indexed: 02/06/2023]
Abstract
We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
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Affiliation(s)
- Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK
| | - Helen Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Dominik Glodzik
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Xueqing Zou
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Ludmil B. Alexandrov
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Peter Van Loo
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Department of Human Genetics, University of Leuven, B-3000 Leuven, Belgium
| | - Young Seok Ju
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marcel Smid
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Arie B Brinkman
- Radboud University, Department of Molecular Biology, Faculties of Science and Medicine, Nijmegen, Netherlands
| | - Sandro Morganella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire, CB10 1SD
| | - Miriam R. Aure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ole Christian Lingjærde
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Computer Science, University of Oslo, Oslo, Norway
| | - Anita Langerød
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Sung-Min Ahn
- Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon, South Korea
| | - Sandrine Boyault
- Translational Research Lab, Centre Léon Bérard, 28, rue Laënnec, 69373 Lyon Cedex 08, France
| | - Jane E. Brock
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Annegien Broeks
- The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Adam Butler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium
| | - Luc Dirix
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Serge Dronov
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - John A. Foekens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Moritz Gerstung
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Gerrit KJ Hooijer
- Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, College of Medicine, Ulsan University, South Korea
| | - David R. Jones
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Hyung-Yong Kim
- Department of Pathology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Tari A. King
- Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, United States
| | - Savitri Krishnamurthy
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030
| | - Hee Jin Lee
- Department of Pathology, Asan Medical Center, College of Medicine, Ulsan University, South Korea
| | - Jeong-Yeon Lee
- Institute for Bioengineering and Biopharmaceutical Research (IBBR), Hanyang University, Seoul, South Korea
| | - Yilong Li
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Stuart McLaren
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Andrew Menzies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Ville Mustonen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah O’Meara
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Iris Pauporté
- Institut National du Cancer, Research Division, Clinical Research Department, 52 avenue Morizet, 92513 Boulogne-Billancourt, France
| | - Xavier Pivot
- University Hospital of Minjoz, INSERM UMR 1098, Bd Fleming, Besançon 25000, France
| | - Colin A. Purdie
- Pathology Department, Ninewells Hospital & Medical School, Dundee DD1 9SY, UK
| | - Keiran Raine
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - F. Germán Rodríguez-González
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Gilles Romieu
- Oncologie Sénologie, ICM Institut Régional du Cancer, Montpellier, France
| | - Anieta M. Sieuwerts
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Peter T Simpson
- The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane, Australia
| | - Rebecca Shepherd
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Lucy Stebbings
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Olafur A Stefansson
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Jon Teague
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Isabelle Treilleux
- Department of Pathology, Centre Léon Bérard, 28 rue Laënnec, 69373 Lyon Cédex 08, France
| | - Gert G. Van den Eynden
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Pathology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Peter Vermeulen
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Pathology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Anne Vincent-Salomon
- Institut Curie, Department of Pathology and INSERM U934, 26 rue d’Ulm, 75248 Paris Cedex 05, France
| | - Lucy Yates
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Laura van’t Veer
- The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Andrew Tutt
- Breast Cancer Now Toby Research Unit, King’s College London
- Breast Cancer Now Toby Robin’s Research Centre, Institute of Cancer Research, London
| | - Stian Knappskog
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
- Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Benita Kiat Tee Tan
- National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610
- Singapore General Hospital, Outram Road, Singapore 169608
| | - Jos Jonkers
- The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Naoto T Ueno
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium
| | - Alain Viari
- Equipe Erable, INRIA Grenoble-Rhône-Alpes, 655, Av. de l’Europe, 38330 Montbonnot-Saint Martin, France
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
| | - P. Andrew Futreal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX, 77230
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Paul N. Span
- Department of Radiation Oncology, and department of Laboratory Medicine, Radboud university medical center, Nijmegen, the Netherlands
| | - Steven Van Laere
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Sunil R Lakhani
- The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane, Australia
- Pathology Queensland, The Royal Brisbane and Women’s Hospital, Brisbane, Australia
| | - Jorunn E. Eyfjord
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Alastair M. Thompson
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, 1400 Pressler Street,Houston, Texas 77030
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire, CB10 1SD
| | - Hendrik G Stunnenberg
- Radboud University, Department of Molecular Biology, Faculties of Science and Medicine, Nijmegen, Netherlands
| | - Marc J van de Vijver
- Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - John W.M. Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andrea L. Richardson
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115 USA
- Dana-Farber Cancer Institute, Boston, MA 02215 USA
| | - Gu Kong
- Department of Pathology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Gilles Thomas
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
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481
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Wang X, Sun W, Shen W, Xia M, Chen C, Xiang D, Ning B, Cui X, Li H, Li X, Ding J, Wang H. Long non-coding RNA DILC regulates liver cancer stem cells via IL-6/STAT3 axis. J Hepatol 2016; 64:1283-94. [PMID: 26812074 DOI: 10.1016/j.jhep.2016.01.019] [Citation(s) in RCA: 242] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Emerging evidence has demonstrated the aberrant expression of long non-coding RNAs (lncRNAs) in various malignancies including HCC. However, the knowledge of cancer stem cell-related lncRNAs remains limited. METHODS lnc-DILC (lncRNA downregulated in liver cancer stem cells (LCSCs)) was identified by microarray and validated by real-time PCR. The role of lnc-DILC in LCSCs was assessed both in vitro and in vivo. Pull down assay and oligoribonucleotides or oligodeoxynucleotides treatment were conducted to evaluate the interaction between lnc-DILC and interleukin-6 (IL-6) promoter. RESULTS Depletion of lnc-DILC markedly enhanced LCSC expansion and facilitated HCC initiation and progression, whereas ectopic expression of lnc-DILC dramatically inhibited LCSC expansion. Mechanistically, lnc-DILC inhibited the autocrine IL-6/STAT3 signaling. The putative binding locus of lnc-DILC within IL-6 promoter was confirmed by pull down assay. Consistently, the oligoribonucleotide mimics and an oligodeoxynucleotide decoy of lnc-DILC abrogated the effects on IL-6 transcription, STAT3 activation and LCSC expansion triggered by lnc-DILC depletion and lnc-DILC overexpression. Moreover, our data suggested that lnc-DILC mediated the crosstalk between TNF-α/NF-κB signaling and IL-6/STAT3 cascade. Clinical investigation demonstrated the reduction of lnc-DILC in patient HCCs, and suggested the correlation between lnc-DILC levels and IL-6, EpCAM or CD24 expression. Decreased lnc-DILC expression in HCCs predicts early recurrence and short survival of patients, highlighting its prognostic value. CONCLUSIONS lnc-DILC mediates the crosstalk between TNF-α/NF-κB signaling and autocrine IL-6/STAT3 cascade and connects hepatic inflammation with LCSC expansion, suggesting that lnc-DILC could be not only a potential prognostic biomarker, but also a possible therapeutic target against LCSCs.
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Affiliation(s)
- Xue Wang
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China
| | - Wen Sun
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China
| | - Weifeng Shen
- The Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China
| | - Mingyang Xia
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China
| | - Cheng Chen
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China
| | - Daimin Xiang
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China
| | - Beifang Ning
- The Department of Gastroenterology, Changzheng Hospital, 200003 Shanghai, China
| | - Xiuliang Cui
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China
| | - Hengyu Li
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China
| | - Xiaofeng Li
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China
| | - Jin Ding
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China; National Center for Liver Cancer, 201805 Shanghai, China.
| | - Hongyang Wang
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China; National Center for Liver Cancer, 201805 Shanghai, China.
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482
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Li J, Tian H, Yang J, Gong Z. Long Noncoding RNAs Regulate Cell Growth, Proliferation, and Apoptosis. DNA Cell Biol 2016; 35:459-70. [PMID: 27213978 DOI: 10.1089/dna.2015.3187] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The revolutionary findings in nonprotein-coding part of human genome analysis have revealed a large number of RNA transcripts longer than 200 nucleotides that lack coding protein function, termed long noncoding RNAs (lncRNAs). Recently, accumulating shreds of evidence suggest that lncRNAs are widely distributed in human genome and deeply involved in cellular activities such as cell growth, proliferation, and apoptosis. Generally, lncRNAs regulate cell behaviors by targeting cell cycle-associated cyclins, cyclin-dependent kinases (CDKs), and/or CDK inhibitors. Specifically, lncRNAs serve as scaffolds or guides for chromatin-modifying complexes and act as signals in response to DNA damage. In addition, lncRNAs function as protein decoys and microRNA decoys, as well as interveners in cell division by modulating oncogenes and/or tumor suppressors. In this review, we mainly focus on the current understanding of the molecular mechanisms, how lncRNAs influence cellular processes and cancer progression. Finally, we also prospect the limitations of lncRNAs in cell behaviors and the novel roles of lncRNAs in epigenetic regulations.
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Affiliation(s)
- Jingqiu Li
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
| | - Haihua Tian
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China .,3 Department of Laboratory Medicine, Ningbo Kangning Hospital , Ningbo, China
| | - Jie Yang
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
| | - Zhaohui Gong
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
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483
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Li R, Zhu H, Luo Y. Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures. Int J Mol Sci 2016; 17:ijms17050702. [PMID: 27196897 PMCID: PMC4881525 DOI: 10.3390/ijms17050702] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/28/2016] [Accepted: 05/04/2016] [Indexed: 02/08/2023] Open
Abstract
Although thousands of long non-coding RNAs (lncRNAs) have been discovered in eukaryotes, very few molecular mechanisms have been characterized due to an insufficient understanding of lncRNA structure. Therefore, investigations of lncRNA structure and subsequent elucidation of the regulatory mechanisms are urgently needed. However, since lncRNA are high molecular weight molecules, which makes their crystallization difficult, obtaining information about their structure is extremely challenging, and the structures of only several lncRNAs have been determined so far. Here, we review the structure-function relationships of the widely studied lncRNAs found in the animal and plant kingdoms, focusing on the principles and applications of both in vitro and in vivo technologies for the study of RNA structures, including dimethyl sulfate-sequencing (DMS-seq), selective 2'-hydroxyl acylation analyzed by primer extension-sequencing (SHAPE-seq), parallel analysis of RNA structure (PARS), and fragmentation sequencing (FragSeq). The aim of this review is to provide a better understanding of lncRNA biological functions by studying them at the structural level.
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Affiliation(s)
- Rui Li
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Hongliang Zhu
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yunbo Luo
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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484
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Rutenberg-Schoenberg M, Sexton AN, Simon MD. The Properties of Long Noncoding RNAs That Regulate Chromatin. Annu Rev Genomics Hum Genet 2016; 17:69-94. [PMID: 27147088 DOI: 10.1146/annurev-genom-090314-024939] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Beyond coding for proteins, RNA molecules have well-established functions in the posttranscriptional regulation of gene expression. Less clear are the upstream roles of RNA in regulating transcription and chromatin-based processes in the nucleus. RNA is transcribed in the nucleus, so it is logical that RNA could play diverse and broad roles that would impact human physiology. Indeed, this idea is supported by well-established examples of noncoding RNAs that affect chromatin structure and function. There has been dramatic growth in studies focused on the nuclear roles of long noncoding RNAs (lncRNAs). Although little is known about the biochemical mechanisms of these lncRNAs, there is a developing consensus regarding the challenges of defining lncRNA function and mechanism. In this review, we examine the definition, discovery, functions, and mechanisms of lncRNAs. We emphasize areas where challenges remain and where consensus among laboratories has underscored the exciting ways in which human lncRNAs may affect chromatin biology.
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Affiliation(s)
- Michael Rutenberg-Schoenberg
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Alec N Sexton
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
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485
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Latorre E, Carelli S, Raimondi I, D'Agostino V, Castiglioni I, Zucal C, Moro G, Luciani A, Ghilardi G, Monti E, Inga A, Di Giulio AM, Gorio A, Provenzani A. The Ribonucleic Complex HuR-MALAT1 Represses CD133 Expression and Suppresses Epithelial-Mesenchymal Transition in Breast Cancer. Cancer Res 2016; 76:2626-36. [PMID: 27197265 DOI: 10.1158/0008-5472.can-15-2018] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 03/01/2016] [Indexed: 11/16/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a core process underlying cell movement during embryonic development and morphogenesis. Cancer cells hijack this developmental program to execute a multi-step cascade, leading to tumorigenesis and metastasis. CD133 (PROM1), a marker of cancer stem cells, has been shown to facilitate EMT in various cancers, but the regulatory networks controlling CD133 gene expression and function in cancer remain incompletely delineated. In this study, we show that a ribonucleoprotein complex including the long noncoding RNA MALAT1 and the RNA-binding protein HuR (ELAVL1) binds the CD133 promoter region to regulate its expression. In luminal nonmetastatic MCF-7 breast cancer cells, HuR silencing was sufficient to upregulate N-cadherin (CDH2) and CD133 along with a migratory and mesenchymal-like phenotype. Furthermore, we found that in the basal-like metastatic cell line MDA-MB-231 and primary triple-negative breast cancer tumor cells, the repressor complex was absent from the CD133-regulatory region, but was present in the MCF-7 and primary ER+ tumor cells. The absence of the complex from basal-like cells was attributed to diminished expression of MALAT1, which, when overexpressed, dampened CD133 levels. In conclusion, our findings suggest that the failure of a repressive complex to form or stabilize in breast cancer promotes CD133 upregulation and an EMT-like program, providing new mechanistic insights underlying the control of prometastatic processes. Cancer Res; 76(9); 2626-36. ©2016 AACR.
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Affiliation(s)
- Elisa Latorre
- Laboratory of Genomic Screening, Center for Integrative Biology, University of Trento, Trento, Italy. Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy.
| | - Stephana Carelli
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy
| | - Ivan Raimondi
- Laboratory of Transcriptional Networks, Center for Integrative Biology, University of Trento, Trento, Italy
| | - Vito D'Agostino
- Laboratory of Genomic Screening, Center for Integrative Biology, University of Trento, Trento, Italy
| | - Ilaria Castiglioni
- Laboratory of Genomic Screening, Center for Integrative Biology, University of Trento, Trento, Italy
| | - Chiara Zucal
- Laboratory of Genomic Screening, Center for Integrative Biology, University of Trento, Trento, Italy
| | | | | | - Giorgio Ghilardi
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy. San Paolo Hospital, Milan, Italy
| | - Eleonora Monti
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy. San Paolo Hospital, Milan, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Center for Integrative Biology, University of Trento, Trento, Italy
| | - Anna Maria Di Giulio
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy
| | - Alfredo Gorio
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy
| | - Alessandro Provenzani
- Laboratory of Genomic Screening, Center for Integrative Biology, University of Trento, Trento, Italy.
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486
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Schmitt AM, Chang HY. Long Noncoding RNAs in Cancer Pathways. Cancer Cell 2016; 29:452-463. [PMID: 27070700 PMCID: PMC4831138 DOI: 10.1016/j.ccell.2016.03.010] [Citation(s) in RCA: 2393] [Impact Index Per Article: 265.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/01/2016] [Accepted: 03/14/2016] [Indexed: 12/16/2022]
Abstract
Genome-wide cancer mutation analyses are revealing an extensive landscape of functional mutations within the noncoding genome, with profound effects on the expression of long noncoding RNAs (lncRNAs). While the exquisite regulation of lncRNA transcription can provide signals of malignant transformation, we now understand that lncRNAs drive many important cancer phenotypes through their interactions with other cellular macromolecules including DNA, protein, and RNA. Recent advancements in surveying lncRNA molecular mechanisms are now providing the tools to functionally annotate these cancer-associated transcripts, making these molecules attractive targets for therapeutic intervention in the fight against cancer.
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Affiliation(s)
- Adam M Schmitt
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.
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487
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Pinter SF. A Tale of Two Cities: How Xist and its partners localize to and silence the bicompartmental X. Semin Cell Dev Biol 2016; 56:19-34. [PMID: 27072488 DOI: 10.1016/j.semcdb.2016.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/30/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
Abstract
Sex chromosomal dosage compensation in mammals takes the form of X chromosome inactivation (XCI), driven by the non-coding RNA Xist. In contrast to dosage compensation systems of flies and worms, mammalian XCI has to restrict its function to the Xist-producing X chromosome, while leaving autosomes and active X untouched. The mechanisms behind the long-range yet cis-specific localization and silencing activities of Xist have long been enigmatic, but genomics, proteomics, super-resolution microscopy, and innovative genetic approaches have produced significant new insights in recent years. In this review, I summarize and integrate these findings with a particular focus on the redundant yet mutually reinforcing pathways that enable long-term transcriptional repression throughout the soma. This includes an exploration of concurrent epigenetic changes acting in parallel within two distinct compartments of the inactive X. I also examine how Polycomb repressive complexes 1 and 2 and macroH2A may bridge XCI establishment and maintenance. XCI is a remarkable phenomenon that operates across multiple scales, combining changes in nuclear architecture, chromosome topology, chromatin compaction, and nucleosome/nucleotide-level epigenetic cues. Learning how these pathways act in concert likely holds the answer to the riddle posed by Cattanach's and other autosomal translocations: What makes the X especially receptive to XCI?
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Affiliation(s)
- Stefan F Pinter
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT 06030-6403, USA.
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488
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Meng Y, Yi X, Li X, Hu C, Wang J, Bai L, Czajkowsky DM, Shao Z. The non-coding RNA composition of the mitotic chromosome by 5'-tag sequencing. Nucleic Acids Res 2016; 44:4934-46. [PMID: 27016738 PMCID: PMC4889943 DOI: 10.1093/nar/gkw195] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 03/15/2016] [Indexed: 12/16/2022] Open
Abstract
Mitotic chromosomes are one of the most commonly recognized sub-cellular structures in eukaryotic cells. Yet basic information necessary to understand their structure and assembly, such as their composition, is still lacking. Recent proteomic studies have begun to fill this void, identifying hundreds of RNA-binding proteins bound to mitotic chromosomes. However, by contrast, there are only two RNA species (U3 snRNA and rRNA) that are known to be associated with the mitotic chromosome, suggesting that there are many mitotic chromosome-associated RNAs (mCARs) not yet identified. Here, using a targeted protocol based on 5'-tag sequencing to profile the mammalian mCAR population, we report the identification of 1279 mCARs, the majority of which are ncRNAs, including lncRNAs that exhibit greater conservation across 60 vertebrate species than the entire population of lncRNAs. There is also a significant enrichment of snoRNAs and specific SINE RNAs. Finally, ∼40% of the mCARs are presently unannotated, many of which are as abundant as the annotated mCARs, suggesting that there are also many novel ncRNAs in the mCARs. Overall, the mCARs identified here, together with the previous proteomic and genomic data, constitute the first comprehensive catalogue of the molecular composition of the eukaryotic mitotic chromosomes.
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Affiliation(s)
- Yicong Meng
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Xinhui Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ju Wang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Ling Bai
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes & Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
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489
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Zhu Y, Chen Z, Zhang K, Wang M, Medovoy D, Whitaker JW, Ding B, Li N, Zheng L, Wang W. Constructing 3D interaction maps from 1D epigenomes. Nat Commun 2016; 7:10812. [PMID: 26960733 PMCID: PMC4792925 DOI: 10.1038/ncomms10812] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/24/2016] [Indexed: 12/28/2022] Open
Abstract
The human genome is tightly packaged into chromatin whose functional output depends on both one-dimensional (1D) local chromatin states and three-dimensional (3D) genome organization. Currently, chromatin modifications and 3D genome organization are measured by distinct assays. An emerging question is whether it is possible to deduce 3D interactions by integrative analysis of 1D epigenomic data and associate 3D contacts to functionality of the interacting loci. Here we present EpiTensor, an algorithm to identify 3D spatial associations within topologically associating domains (TADs) from 1D maps of histone modifications, chromatin accessibility and RNA-seq. We demonstrate that active promoter–promoter, promoter–enhancer and enhancer–enhancer associations identified by EpiTensor are highly concordant with those detected by Hi-C, ChIA-PET and eQTL analyses at 200 bp resolution. Moreover, EpiTensor has identified a set of interaction hotspots, characterized by higher chromatin and transcriptional activity as well as enriched TF and ncRNA binding across diverse cell types, which may be critical for stabilizing the local 3D interactions. The human genome is highly organized, with one-dimensional chromatin states packaged into higher level three-dimensional architecture. Here, the authors present EpiTensor that can identify 3D spatial associations from 1D epigenetic information.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Zhao Chen
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Kai Zhang
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Mengchi Wang
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - David Medovoy
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - John W Whitaker
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Bo Ding
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Nan Li
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Lina Zheng
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093-0359, USA
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490
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Dhamija S, Diederichs S. From junk to master regulators of invasion: lncRNA functions in migration, EMT and metastasis. Int J Cancer 2016; 139:269-80. [PMID: 26875870 DOI: 10.1002/ijc.30039] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/04/2016] [Indexed: 01/17/2023]
Abstract
Metastasis is a multistep process that involves the dissemination of cells from the primary tumor and colonization of distant secondary organs. Epithelial cells at the invasive front of a carcinoma acquire an enhanced migratory phenotype in a process called epithelial-to-mesenchymal transition (EMT). This cellular plasticity seems to drive the initiation of metastasis. Identifying important molecules and understanding their molecular mechanisms is a key to cancer prognosis and the development of therapeutics for late stage malignancies. Recent advances in sequencing technology uncovered that the mammalian genome is pervasively transcribed into many nonprotein-coding RNAs including the class of long noncoding RNA, a.k.a. lncRNA. Several lncRNAs are differentially expressed in carcinomas and they are emerging as potent regulators of tumor progression and metastasis. Here, we review the diverse molecular mechanisms, cellular roles and regulatory patterns that are becoming apparent for the noncoding transcriptome. Chromatin modification, epigenetic regulation, alternative splicing and translational control by MALAT1, HOTAIR and TRE lncRNAs represent important examples of lncRNA-mediated control of cell migration and invasion, EMT and metastasis. Beyond these better characterized examples, numerous additional transcripts have been associated with cancer metastasis, but their functional roles await their discovery.
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Affiliation(s)
- Sonam Dhamija
- Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,CellNetworks Excellence Cluster, University of Heidelberg, Heidelberg, Germany
| | - Sven Diederichs
- Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,CellNetworks Excellence Cluster, University of Heidelberg, Heidelberg, Germany
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491
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Noberini R, Sigismondo G, Bonaldi T. The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics 2016; 8:429-45. [DOI: 10.2217/epi.15.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin is a macromolecular complex composed of DNA and histones that regulate gene expression and nuclear architecture. The concerted action of DNA methylation, histone post-translational modifications and chromatin-associated proteins control the epigenetic regulation of the genome, ultimately determining cell fate and the transcriptional outputs of differentiated cells. Deregulation of this complex machinery leads to disease states, and exploiting epigenetic drugs is becoming increasingly attractive for therapeutic intervention. Mass spectrometry (MS)-based proteomics emerged as a powerful tool complementary to genomic approaches for epigenetic research, allowing the unbiased and comprehensive analysis of histone post-translational modifications and the characterization of chromatin constituents and chromatin-associated proteins. Furthermore, MS holds great promise for epigenetic biomarker discovery and represents a useful tool for deconvolution of epigenetic drug targets. Here, we will provide an overview of the applications of MS-based proteomics in various areas of chromatin biology.
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Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, via Adamello 16, Milano, Italy
| | - Gianluca Sigismondo
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
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492
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Peters T, Hermans-Beijnsberger S, Beqqali A, Bitsch N, Nakagawa S, Prasanth KV, de Windt LJ, van Oort RJ, Heymans S, Schroen B. Long Non-Coding RNA Malat-1 Is Dispensable during Pressure Overload-Induced Cardiac Remodeling and Failure in Mice. PLoS One 2016; 11:e0150236. [PMID: 26919721 PMCID: PMC4769011 DOI: 10.1371/journal.pone.0150236] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/10/2016] [Indexed: 12/30/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are a class of RNA molecules with diverse regulatory functions during embryonic development, normal life, and disease in higher organisms. However, research on the role of lncRNAs in cardiovascular diseases and in particular heart failure is still in its infancy. The exceptionally well conserved nuclear lncRNA Metastasis associated in lung adenocarcinoma transcript 1 (Malat-1) is a regulator of mRNA splicing and highly expressed in the heart. Malat-1 modulates hypoxia-induced vessel growth, activates ERK/MAPK signaling, and scavenges the anti-hypertrophic microRNA-133. We therefore hypothesized that Malat-1 may act as regulator of cardiac hypertrophy and failure during cardiac pressure overload induced by thoracic aortic constriction (TAC) in mice. Results Absence of Malat-1 did not affect cardiac hypertrophy upon pressure overload: Heart weight to tibia length ratio significantly increased in WT mice (sham: 5.78±0.55, TAC 9.79±1.82 g/mm; p<0.001) but to a similar extend also in Malat-1 knockout (KO) mice (sham: 6.21±1.12, TAC 8.91±1.74 g/mm; p<0.01) with no significant difference between genotypes. As expected, TAC significantly reduced left ventricular fractional shortening in WT (sham: 38.81±6.53%, TAC: 23.14±11.99%; p<0.01) but to a comparable degree also in KO mice (sham: 37.01±4.19%, TAC: 25.98±9.75%; p<0.05). Histological hallmarks of myocardial remodeling, such as cardiomyocyte hypertrophy, increased interstitial fibrosis, reduced capillary density, and immune cell infiltration, did not differ significantly between WT and KO mice after TAC. In line, the absence of Malat-1 did not significantly affect angiotensin II-induced cardiac hypertrophy, dysfunction, and overall remodeling. Above that, pressure overload by TAC significantly induced mRNA levels of the hypertrophy marker genes Nppa, Nppb and Acta1, to a similar extend in both genotypes. Alternative splicing of Ndrg2 after TAC was apparent in WT (isoform ratio; sham: 2.97±0.26, TAC 1.57±0.40; p<0.0001) and KO mice (sham: 3.64±0.37; TAC: 2.24±0.76; p<0.0001) and interestingly differed between genotypes both at baseline and after pressure overload (p<0.05 each). Conclusion These findings confirm a role for the lncRNA Malat-1 in mRNA splicing. However, no critical role for Malat-1 was found in pressure overload-induced heart failure in mice, despite its reported role in vascularization, ERK/MAPK signaling, and regulation of miR-133.
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Affiliation(s)
- Tim Peters
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Steffie Hermans-Beijnsberger
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Abdelaziz Beqqali
- Department of Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Nicole Bitsch
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | | | - Kannanganattu V. Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Leon J. de Windt
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Ralph J. van Oort
- Department of Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Stephane Heymans
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
- Netherlands Heart Institute (ICIN), Utrecht, The Netherlands
- Centre for Molecular and Vascular Biology (CMVB), Department of Cardiovascular Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Blanche Schroen
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
- * E-mail:
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493
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Ma Y, Liu L, Yan F, Wei W, Deng J, Sun J. Enhanced expression of long non-coding RNA NEAT1 is associated with the progression of gastric adenocarcinomas. World J Surg Oncol 2016; 14:41. [PMID: 26911892 PMCID: PMC4765228 DOI: 10.1186/s12957-016-0799-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 02/16/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are emerging as new players in the cancer. The aim of this study was to examine the abnormalities of NEAT1 (nuclear paraspeckle assembly transcript 1, also known as MENε/β) in gastric adenocarcinomas (GACs). METHODS One hundred thirty-one GAC tissues and matched adjacent normal tissues (ANTs) were collected from patients who undergone surgery. Differences in of NEAT1 expression were examined via quantitative reverse transcriptase PCR (qRT-PCR). WST-1 assay and transwell assay were carried out in vitro to investigate the proliferation and migration of GAC cells with alteration in NEAT1 long non-coding RNA (lncRNA) expression. RESULTS The expression levels of lncRNA NEAT1 were significantly elevated in GAC tissues (P<0.001) compared with ANTs. There was also a statistical difference in NEAT1 expression between early and advanced GACs (P=0.0111). GACs with lymph node metastasis (LNM) expressed higher levels of NEAT1 lncRNA compared with those without LNM (P=0.004). In the in vitro experiments, the proliferation but not migration of GAC cells was attenuated after NEAT1 knockdown by RNA interference. CONCLUSIONS Expression of NEAT1 lncRNA was enhanced in GACs; and NEAT1 may influence GAC progression by promoting tumor growth.
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Affiliation(s)
- Yanling Ma
- Department of Oncology of Zhongshan Hospital, Wuhan University, No. 26 Zhongshan Road, Wuhan, Hubei, 430033, China.
| | - Li Liu
- Department of Oncology of Zhongshan Hospital, Wuhan University, No. 26 Zhongshan Road, Wuhan, Hubei, 430033, China.
| | - Fei Yan
- Department of Oncology of Zhongshan Hospital, Wuhan University, No. 26 Zhongshan Road, Wuhan, Hubei, 430033, China.
| | - Wujie Wei
- Department of Oncology of Zhongshan Hospital, Wuhan University, No. 26 Zhongshan Road, Wuhan, Hubei, 430033, China.
| | - Jie Deng
- Department of Oncology of Zhongshan Hospital, Wuhan University, No. 26 Zhongshan Road, Wuhan, Hubei, 430033, China.
| | - Jianhai Sun
- Department of Oncology of Zhongshan Hospital, Wuhan University, No. 26 Zhongshan Road, Wuhan, Hubei, 430033, China.
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494
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Abstract
It is increasingly evident that many of the genomic mutations in cancer reside inside regions that do not encode proteins. However, these regions are often transcribed into long noncoding RNAs (lncRNAs). The recent application of next-generation sequencing to a growing number of cancer transcriptomes has indeed revealed thousands of lncRNAs whose aberrant expression is associated with different cancer types. Among the few that have been functionally characterized, several have been linked to malignant transformation. Notably, these lncRNAs have key roles in gene regulation and thus affect various aspects of cellular homeostasis, including proliferation, survival, migration or genomic stability. This review aims to summarize current knowledge of lncRNAs from the cancer perspective. It discusses the strategies that led to the identification of cancer-related lncRNAs and the methodologies and challenges involving the study of these molecules, as well as the imminent applications of these findings to the clinic.
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495
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Lima WF, De Hoyos CL, Liang XH, Crooke ST. RNA cleavage products generated by antisense oligonucleotides and siRNAs are processed by the RNA surveillance machinery. Nucleic Acids Res 2016; 44:3351-63. [PMID: 26843429 PMCID: PMC4838368 DOI: 10.1093/nar/gkw065] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/25/2016] [Indexed: 01/22/2023] Open
Abstract
DNA-based antisense oligonucleotides (ASOs) elicit cleavage of the targeted RNA by the endoribonuclease RNase H1, whereas siRNAs mediate cleavage through the RNAi pathway. To determine the fates of the cleaved RNA in cells, we lowered the levels of the factors involved in RNA surveillance prior to treating cells with ASOs or siRNA and analyzed cleavage products by RACE. The cytoplasmic 5' to 3' exoribonuclease XRN1 was responsible for the degradation of the downstream cleavage products generated by ASOs or siRNA targeting mRNAs. In contrast, downstream cleavage products generated by ASOs targeting nuclear long non-coding RNA Malat 1 and pre-mRNA were degraded by nuclear XRN2. The downstream cleavage products did not appear to be degraded in the 3' to 5' direction as the majority of these products contained intact poly(A) tails and were bound by the poly(A) binding protein. The upstream cleavage products of Malat1 were degraded in the 3' to 5' direction by the exosome complex containing the nuclear exoribonuclease Dis3. The exosome complex containing Dis3 or cytoplasmic Dis3L1 degraded mRNA upstream cleavage products, which were not bound by the 5'-cap binding complex and, consequently, were susceptible to degradation in the 5' to 3' direction by the XRN exoribonucleases.
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Affiliation(s)
- Walt F Lima
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
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496
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Stojic L, Niemczyk M, Orjalo A, Ito Y, Ruijter AEM, Uribe-Lewis S, Joseph N, Weston S, Menon S, Odom DT, Rinn J, Gergely F, Murrell A. Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions. Nat Commun 2016; 7:10406. [PMID: 26832224 PMCID: PMC4740813 DOI: 10.1038/ncomms10406] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/08/2015] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate gene expression via their RNA product or through transcriptional interference, yet a strategy to differentiate these two processes is lacking. To address this, we used multiple small interfering RNAs (siRNAs) to silence GNG12-AS1, a nuclear lncRNA transcribed in an antisense orientation to the tumour-suppressor DIRAS3. Here we show that while most siRNAs silence GNG12-AS1 post-transcriptionally, siRNA complementary to exon 1 of GNG12-AS1 suppresses its transcription by recruiting Argonaute 2 and inhibiting RNA polymerase II binding. Transcriptional, but not post-transcriptional, silencing of GNG12-AS1 causes concomitant upregulation of DIRAS3, indicating a function in transcriptional interference. This change in DIRAS3 expression is sufficient to impair cell cycle progression. In addition, the reduction in GNG12-AS1 transcripts alters MET signalling and cell migration, but these are independent of DIRAS3. Thus, differential siRNA targeting of a lncRNA allows dissection of the functions related to the process and products of its transcription.
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Affiliation(s)
- Lovorka Stojic
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Malwina Niemczyk
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Arturo Orjalo
- Biosearch Technologies Inc., 2199S. McDowell Boulevard, Petaluma, California 94954, USA
| | - Yoko Ito
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Anna Elisabeth Maria Ruijter
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Santiago Uribe-Lewis
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Nimesh Joseph
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Stephen Weston
- Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Duncan T. Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - John Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Adele Murrell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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497
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The Association between Abnormal Long Noncoding RNA MALAT-1 Expression and Cancer Lymph Node Metastasis: A Meta-Analysis. BIOMED RESEARCH INTERNATIONAL 2016; 2016:1823482. [PMID: 26989678 PMCID: PMC4773549 DOI: 10.1155/2016/1823482] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/14/2015] [Indexed: 01/08/2023]
Abstract
Previous studies have investigated that the expression levels of MALAT-1 were higher in cancerous tissues than matched histologically normal tissues. And, to some extent, overexpression of MALAT-1 was inclined to lymph node metastasis. This meta-analysis collected all relevant articles and explored the association between MALAT-1 expression levels and lymph node metastasis. We searched PubMed, EmBase, Web of Science, Cochrane Library, and OVID to address the level of MALAT-1 expression in cancer cases and noncancerous controls (accessed February 2015). And 8 studies comprising 696 multiple cancer patients were included to assess this association. The odds ratio (OR) and its corresponding 95% confidence interval (CI) were calculated to assess the strength of the association using Stata 12.0 version software. The results revealed there was a significant difference in the incidence of lymph node metastasis between high MALAT-1 expression group and low MALAT-1 expression group (OR = 1.94, 95% CI 1.15–3.28, P = 0.013 random-effects model). Subgroup analysis indicated that MALAT-1 high expression had an unfavorable impact on lymph node metastasis in Chinese patients (OR = 1.87, 95% CI 1.01–2.46). This study demonstrated that the incidence of lymph node metastasis in patients detected with high MALAT-1 expression was higher than that in patients with low MALAT-1 expression in China.
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498
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Arun G, Diermeier S, Akerman M, Chang KC, Wilkinson JE, Hearn S, Kim Y, MacLeod AR, Krainer AR, Norton L, Brogi E, Egeblad M, Spector DL. Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss. Genes Dev 2016; 30:34-51. [PMID: 26701265 PMCID: PMC4701977 DOI: 10.1101/gad.270959.115] [Citation(s) in RCA: 463] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/24/2015] [Indexed: 12/29/2022]
Abstract
Genome-wide analyses have identified thousands of long noncoding RNAs (lncRNAs). Malat1 (metastasis-associated lung adenocarcinoma transcript 1) is among the most abundant lncRNAs whose expression is altered in numerous cancers. Here we report that genetic loss or systemic knockdown of Malat1 using antisense oligonucleotides (ASOs) in the MMTV (mouse mammary tumor virus)-PyMT mouse mammary carcinoma model results in slower tumor growth accompanied by significant differentiation into cystic tumors and a reduction in metastasis. Furthermore, Malat1 loss results in a reduction of branching morphogenesis in MMTV-PyMT- and Her2/neu-amplified tumor organoids, increased cell adhesion, and loss of migration. At the molecular level, Malat1 knockdown results in alterations in gene expression and changes in splicing patterns of genes involved in differentiation and protumorigenic signaling pathways. Together, these data demonstrate for the first time a functional role of Malat1 in regulating critical processes in mammary cancer pathogenesis. Thus, Malat1 represents an exciting therapeutic target, and Malat1 ASOs represent a potential therapy for inhibiting breast cancer progression.
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Affiliation(s)
- Gayatri Arun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sarah Diermeier
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Martin Akerman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Kung-Chi Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York 11790, USA
| | - J Erby Wilkinson
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stephen Hearn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Youngsoo Kim
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, USA
| | | | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York 11790, USA
| | - Larry Norton
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Edi Brogi
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Mikala Egeblad
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York 11790, USA
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499
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Wilusz JE. Long noncoding RNAs: Re-writing dogmas of RNA processing and stability. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:128-38. [PMID: 26073320 PMCID: PMC4676738 DOI: 10.1016/j.bbagrm.2015.06.003] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/16/2015] [Accepted: 06/04/2015] [Indexed: 12/14/2022]
Abstract
Most of the human genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs. Many of these transcripts have a 5' cap and a poly(A) tail, yet some of the most abundant long noncoding RNAs are processed in unexpected ways and lack these canonical structures. Here, I highlight the mechanisms by which several of these well-characterized noncoding RNAs are generated, stabilized, and function. The MALAT1 and MEN β (NEAT1_2) long noncoding RNAs each accumulate to high levels in the nucleus, where they play critical roles in cancer progression and the formation of nuclear paraspeckles, respectively. Nevertheless, MALAT1 and MEN β are not polyadenylated as the tRNA biogenesis machinery generates their mature 3' ends. In place of a poly(A) tail, these transcripts are stabilized by highly conserved triple helical structures. Sno-lncRNAs likewise lack poly(A) tails and instead have snoRNA structures at their 5' and 3' ends. Recent work has additionally identified a number of abundant circular RNAs generated by the pre-mRNA splicing machinery that are resistant to degradation by exonucleases. As these various transcripts use non-canonical strategies to ensure their stability, it is becoming increasingly clear that long noncoding RNAs may often be regulated by unique post-transcriptional control mechanisms. 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)
- Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States.
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Gernapudi R, Wolfson B, Zhang Y, Yao Y, Yang P, Asahara H, Zhou Q. MicroRNA 140 Promotes Expression of Long Noncoding RNA NEAT1 in Adipogenesis. Mol Cell Biol 2016; 36:30-8. [PMID: 26459763 PMCID: PMC4702608 DOI: 10.1128/mcb.00702-15] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/15/2015] [Accepted: 10/02/2015] [Indexed: 02/06/2023] Open
Abstract
More than 40% of the U.S. population are clinically obese and suffer from metabolic syndrome with an increased risk of postmenopausal estrogen receptor-positive breast cancer. Adipocytes are the primary component of adipose tissue and are formed through adipogenesis from precursor mesenchymal stem cells. While the major molecular pathways of adipogenesis are understood, little is known about the noncoding RNA signaling networks involved in adipogenesis. Using adipocyte-derived stem cells (ADSCs) isolated from wild-type and microRNA 140 (miR-140) knockout mice, we identify a novel miR-140/long noncoding RNA (lncRNA) NEAT1 signaling network necessary for adipogenesis. miR-140 knockout ADSCs have dramatically decreased adipogenic capabilities associated with downregulation of NEAT1 expression. We identified a miR-140 binding site in NEAT1 and found that mature miR-140 in the nucleus can physically interact with NEAT1, leading to increased NEAT1 expression. We demonstrated that reexpression of NEAT1 in miR-140 knockout ADSCs is sufficient to restore their ability to undergo differentiation. Our results reveal an exciting new noncoding RNA signaling network that regulates adipogenesis and that is a potential new target in the prevention or treatment of obesity.
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Affiliation(s)
- Ramkishore Gernapudi
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Benjamin Wolfson
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yongshu Zhang
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yuan Yao
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Peixin Yang
- Department of Obstetrics, Gynecology and Reproductive Sciences at University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Hiroshi Asahara
- The Scripps Research Institute Department of Molecular and Experimental Medicine, La Jolla, California, USA Department of Systems Biomedicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Qun Zhou
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
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