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Chen G, Yu D, Yang Y, Li X, Wang X, Sun D, Lu Y, Ke R, Zhang G, Cui J, Feng S. Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events. Nat Commun 2024; 15:3151. [PMID: 38605055 PMCID: PMC11009239 DOI: 10.1038/s41467-024-47501-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
Endogenous retroviruses (ERVs) are ancient retroviral remnants integrated in host genomes, and commonly deleted through unequal homologous recombination, leaving solitary long terminal repeats (solo-LTRs). This study, analysing the genomes of 362 bird species and their reptilian and mammalian outgroups, reveals an unusually higher level of solo-LTRs formation in birds, indicating evolutionary forces might have purged ERVs during evolution. Strikingly in the order Passeriformes, and especially the parvorder Passerida, endogenous retrovirus K (ERVK) solo-LTRs showed bursts of formation and recurrent accumulations coinciding with speciation events over past 22 million years. Moreover, our results indicate that the ongoing expansion of ERVK solo-LTRs in these bird species, marked by high transcriptional activity of ERVK retroviral genes in reproductive organs, caused variation of solo-LTRs between individual zebra finches. We experimentally demonstrated that cis-regulatory activity of recently evolved ERVK solo-LTRs may significantly increase the expression level of ITGA2 in the brain of zebra finches compared to chickens. These findings suggest that ERVK solo-LTRs expansion may introduce novel genomic sequences acting as cis-regulatory elements and contribute to adaptive evolution. Overall, our results underscore that the residual sequences of ancient retroviruses could influence the adaptive diversification of species by regulating host gene expression.
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Affiliation(s)
- Guangji Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- BGI Research, Wuhan, China
| | - Dan Yu
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Yang
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Xiang Li
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Danyang Sun
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yanlin Lu
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jie Cui
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Huashan Hospital, Institute of Infection and Health Research, Fudan University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, 200052, China.
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China.
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China.
- Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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2
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Heruye S, Myslinski J, Zeng C, Zollman A, Makino S, Nanamatsu A, Mir Q, Janga SC, Doud EH, Eadon MT, Maier B, Hamada M, Tran TM, Dagher PC, Hato T. Inflammation primes the kidney for recovery by activating AZIN1 A-to-I editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566426. [PMID: 37986799 PMCID: PMC10659426 DOI: 10.1101/2023.11.09.566426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The progression of kidney disease varies among individuals, but a general methodology to quantify disease timelines is lacking. Particularly challenging is the task of determining the potential for recovery from acute kidney injury following various insults. Here, we report that quantitation of post-transcriptional adenosine-to-inosine (A-to-I) RNA editing offers a distinct genome-wide signature, enabling the delineation of disease trajectories in the kidney. A well-defined murine model of endotoxemia permitted the identification of the origin and extent of A-to-I editing, along with temporally discrete signatures of double-stranded RNA stress and Adenosine Deaminase isoform switching. We found that A-to-I editing of Antizyme Inhibitor 1 (AZIN1), a positive regulator of polyamine biosynthesis, serves as a particularly useful temporal landmark during endotoxemia. Our data indicate that AZIN1 A-to-I editing, triggered by preceding inflammation, primes the kidney and activates endogenous recovery mechanisms. By comparing genetically modified human cell lines and mice locked in either A-to-I edited or uneditable states, we uncovered that AZIN1 A-to-I editing not only enhances polyamine biosynthesis but also engages glycolysis and nicotinamide biosynthesis to drive the recovery phenotype. Our findings implicate that quantifying AZIN1 A-to-I editing could potentially identify individuals who have transitioned to an endogenous recovery phase. This phase would reflect their past inflammation and indicate their potential for future recovery.
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Affiliation(s)
- Segewkal Heruye
- Department of Medicine, Indiana University School of Medicine
| | - Jered Myslinski
- Department of Medicine, Indiana University School of Medicine
| | - Chao Zeng
- Faculty of Science and Engineering, Waseda University, Tokyo
| | - Amy Zollman
- Department of Medicine, Indiana University School of Medicine
| | - Shinichi Makino
- Department of Medicine, Indiana University School of Medicine
| | - Azuma Nanamatsu
- Department of Medicine, Indiana University School of Medicine
| | - Quoseena Mir
- Luddy School of Informatics, Computing, and Engineering, Indiana University
| | | | - Emma H Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine
| | - Michael T Eadon
- Department of Medicine, Indiana University School of Medicine
| | - Bernhard Maier
- Department of Medicine, Indiana University School of Medicine
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, Tokyo
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo
- Graduate School of Medicine, Nippon Medical School, Tokyo
| | - Tuan M Tran
- Department of Medicine, Indiana University School of Medicine
- Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis
| | - Pierre C Dagher
- Department of Medicine, Indiana University School of Medicine
| | - Takashi Hato
- Department of Medicine, Indiana University School of Medicine
- Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis
- Department of Medical and Molecular Genetics, Indiana University School of Medicine
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3
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Tang RY, Yin L, Yao L, Zhang QF, Chen XP. A Co-Expressed Natural Antisense RNA FCER1A-AS Controls IgE-Dependent Immunity by Promoting Expression of FcεRIα. Microbiol Spectr 2023; 11:e0073323. [PMID: 37154775 PMCID: PMC10269606 DOI: 10.1128/spectrum.00733-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
As the α-subunit of the high-affinity receptor for the Fc portion of immunoglobulin E (FcεRIα), FcεRIα plays a central role in IgE-mediated allergic disorders and in the immunity and immunopathology of some parasitic infections. FcεRIα is specifically expressed on basophils and mast cells, but the mechanism that controls FcεRIα expression in these cells is poorly understood. In this study, we found that the natural antisense transcript (NAT) of FcεRIα (FCER1A-AS) is co-expressed with the sense transcript (FCER1A-S) in both interleukin (IL)-3-induced FcεRIα-expressing cells and in the high FcεRIα-expressing cell line MC/9. When FCER1A-AS is selectively knocked down by the CRISPR/RfxCas13d (CasRx) approach in MC/9 cells, the expression of both FCER1A-S mRNA and proteins is markedly decreased. Furthermore, FCER1A-AS deficiency was also found to be associated with a lack of FCER1A-S expression in vivo. Correspondingly, homozygous mice deficient in FCER1A-AS demonstrated a similar phenotype to FCER1A knockout mice in Schistosoma japonicum infection and in IgE-FcεRIα-mediated cutaneous anaphylaxis. Thus, we uncovered a novel pathway for the control of FcεRIα expression by its co-expressed natural antisense transcript. IMPORTANCE FcεRIα is responsible for high-affinity binding with the Fc portion of IgE, which is critical for IgE-dependent disease responses such as allergy responses and anti-parasite immunity. FcεRIα is expressed on a few cell types, including mast cells and basophils. Although the expression of FcεRIα is known to be promoted by the IL-3-GATA-2 pathway during its differentiation, the mechanism by which FcεRIα expression is maintained remains unknown. In this study, we discovered that a natural antisense transcript, FCER1A-AS, is co-expressed with the sense transcript. The presence of FCER1A-AS is essential for sense transcript expression in mast cells and basophils, but not for the differentiation of these cells through cis-regulation. Like FcεRIα knockout mice, mice lacking FCER1A-AS also exhibit reduced survival after Schistosoma japonicum infection and a lack of IgE-mediated cutaneous anaphylaxis. Thus, a novel pathway for regulating IgE-mediated allergic diseases through noncoding RNAs has been revealed.
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Affiliation(s)
- Ruo-yu Tang
- Department of Microbiology and Immunology, School of Medicine, Tongji University, Shanghai, China
| | - Lan Yin
- Department of Microbiology and Immunology, School of Medicine, Tongji University, Shanghai, China
| | - Liang Yao
- Department of Microbiology and Immunology, School of Medicine, Tongji University, Shanghai, China
| | - Qing-Feng Zhang
- Department of Microbiology and Immunology, School of Medicine, Tongji University, Shanghai, China
| | - Xiao-Ping Chen
- Department of Microbiology and Immunology, School of Medicine, Tongji University, Shanghai, China
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4
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The retroelement Lx9 puts a brake on the immune response to virus infection. Nature 2022; 608:757-765. [PMID: 35948641 DOI: 10.1038/s41586-022-05054-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 06/30/2022] [Indexed: 11/08/2022]
Abstract
The notion that mobile units of nucleic acid known as transposable elements can operate as genomic controlling elements was put forward over six decades ago1,2. However, it was not until the advancement of genomic sequencing technologies that the abundance and repertoire of transposable elements were revealed, and they are now known to constitute up to two-thirds of mammalian genomes3,4. The presence of DNA regulatory regions including promoters, enhancers and transcription-factor-binding sites within transposable elements5-8 has led to the hypothesis that transposable elements have been co-opted to regulate mammalian gene expression and cell phenotype8-14. Mammalian transposable elements include recent acquisitions and ancient transposable elements that have been maintained in the genome over evolutionary time. The presence of ancient conserved transposable elements correlates positively with the likelihood of a regulatory function, but functional validation remains an essential step to identify transposable element insertions that have a positive effect on fitness. Here we show that CRISPR-Cas9-mediated deletion of a transposable element-namely the LINE-1 retrotransposon Lx9c11-in mice results in an exaggerated and lethal immune response to virus infection. Lx9c11 is critical for the neogenesis of a non-coding RNA (Lx9c11-RegoS) that regulates genes of the Schlafen family, reduces the hyperinflammatory phenotype and rescues lethality in virus-infected Lx9c11-/- mice. These findings provide evidence that a transposable element can control the immune system to favour host survival during virus infection.
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5
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Guo Y, Xie Y, Luo Y. The Role of Long Non-Coding RNAs in the Tumor Immune Microenvironment. Front Immunol 2022; 13:851004. [PMID: 35222443 PMCID: PMC8863945 DOI: 10.3389/fimmu.2022.851004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/24/2022] [Indexed: 02/05/2023] Open
Abstract
Tumorigenesis is a complicated process caused by successive genetic and epigenetic alterations. The past decades demonstrated that the immune system affects tumorigenesis, tumor progression, and metastasis. Although increasing immunotherapies are revealed, only a tiny proportion of them are effective. Long non-coding RNAs (lncRNAs) are a class of single-stranded RNA molecules larger than 200 nucleotides and are essential in the molecular network of oncology and immunology. Increasing researches have focused on the connection between lncRNAs and cancer immunotherapy. However, the in-depth mechanisms are still elusive. In this review, we outline the latest studies on the functions of lncRNAs in the tumor immune microenvironment. Via participating in various biological processes such as neutrophil recruitment, macrophage polarization, NK cells cytotoxicity, and T cells functions, lncRNAs regulate tumorigenesis, tumor invasion, epithelial-mesenchymal transition (EMT), and angiogenesis. In addition, we reviewed the current understanding of the relevant strategies for targeting lncRNAs. LncRNAs-based therapeutics may represent promising approaches in serving as prognostic biomarkers or potential therapeutic targets in cancer, providing ideas for future research and clinical application on cancer diagnosis and therapies.
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Affiliation(s)
- Yingli Guo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yajuan Xie
- Department of Orthodontics, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yao Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
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Hermant C, Torres-Padilla ME. TFs for TEs: the transcription factor repertoire of mammalian transposable elements. Genes Dev 2021; 35:22-39. [PMID: 33397727 PMCID: PMC7778262 DOI: 10.1101/gad.344473.120] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Hermant and Torres-Padilla summarize and discuss the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific transposable element families or subfamilies. Transposable elements (TEs) are genetic elements capable of changing position within the genome. Although their mobilization can constitute a threat to genome integrity, nearly half of modern mammalian genomes are composed of remnants of TE insertions. The first critical step for a successful transposition cycle is the generation of a full-length transcript. TEs have evolved cis-regulatory elements enabling them to recruit host-encoded factors driving their own, selfish transcription. TEs are generally transcriptionally silenced in somatic cells, and the mechanisms underlying their repression have been extensively studied. However, during germline formation, preimplantation development, and tumorigenesis, specific TE families are highly expressed. Understanding the molecular players at stake in these contexts is of utmost importance to establish the mechanisms regulating TEs, as well as the importance of their transcription to the biology of the host. Here, we review the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific TE families or subfamilies. We discuss the diversity of TE regulatory elements within mammalian genomes and highlight the importance of TE mobilization in the dispersal of transcription factor-binding sites over the course of evolution.
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Affiliation(s)
- Clara Hermant
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany.,Faculty of Biology, Ludwig-Maximilians Universität München, D-82152 Planegg-Martinsried, Germany
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7
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Wong JYY, Cawthon R, Dai Y, Vermeulen R, Bassig BA, Hu W, Duan H, Niu Y, Downward GS, Leng S, Ji BT, Fu W, Xu J, Meliefste K, Zhou B, Yang J, Ren D, Ye M, Jia X, Meng T, Bin P, Hosgood Iii HD, Silverman DT, Rothman N, Zheng Y, Lan Q. Elevated Alu retroelement copy number among workers exposed to diesel engine exhaust. Occup Environ Med 2021; 78:823-828. [PMID: 34039759 DOI: 10.1136/oemed-2021-107462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Millions of workers worldwide are exposed to diesel engine exhaust (DEE), a known genotoxic carcinogen. Alu retroelements are repetitive DNA sequences that can multiply and compromise genomic stability. There is some evidence linking altered Alu repeats to cancer and elevated mortality risks. However, whether Alu repeats are influenced by environmental pollutants is unexplored. In an occupational setting with high DEE exposure levels, we investigated associations with Alu repeat copy number. METHODS A cross-sectional study of 54 male DEE-exposed workers from an engine testing facility and a comparison group of 55 male unexposed controls was conducted in China. Personal air samples were assessed for elemental carbon, a DEE surrogate, using NIOSH Method 5040. Quantitative PCR (qPCR) was used to measure Alu repeat copy number relative to albumin (Alb) single-gene copy number in leucocyte DNA. The unitless Alu/Alb ratio reflects the average quantity of Alu repeats per cell. Linear regression models adjusted for age and smoking status were used to estimate relations between DEE-exposed workers versus unexposed controls, DEE tertiles (6.1-39.0, 39.1-54.5 and 54.6-107.7 µg/m3) and Alu/Alb ratio. RESULTS DEE-exposed workers had a higher average Alu/Alb ratio than the unexposed controls (p=0.03). Further, we found a positive exposure-response relationship (p=0.02). The Alu/Alb ratio was highest among workers exposed to the top tertile of DEE versus the unexposed controls (1.12±0.08 SD vs 1.06±0.07 SD, p=0.01). CONCLUSION Our findings suggest that DEE exposure may contribute to genomic instability. Further investigations of environmental pollutants, Alu copy number and carcinogenesis are warranted.
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Affiliation(s)
- Jason Y Y Wong
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Richard Cawthon
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Yufei Dai
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Roel Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Bryan A Bassig
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Wei Hu
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Huawei Duan
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yong Niu
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - George S Downward
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Shuguang Leng
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Bu-Tian Ji
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Wei Fu
- Chaoyang Center for Disease Control and Prevention, Chaoyang, Liaoning, China
| | - Jun Xu
- Hong Kong University, Hong Kong, China
| | - Kees Meliefste
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Baosen Zhou
- China Medical University, Shenyang, Liaoning, China
| | - Jufang Yang
- Chaoyang Center for Disease Control and Prevention, Chaoyang, Liaoning, China
| | - Dianzhi Ren
- Chaoyang Center for Disease Control and Prevention, Chaoyang, Liaoning, China
| | - Meng Ye
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaowei Jia
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tao Meng
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ping Bin
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - H Dean Hosgood Iii
- Division of Epidemiology, Albert Einstein College of Medicine, Yeshiva University, New York, New York, USA
| | - Debra T Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Yuxin Zheng
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qing Lan
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
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Li R, Sklutuis R, Groebner JL, Romerio F. HIV-1 Natural Antisense Transcription and Its Role in Viral Persistence. Viruses 2021; 13:v13050795. [PMID: 33946840 PMCID: PMC8145503 DOI: 10.3390/v13050795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
Natural antisense transcripts (NATs) represent a class of RNA molecules that are transcribed from the opposite strand of a protein-coding gene, and that have the ability to regulate the expression of their cognate protein-coding gene via multiple mechanisms. NATs have been described in many prokaryotic and eukaryotic systems, as well as in the viruses that infect them. The human immunodeficiency virus (HIV-1) is no exception, and produces one or more NAT from a promoter within the 3’ long terminal repeat. HIV-1 antisense transcripts have been the focus of several studies spanning over 30 years. However, a complete appreciation of the role that these transcripts play in the virus lifecycle is still lacking. In this review, we cover the current knowledge about HIV-1 NATs, discuss some of the questions that are still open and identify possible areas of future research.
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Affiliation(s)
- Rui Li
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | - Rachel Sklutuis
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Jennifer L. Groebner
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
- Correspondence:
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9
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Evans TA, Erwin JA. Retroelement-derived RNA and its role in the brain. Semin Cell Dev Biol 2020; 114:68-80. [PMID: 33229216 DOI: 10.1016/j.semcdb.2020.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 10/20/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022]
Abstract
Comprising ~40% of the human genome, retroelements are mobile genetic elements which are transcribed into RNA, then reverse-transcribed into DNA and inserted into a new site in the genome. Retroelements are referred to as "genetic parasites", residing among host genes and relying on host machinery for transcription and evolutionary propagation. The healthy brain has the highest expression of retroelement-derived sequences compared to other somatic tissue, which leads to the question: how does retroelement-derived RNA influence human traits and cellular states? While the functional importance of upregulating retroelement expression in the brain is an active area of research, RNA species derived from retroelements influence both self- and host gene expression by contributing to chromatin remodeling, alternative splicing, somatic mosaicism and translational repression. Here, we review the emerging evidence that the functional importance of RNA derived from retroelements is multifaceted. Retroelements can influence organismal states through the seeding of epigenetic states in chromatin, the production of structured RNA and even catalytically active ribozymes, the generation of cytoplasmic ssDNA and RNA/DNA hybrids, the production of viral-like proteins, and the generation of somatic mutations. Comparative sequencing suggests that retroelements can contribute to intraspecies variation through these mechanisms to alter transcript identity and abundance. In humans, an increasing number of neurodevelopmental and neurodegenerative conditions are associated with dysregulated retroelements, including Aicardi-Goutieres syndrome (AGS), Rett syndrome (RTT), Amyotrophic Lateral Sclerosis (ALS), Alzheimer's disease (AD), multiple sclerosis (MS), schizophrenia (SZ), and aging. Taken together, these concepts suggest a larger functional role for RNA derived from retroelements. This review aims to define retroelement-derived RNA, discuss how it impacts the mammalian genome, as well as summarize data supporting phenotypic consequences of this unique RNA subset in the brain.
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Affiliation(s)
- Taylor A Evans
- Lieber Institute for Brain Development, Baltimore, MD, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer Ann Erwin
- Lieber Institute for Brain Development, Baltimore, MD, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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10
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Xue B, Sechi LA, Kelvin DJ. Human Endogenous Retrovirus K (HML-2) in Health and Disease. Front Microbiol 2020; 11:1690. [PMID: 32765477 PMCID: PMC7380069 DOI: 10.3389/fmicb.2020.01690] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/29/2020] [Indexed: 02/05/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are derived from exogenous retrovirus infections in the evolution of primates and account for about 8% of the human genome. They were considered as silent passengers within our genomes for a long time, however, reactivation of HERVs has been associated with tumors and autoimmune diseases, especially the HERV-K (HML-2) family, the most recent integration groups with the least number of mutations and the most biologically active to encode functional retroviral proteins and produce retrovirus-like particles. Increasing studies are committed to determining the potential role of HERV-K (HML-2) in pathogenicity. Although there is still no evidence for HERV-K (HML-2) as a direct cause of diseases, aberrant expression profiles of the HERV-K (HML-2) transcripts and their regulatory function to their proximal host-genes were identified in different diseases. In this review, we summarized the advances between HERV-K (HML-2) and diseases to provide basis for further studies on the causal relationship between HERV-K (HML-2) and diseases. We recommended more attention to polymorphic integrated HERV-K (HML-2) loci which could be genetic causative factors and be associated with inter-individual differences in tumorigenesis and autoimmune diseases.
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Affiliation(s)
- Bei Xue
- Division of Immunology, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Mediterranean Center for Disease Control, University of Sassari, Sassari, Italy
| | - David J. Kelvin
- Division of Immunology, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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11
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Clayton EA, Rishishwar L, Huang TC, Gulati S, Ban D, McDonald JF, Jordan IK. An atlas of transposable element-derived alternative splicing in cancer. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190342. [PMID: 32075558 PMCID: PMC7061986 DOI: 10.1098/rstb.2019.0342] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2019] [Indexed: 12/18/2022] Open
Abstract
Transposable element (TE)-derived sequences comprise more than half of the human genome, and their presence has been documented to alter gene expression in a number of different ways, including the generation of alternatively spliced transcript isoforms. Alternative splicing has been associated with tumorigenesis for a number of different cancers. The objective of this study was to broadly characterize the role of human TEs in generating alternatively spliced transcript isoforms in cancer. To do so, we screened for the presence of TE-derived sequences co-located with alternative splice sites that are differentially used in normal versus cancer tissues. We analysed a comprehensive set of alternative splice variants characterized for 614 matched normal-tumour tissue pairs across 13 cancer types, resulting in the discovery of 4820 TE-generated alternative splice events distributed among 723 cancer-associated genes. Short interspersed nuclear elements (Alu) and long interspersed nuclear elements (L1) were found to contribute the majority of TE-generated alternative splice sites in cancer genes. A number of cancer-associated genes, including MYH11, WHSC1 and CANT1, were shown to have overexpressed TE-derived isoforms across a range of cancer types. TE-derived isoforms were also linked to cancer-specific fusion transcripts, suggesting a novel mechanism for the generation of transcriptome diversity via trans-splicing mediated by dispersed TE repeats. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Evan A. Clayton
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Tzu-Chuan Huang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Saurabh Gulati
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Dongjo Ban
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - John F. McDonald
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
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12
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Zeng Y, Cao Y, Halevy RS, Nguyen P, Liu D, Zhang X, Ahituv N, Han JDJ. Characterization of functional transposable element enhancers in acute myeloid leukemia. SCIENCE CHINA-LIFE SCIENCES 2020; 63:675-687. [PMID: 32170627 DOI: 10.1007/s11427-019-1574-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
Transposable elements (TEs) have been shown to have important gene regulatory functions and their alteration could lead to disease phenotypes. Acute myeloid leukemia (AML) develops as a consequence of a series of genetic changes in hematopoietic precursor cells, including mutations in epigenetic factors. Here, we set out to study the gene regulatory role of TEs in AML. We first explored the epigenetic landscape of TEs in AML patients using ATAC-seq data. We show that a large number of TEs in general, and more specifically mammalian-wide interspersed repeats (MIRs), are more enriched in AML cells than in normal blood cells. We obtained a similar finding when analyzing histone modification data in AML patients. Gene Ontology enrichment analysis showed that genes near MIRs in open chromatin regions are involved in leukemogenesis. To functionally validate their regulatory role, we selected 19 MIR regions in AML cells, and tested them for enhancer activity in an AML cell line (Kasumi-1) and a chronic myeloid leukemia (CML) cell line (K562); the results revealed several MIRs to be functional enhancers. Taken together, our results suggest that TEs are potentially involved in myeloid leukemogenesis and highlight these sequences as potential candidates harboring AML-associated variation.
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Affiliation(s)
- Yingying Zeng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yaqiang Cao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rivka Sukenik Halevy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, 94143, USA.,Sackler School of Medicine, Tel-Aviv University, Tel Aviv, 6997801, Israel
| | - Picard Nguyen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, 94143, USA
| | - Denghui Liu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiaoli Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, USA. .,Institute for Human Genetics, University of California San Francisco, San Francisco, 94143, USA.
| | - Jing-Dong J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. .,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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13
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Zhao X, Xiong J, Mao F, Sheng Y, Chen X, Feng L, Dui W, Yang W, Kapusta A, Feschotte C, Coyne RS, Miao W, Gao S, Liu Y. RNAi-dependent Polycomb repression controls transposable elements in Tetrahymena. Genes Dev 2019; 33:348-364. [PMID: 30808657 PMCID: PMC6411011 DOI: 10.1101/gad.320796.118] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/02/2019] [Indexed: 12/30/2022]
Abstract
In this study, Zhao et al. show that in the protozoan Tetrahymena thermophila, germline-specific internally eliminated sequences (IESs) become transcriptionally activated in mutants deficient in the RNAi-dependent Polycomb repression pathway. Their findings suggest that the interplay between RNAi and Polycomb repression is a widely conserved phenomenon whose ancestral role is epigenetic silencing of TEs. RNAi and Polycomb repression play evolutionarily conserved and often coordinated roles in transcriptional silencing. Here, we show that, in the protozoan Tetrahymena thermophila, germline-specific internally eliminated sequences (IESs)—many related to transposable elements (TEs)—become transcriptionally activated in mutants deficient in the RNAi-dependent Polycomb repression pathway. Germline TE mobilization also dramatically increases in these mutants. The transition from noncoding RNA (ncRNA) to mRNA production accompanies transcriptional activation of TE-related sequences and vice versa for transcriptional silencing. The balance between ncRNA and mRNA production is potentially affected by cotranscriptional processing as well as RNAi and Polycomb repression. We posit that interplay between RNAi and Polycomb repression is a widely conserved phenomenon, whose ancestral role is epigenetic silencing of TEs.
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Affiliation(s)
- Xiaolu Zhao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yalan Sheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Xiao Chen
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Lifang Feng
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Wen Dui
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Wentao Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Robert S Coyne
- J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shan Gao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
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14
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Zhao CN, Mao YM, Liu LN, Li XM, Wang DG, Pan HF. Emerging role of lncRNAs in systemic lupus erythematosus. Biomed Pharmacother 2018; 106:584-592. [DOI: 10.1016/j.biopha.2018.06.175] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/26/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
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15
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Jung J, Lee S, Cho HS, Park K, Ryu JW, Jung M, Kim J, Kim H, Kim DS. Bioinformatic analysis of regulation of natural antisense transcripts by transposable elements in human mRNA. Genomics 2018; 111:159-166. [PMID: 29366860 DOI: 10.1016/j.ygeno.2018.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/19/2022]
Abstract
Non-coding RNA is no longer considered to be "junk" DNA, based on evidence uncovered in recent decades. In particular, the important role played by natural antisense transcripts (NATs) in regulating the expression of genes is receiving increasing attention. However, the regulatory mechanisms of NATs remain incompletely understood. It is well-known that the insertion of transposable elements (TEs) can affect gene transcription. Using a bioinformatics approach, we identified NATs using human mRNA sequences from the UCSC Genome Browser Database. Our in silico analysis identified 1079 NATs and 700 sense-antisense gene pairs. We identified 179 NATs that showed evidence of having been affected by TEs during cellular gene expression. These findings may provide an understanding of the complex regulation mechanisms of NATs. If our understanding of NATs as modulators of gene expression is further enhanced, we can develop ways to control gene expression.
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Affiliation(s)
- Jaeeun Jung
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sugi Lee
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyun-Soo Cho
- Department of Stem Cell Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Kunhyang Park
- Department of Core Facility Management Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jea-Woon Ryu
- Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Minah Jung
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jeongkil Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - HyeRan Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Plant Systems Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Dae-Soo Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea.
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16
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Zhang H, Liu J, Tai Y, Zhang X, Zhang J, Liu S, Lv J, Liu Z, Kong Q. Identification and characterization of L1-specific endo-siRNAs essential for early embryonic development in pig. Oncotarget 2017; 8:23167-23176. [PMID: 28423565 PMCID: PMC5410294 DOI: 10.18632/oncotarget.15517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/08/2017] [Indexed: 01/17/2023] Open
Abstract
Small noncoding RNAs (sncRNAs) play important roles in RNA interference (RNAi). In addition to microRNA (miRNA) and Piwi-interacting RNA (piRNA), one key member of sncRNAs group is endogenous small interfering RNA (endo-siRNA). Some studies do show the role of endo-siRNAs in Dicer and/or Ago mutants, however, the biological functions of specific endo-siRNAs remains mostly unanswered. In the study, we have performed a comparative analysis of endo-siRNAs present in porcine sperms, oocytes and zygotes, identified by deep sequencing and bioinformatics analysis. Further, we observe a large amount of endo-siRNAs specific binding on ORF2 and 3′ UTR of porcine L1 (L1-siRNAs). And, 9 L1-siRNAs generated from a dsRNA formed between L1 transcript and a newly identified an antisense noncoding RNA was characterized. We show the L1-siRNAs regulate early embryonic development by inhibiting the activity of L1 retrotransposition. This work can contribute to understanding the functional role of abundant endo-siRNAs in embryonic development.
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Affiliation(s)
- Heng Zhang
- Laboratory of Embryo Biotechnology, College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, China
| | - Jilong Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou Province 510642, China
| | - Yurong Tai
- Laboratory of Embryo Biotechnology, College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, China
| | - Xiaolei Zhang
- Laboratory of Embryo Biotechnology, College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, China
| | - Jiaming Zhang
- Laboratory of Embryo Biotechnology, College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, China
| | - Shichao Liu
- Laboratory of Embryo Biotechnology, College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, China
| | - Jiawei Lv
- Laboratory of Embryo Biotechnology, College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, China
| | - Zhonghua Liu
- Laboratory of Embryo Biotechnology, College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, China
| | - Qingran Kong
- Laboratory of Embryo Biotechnology, College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, China
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17
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Zinad HS, Natasya I, Werner A. Natural Antisense Transcripts at the Interface between Host Genome and Mobile Genetic Elements. Front Microbiol 2017; 8:2292. [PMID: 29209299 PMCID: PMC5701935 DOI: 10.3389/fmicb.2017.02292] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/06/2017] [Indexed: 12/26/2022] Open
Abstract
Non-coding RNAs are involved in epigenetic processes, playing a role in the regulation of gene expression at the transcriptional and post-transcriptional levels. A particular group of ncRNA are natural antisense transcripts (NATs); these are transcribed in the opposite direction to protein coding transcripts and are widespread in eukaryotes. Their abundance, evidence of phylogenetic conservation and an increasing number of well-characterized examples of antisense-mediated gene regulation are indicative of essential biological roles of NATs. There is evidence to suggest that they interfere with their corresponding sense transcript to elicit concordant and discordant regulation. The main mechanisms involved include transcriptional interference as well as dsRNA formation. Sense–antisense hybrid formation can trigger RNA interference, RNA editing or protein kinase R. However, the exact molecular mechanisms elicited by NATs in the context of these regulatory roles are currently poorly understood. Several examples confirm that ectopic expression of antisense transcripts trigger epigenetic silencing of the related sense transcript. Genomic approaches suggest that the antisense transcriptome carries a broader biological significance which goes beyond the physiological regulation of the directly related sense transcripts. Because NATs show evidence of conservation we speculate that they played a role in evolution, with early eukaryotes gaining selective advantage through the regulatory effects. With the surge of genome and transcriptome sequencing projects, there is promise of a more comprehensive understanding of the biological role of NATs and the regulatory mechanisms involved.
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Affiliation(s)
- Hany S Zinad
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Inas Natasya
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andreas Werner
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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18
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Casa V, Runfola V, Micheloni S, Aziz A, Dilworth FJ, Gabellini D. Polycomb repressive complex 1 provides a molecular explanation for repeat copy number dependency in FSHD muscular dystrophy. Hum Mol Genet 2017; 26:753-767. [PMID: 28040729 PMCID: PMC5409123 DOI: 10.1093/hmg/ddw426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/15/2016] [Indexed: 11/13/2022] Open
Abstract
Repression of repetitive elements is crucial to preserve genome integrity and has been traditionally ascribed to constitutive heterochromatin pathways. FacioScapuloHumeral Muscular Dystrophy (FSHD), one of the most common myopathies, is characterized by a complex interplay of genetic and epigenetic events. The main FSHD form is linked to a reduced copy number of the D4Z4 macrosatellite repeat on 4q35, causing loss of silencing and aberrant expression of the D4Z4-embedded DUX4 gene leading to disease. By an unknown mechanism, D4Z4 copy-number correlates with FSHD phenotype. Here we show that the DUX4 proximal promoter (DUX4p) is sufficient to nucleate the enrichment of both constitutive and facultative heterochromatin components and to mediate a copy-number dependent gene silencing. We found that both the CpG/GC dense DNA content and the repetitive nature of DUX4p arrays are important for their repressive ability. We showed that DUX4p mediates a copy number-dependent Polycomb Repressive Complex 1 (PRC1) recruitment, which is responsible for the copy-number dependent gene repression. Overall, we directly link genetic and epigenetic defects in FSHD by proposing a novel molecular explanation for the copy number-dependency in FSHD pathogenesis, and offer insight into the molecular functions of repeats in chromatin regulation.
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Affiliation(s)
- Valentina Casa
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Università Vita-Salute San Raffaele, Milan 20132, Italy
| | - Valeria Runfola
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Stefano Micheloni
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Arif Aziz
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - F Jeffrey Dilworth
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Dulbecco Telethon Institute, Milan 20132, Italy
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19
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Broecker F, Horton R, Heinrich J, Franz A, Schweiger MR, Lehrach H, Moelling K. The intron-enriched HERV-K(HML-10) family suppresses apoptosis, an indicator of malignant transformation. Mob DNA 2016; 7:25. [PMID: 27980690 PMCID: PMC5142424 DOI: 10.1186/s13100-016-0081-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/19/2016] [Indexed: 02/06/2023] Open
Abstract
Background Human endogenous retroviruses (HERVs) constitute 8% of the human genome and contribute substantially to the transcriptome. HERVs have been shown to generate RNAs that modulate host gene expression. However, experimental evidence for an impact of these regulatory transcripts on the cellular phenotype has been lacking. Results We characterized the previously little described HERV-K(HML-10) endogenous retrovirus family on a genome-wide scale. HML-10 invaded the ancestral genome of Old World monkeys about 35 Million years ago and is enriched within introns of human genes when compared to other HERV families. We show that long terminal repeats (LTRs) of HML-10 exhibit variable promoter activity in human cancer cell lines. One identified HML-10 LTR-primed RNA was in opposite orientation to the pro-apoptotic Death-associated protein 3 (DAP3). In HeLa cells, experimental inactivation of HML-10 LTR-primed transcripts induced DAP3 expression levels, which led to apoptosis. Conclusions Its enrichment within introns suggests that HML-10 may have been evolutionary co-opted for gene regulation more than other HERV families. We demonstrated such a regulatory activity for an HML-10 RNA that suppressed DAP3-mediated apoptosis in HeLa cells. Since HML-10 RNA appears to be upregulated in various tumor cell lines and primary tumor samples, it may contribute to evasion of apoptosis in malignant cells. However, the overall weak expression of HML-10 transcripts described here raises the question whether our result described for HeLa represent a rare event in cancer. A possible function in other cells or tissues requires further investigation. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0081-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Felix Broecker
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Institute of Medical Microbiology, University of Zurich, Gloriastr. 32, 8006 Zurich, Switzerland ; Current affiliation: Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Roger Horton
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Jochen Heinrich
- Institute of Medical Microbiology, University of Zurich, Gloriastr. 32, 8006 Zurich, Switzerland
| | - Alexandra Franz
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Current affiliation: University of Zurich, Institute of Molecular Life Sciences, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Michal-Ruth Schweiger
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Current affiliation: Functional Epigenomics, CCG, Cologne University Hospital, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Hans Lehrach
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Dahlem Centre for Genome Research and Medical Systems Biology, Fabeckstr. 60-62, 14195 Berlin, Germany
| | - Karin Moelling
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Institute of Medical Microbiology, University of Zurich, Gloriastr. 32, 8006 Zurich, Switzerland
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20
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Abstract
Understanding the molecular mechanisms behind the capacity of cancer cells to adapt to the tumor microenvironment and to anticancer therapies is a major challenge. In this context, cancer is believed to be an evolutionary process where random mutations and the selection process shape the mutational pattern and phenotype of cancer cells. This article challenges the notion of randomness of some cancer-associated mutations by describing molecular mechanisms involving stress-mediated biogenesis of mRNA-derived small RNAs able to target and increase the local mutation rate of the genomic loci they originate from. It is proposed that the probability of some mutations at specific loci could be increased in a stress-specific and RNA-depending manner. This would increase the probability of generating mutations that could alleviate stress situations, such as those triggered by anticancer drugs. Such a mechanism is made possible because tumor- and anticancer drug-associated stress situations trigger both cellular reprogramming and inflammation, which leads cancer cells to express molecular tools allowing them to “attack” and mutate their own genome in an RNA-directed manner.
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Affiliation(s)
- Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
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21
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Gerdes P, Richardson SR, Mager DL, Faulkner GJ. Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. Genome Biol 2016; 17:100. [PMID: 27161170 PMCID: PMC4862087 DOI: 10.1186/s13059-016-0965-5] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomologous recombination, and other potentially deleterious processes can cause sporadic disease by disrupting genome integrity or inducing abrupt gene expression changes. Here, we discuss recent evidence suggesting that TEs may contribute regulatory innovation to mammalian embryonic and pluripotent states as a means to ward off complete repression by their host genome.
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Affiliation(s)
- Patricia Gerdes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Sandra R Richardson
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Dixie L Mager
- Department of Medical Genetics, Terry Fox Laboratory, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 1L3, Canada.
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia. .,School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
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22
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Abstract
Over 40% of mammalian genomes comprise the products of reverse transcription. Among such retrotransposed sequences are those characterized by the presence of long terminal repeats (LTRs), including the endogenous retroviruses (ERVs), which are inherited genetic elements closely resembling the proviruses formed following exogenous retrovirus infection. Sequences derived from ERVs make up at least 8 to 10% of the human and mouse genomes and range from ancient sequences that predate mammalian divergence to elements that are currently still active. In this chapter we describe the discovery, classification and origins of ERVs in mammals and consider cellular mechanisms that have evolved to control their expression. We also discuss the negative effects of ERVs as agents of genetic disease and cancer and review examples of ERV protein domestication to serve host functions, as in placental development. Finally, we address growing evidence that the gene regulatory potential of ERV LTRs has been exploited multiple times during evolution to regulate genes and gene networks. Thus, although recently endogenized retroviral elements are often pathogenic, those that survive the forces of negative selection become neutral components of the host genome or can be harnessed to serve beneficial roles.
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Lin S, Zhang L, Luo W, Zhang X. Characteristics of Antisense Transcript Promoters and the Regulation of Their Activity. Int J Mol Sci 2015; 17:E9. [PMID: 26703594 PMCID: PMC4730256 DOI: 10.3390/ijms17010009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/23/2015] [Accepted: 12/16/2015] [Indexed: 02/07/2023] Open
Abstract
Recently, an increasing number of studies on natural antisense transcripts have been reported, especially regarding their classification, temporal and spatial expression patterns, regulatory functions and mechanisms. It is well established that natural antisense transcripts are produced from the strand opposite to the strand encoding a protein. Despite the pivotal roles of natural antisense transcripts in regulating the expression of target genes, the transcriptional mechanisms initiated by antisense promoters (ASPs) remain unknown. To date, nearly all of the studies conducted on this topic have focused on the ASP of a single gene of interest, whereas no study has systematically analyzed the locations of ASPs in the genome, ASP activity, or factors influencing this activity. This review focuses on elaborating on and summarizing the characteristics of ASPs to extend our knowledge about the mechanisms of antisense transcript initiation.
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Affiliation(s)
- Shudai Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Li Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
- Agricultural College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
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Carrieri C, Forrest ARR, Santoro C, Persichetti F, Carninci P, Zucchelli S, Gustincich S. Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and in neurochemical models of Parkinson's disease. Front Cell Neurosci 2015; 9:114. [PMID: 25883552 PMCID: PMC4381646 DOI: 10.3389/fncel.2015.00114] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/12/2015] [Indexed: 01/04/2023] Open
Abstract
Antisense (AS) transcripts are RNA molecules that are transcribed from the opposite strand to sense (S) genes forming S/AS pairs. The most prominent configuration is when a lncRNA is antisense to a protein coding gene. Increasing evidences prove that antisense transcription may control sense gene expression acting at distinct regulatory levels. However, its contribution to brain function and neurodegenerative diseases remains unclear. We have recently identified AS Uchl1 as an antisense to the mouse Ubiquitin carboxy-terminal hydrolase L1 (Uchl1) gene (AS Uchl1), the synthenic locus of UCHL1/PARK5. This is mutated in rare cases of early-onset familial Parkinson's Disease (PD) and loss of UCHL1 activity has been reported in many neurodegenerative diseases. Importantly, manipulation of UchL1 expression has been proposed as tool for therapeutic intervention. AS Uchl1 induces UchL1 expression by increasing its translation. It is the representative member of SINEUPs (SINEB2 sequence to UP-regulate translation), a new functional class of natural antisense lncRNAs that activate translation of their sense genes. Here we take advantage of FANTOM5 dataset to identify the transcription start sites associated to S/AS pair at Uchl1 locus. We show that AS Uchl1 expression is under the regulation of Nurr1, a major transcription factor involved in dopaminergic cells' differentiation and maintenance. Furthermore, AS Uch1 RNA levels are strongly down-regulated in neurochemical models of PD in vitro and in vivo. This work positions AS Uchl1 RNA as a component of Nurr1-dependent gene network and target of cellular stress extending our understanding on the role of antisense transcription in the brain.
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Affiliation(s)
- Claudia Carrieri
- Area of Neuroscience, International School for Advanced Studies (SISSA) Trieste, Italy
| | - Alistair R R Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan
| | - Claudio Santoro
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Francesca Persichetti
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan
| | - Silvia Zucchelli
- Area of Neuroscience, International School for Advanced Studies (SISSA) Trieste, Italy ; Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Stefano Gustincich
- Area of Neuroscience, International School for Advanced Studies (SISSA) Trieste, Italy
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25
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Yang X, Xie X, Xiao YF, Xie R, Hu CJ, Tang B, Li BS, Yang SM. The emergence of long non-coding RNAs in the tumorigenesis of hepatocellular carcinoma. Cancer Lett 2015; 360:119-24. [PMID: 25721084 DOI: 10.1016/j.canlet.2015.02.035] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/16/2015] [Accepted: 02/16/2015] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is the third cause of cancer-related death worldwide. However, the treatments for HCC are limited, and most of them are only available to the early stage. In the later stages, traditional chemotherapy has only marginal effects and may include toxicity. Thus, the identification of new predictive markers is urgently needed. New targets for non-conventional treatments will help to accelerate research on the molecular pathogenesis of HCC. A new class of transcripts, long non-coding RNAs (lncRNAs), has recently been found to be pervasively transcribed in the human genome. Aberrant expression of several lncRNAs was found to be involved in the tumorigenesis of HCC. In this review, we describe the possible molecular mechanisms that underlie lncRNA expression changes in HCC, as well as potential future applications of lncRNA research in the diagnosis and treatment of HCC.
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Affiliation(s)
- Xin Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Xia Xie
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Yu-Feng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Rei Xie
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Chang-Jiang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Bo-Sheng Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China.
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26
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Abstract
Rapid development in genome-wide transcriptional analyses has led to the discovery of a large number of non-coding transcripts, also called long non-coding RNA (lncRNA). LncRNAs harbor biological activities including regulation of protein-coding gene expression at epigenetic, transcriptional and post-transcriptional levels. They also take a part in various physiological and pathological processes, participating in cell development, immunity, disease processes and oncogenesis. Here I discuss and summarize, current knowledge about lncRNA origin, function and involvement in human disease.
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Affiliation(s)
- Kyriacos Felekkis
- Department of Life and Health Sciences and University of Nicosia Medical School, University of Nicosia, Nicosia, Cyprus
| | - Konstantinos Voskarides
- Department of Biological Sciences, Molecular Medicine Research Center, University of Cyprus, Nicosia, Cyprus
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27
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Sciamanna I, Gualtieri A, Cossetti C, Osimo EF, Ferracin M, Macchia G, Aricò E, Prosseda G, Vitullo P, Misteli T, Spadafora C. A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines. Oncotarget 2014; 4:2271-87. [PMID: 24345856 PMCID: PMC3926826 DOI: 10.18632/oncotarget.1403] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming RNA:DNA hybrids. We propose that this impairs the formation of double-stranded RNAs and the ensuing production of small regulatory RNAs, with a direct impact on gene expression. RT inhibition restores the ‘normal’ small RNA profile and the regulatory networks that depend on them. Thus, the retrotransposon-encoded RT drives a previously unrecognized mechanism crucial to the transformed state in tumor cells.
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Affiliation(s)
- Ilaria Sciamanna
- Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
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28
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Abstract
The ability to distinguish self from non-self nucleic acids enables eukaryotes to suppress mobile elements and maintain genome integrity. In organisms from protist to human, this function is performed by RNA silencing pathways. There have been major advances in our understanding of the RNA silencing machinery, but the mechanisms by which these pathways distinguish self from non-self remain unclear. Recent studies in the yeast C. neoformans indicate that transposon-derived transcripts encode suboptimal introns and tend to stall in spliceosomes, which promotes the biogenesis of siRNA that targets these transcripts. These findings identify gene expression signal strength as a metric by which a foreign element can be distinguished from a host gene, and reveal a new function for introns and the spliceosome in genome defense. Anticipating that these principles may apply to RNA silencing in other systems, we discuss strong hints in the literature suggesting that the spliceosome may guide small RNA biogenesis in the siRNA and piRNA pathways of plants and animals.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
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29
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Khorkova O, Myers AJ, Hsiao J, Wahlestedt C. Natural antisense transcripts. Hum Mol Genet 2014; 23:R54-63. [PMID: 24838284 DOI: 10.1093/hmg/ddu207] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recent years have seen the increasing understanding of the crucial role of RNA in the functioning of the eukaryotic genome. These discoveries, fueled by the achievements of the FANTOM, and later GENCODE and ENCODE consortia, led to the recognition of the important regulatory roles of natural antisense transcripts (NATs) arising from what was previously thought to be 'junk DNA'. Roughly defined as non-coding regulatory RNA transcribed from the opposite strand of a coding gene locus, NATs are proving to be a heterogeneous group with high potential for therapeutic application. Here, we attempt to summarize the rapidly growing knowledge about this important non-coding RNA subclass.
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Affiliation(s)
- Olga Khorkova
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | | | - Jane Hsiao
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - Claes Wahlestedt
- Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL 33136, USA
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30
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Jjingo D, Conley AB, Wang J, Mariño-Ramírez L, Lunyak VV, Jordan IK. Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. Mob DNA 2014; 5:14. [PMID: 25018785 PMCID: PMC4090950 DOI: 10.1186/1759-8753-5-14] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 04/10/2014] [Indexed: 11/26/2022] Open
Abstract
Background Mammalian-wide interspersed repeats (MIRs) are the most ancient family of transposable elements (TEs) in the human genome. The deep conservation of MIRs initially suggested the possibility that they had been exapted to play functional roles for their host genomes. MIRs also happen to be the only TEs whose presence in-and-around human genes is positively correlated to tissue-specific gene expression. Similar associations of enhancer prevalence within genes and tissue-specific expression, along with MIRs’ previous implication as providing regulatory sequences, suggested a possible link between MIRs and enhancers. Results To test the possibility that MIRs contribute functional enhancers to the human genome, we evaluated the relationship between MIRs and human tissue-specific enhancers in terms of genomic location, chromatin environment, regulatory function, and mechanistic attributes. This analysis revealed MIRs to be highly concentrated in enhancers of the K562 and HeLa human cell-types. Significantly more enhancers were found to be linked to MIRs than would be expected by chance, and putative MIR-derived enhancers are characterized by a chromatin environment highly similar to that of canonical enhancers. MIR-derived enhancers show strong associations with gene expression levels, tissue-specific gene expression and tissue-specific cellular functions, including a number of biological processes related to erythropoiesis. MIR-derived enhancers were found to be a rich source of transcription factor binding sites, underscoring one possible mechanistic route for the element sequences co-option as enhancers. There is also tentative evidence to suggest that MIR-enhancer function is related to the transcriptional activity of non-coding RNAs. Conclusions Taken together, these data reveal enhancers to be an important cis-regulatory platform from which MIRs can exercise a regulatory function in the human genome and help to resolve a long-standing conundrum as to the reason for MIRs’ deep evolutionary conservation.
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Affiliation(s)
- Daudi Jjingo
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Andrew B Conley
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jianrong Wang
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Leonardo Mariño-Ramírez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA ; PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia
| | - Victoria V Lunyak
- PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia ; Buck Institute for Research on Aging, Novato, CA, USA
| | - I King Jordan
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA ; PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia
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31
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Abstract
Alus are transposable elements belonging to the short interspersed element family. They occupy over 10% of human genome and have been spreading through genomes over the past 65 million years. In the past, they were considered junk DNA with little function that took up genome volumes. Today, Alus and other transposable elements emerge to be key players in cellular function, including genomic activities, gene expression regulations, and evolution. Here we summarize the current understanding of Alu function in genome and gene expression regulation in human cell nuclei.
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Affiliation(s)
- Chen Wang
- Department of Cell and Molecular Biology; Northwestern University; Feinberg School of Medicine; Chicago, IL USA
| | - Sui Huang
- Department of Cell and Molecular Biology; Northwestern University; Feinberg School of Medicine; Chicago, IL USA
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32
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Li J, Kannan M, Trivett AL, Liao H, Wu X, Akagi K, Symer DE. An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition. Nucleic Acids Res 2014; 42:4546-62. [PMID: 24493738 PMCID: PMC3985663 DOI: 10.1093/nar/gku091] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Between 6 and 30% of human and mouse transcripts are initiated from transposable elements. However, the promoters driving such transcriptional activity are mostly unknown. We experimentally characterized an antisense (AS) promoter in mouse L1 retrotransposons for the first time, oriented antiparallel to the coding strand of L1 open reading frame-1. We found that AS transcription is mediated by RNA polymerase II. Rapid amplification of cDNA ends cloning mapped transcription start sites adjacent to the AS promoter. We identified >100 novel fusion transcripts, of which many were conserved across divergent mouse lineages, suggesting conservation of potential functions. To evaluate whether AS L1 transcription could regulate L1 retrotransposition, we replaced portions of native open reading frame-1 in donor elements by synonymously recoded sequences. The resulting L1 elements lacked AS promoter activity and retrotransposed more frequently than endogenous L1s. Overexpression of AS L1 transcripts also reduced L1 retrotransposition. This suppression of retrotransposition was largely independent of Dicer. Our experiments shed new light on how AS fusion transcripts are initiated from endogenous L1 elements across the mouse genome. Such AS transcription can contribute substantially both to natural transcriptional variation and to endogenous regulation of L1 retrotransposition.
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Affiliation(s)
- Jingfeng Li
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA, Laboratory of Molecular Technology, Advanced Technology Program, SAIC-Frederick, Inc., Frederick, MD 21702, USA, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA, Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA, Internal Medicine, The Ohio State University, Columbus, OH 43210, USA and Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
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33
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Wood JG, Helfand SL. Chromatin structure and transposable elements in organismal aging. Front Genet 2013; 4:274. [PMID: 24363663 PMCID: PMC3849598 DOI: 10.3389/fgene.2013.00274] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 11/18/2013] [Indexed: 01/23/2023] Open
Abstract
Epigenetic regulatory mechanisms are increasingly appreciated as central to a diverse array of biological processes, including aging. An association between heterochromatic silencing and longevity has long been recognized in yeast, and in more recent years evidence has accumulated of age-related chromatin changes in Caenorhabditis elegans, Drosophila, and mouse model systems, as well as in the tissue culture-based replicative senescence model of cell aging. In addition, a number of studies have linked expression of transposable elements (TEs), as well as changes in the RNAi pathways that cells use to combat TEs, to the aging process. This review summarizes the recent evidence linking chromatin structure and function to aging, with a particular focus on the relationship of heterochromatin structure to organismal aging.
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Affiliation(s)
- Jason G Wood
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University Providence, RI, USA
| | - Stephen L Helfand
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University Providence, RI, USA
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34
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Tufarelli C, Cruickshanks HA, Meehan RR. LINE-1 activation and epigenetic silencing of suppressor genes in cancer: Causally related events? Mob Genet Elements 2013; 3:e26832. [PMID: 24251074 DOI: 10.4161/mge.26832] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/11/2013] [Accepted: 10/15/2013] [Indexed: 01/11/2023] Open
Abstract
The ability of active retrotransposon elements to move within the host genome and alter gene expression with subsequent phenotypic variation led to their initial discovery. In recent years it has become apparent that these elements can also modulate host gene expression independently of their transposition activity. Many retrotransposons maintain endogenous promoter motifs that can potentially drive expression of adjacent DNA modules. Similarly to transposition dependent dysregulation, these proto-promoters can progress disease states when active. Indeed aberrant activation of retrotransposon derived promoters in cancer can lead to transcription of oncogenic isoforms of cellular genes. Here we propose that activation of promoters of transposable elements in cancer can also drive transcription of long non-coding RNAs whose expression leads to silencing of linked tumor suppressor genes. Such transcription driven by aberrantly active transposable elements in cancer can lead to a characteristic reprogramming of epigenetic profiles, thus extending the potential molecular mechanisms whereby retrotransposons can directly contribute to cancer development and subsequent progression.
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Affiliation(s)
- Cristina Tufarelli
- School of Medicine; University of Nottingham; Royal Derby Hospital Centre; Derby, England UK ; Centre for Genetics and Genomics; University of Nottingham; Nottingham, England UK
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35
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Hohn O, Hanke K, Bannert N. HERV-K(HML-2), the Best Preserved Family of HERVs: Endogenization, Expression, and Implications in Health and Disease. Front Oncol 2013; 3:246. [PMID: 24066280 PMCID: PMC3778440 DOI: 10.3389/fonc.2013.00246] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/05/2013] [Indexed: 12/14/2022] Open
Abstract
Retroviruses that have the ability to infect germ line cells can become an integral and inherited part of the host genome. About 8% of the human chromosomal DNA consists of sequences derived from infections by retroviruses that presumably circulated 2-40 millions of years ago, and some elements are actually much older. Post-insertional recombinations, deletions, and mutations have rendered all known human endogenous retroviruses (HERVs) non-infectious. However some, particularly the most recently acquired proviruses of the HERV-K(HML-2) family, can expresses viral proteins and produce viral particles. In this review we will first discuss the major aspects of the endogenization process and peculiarities of the different HERV-K families. We will then focus on the genes and proteins encoded by HERV-K(HML-2) as well as inactivation of these proviruses by postinsertional mutations and their inhibition by antiretroviral factors. After describing the evolutionary interplay between host and endogenous retrovirus we will delve deeper into the currently limited understanding of HERV-K and its possible association with disease, particularly tumorigenesis.
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Affiliation(s)
- Oliver Hohn
- Division for HIV and Other Retroviruses, Robert Koch Institute , Berlin , Germany
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36
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Cruickshanks HA, Vafadar-Isfahani N, Dunican DS, Lee A, Sproul D, Lund JN, Meehan RR, Tufarelli C. Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer. Nucleic Acids Res 2013; 41:6857-69. [PMID: 23703216 PMCID: PMC3737543 DOI: 10.1093/nar/gkt438] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/29/2013] [Accepted: 04/29/2013] [Indexed: 12/18/2022] Open
Abstract
LINE-1 retrotransposons are abundant repetitive elements of viral origin, which in normal cells are kept quiescent through epigenetic mechanisms. Activation of LINE-1 occurs frequently in cancer and can enable LINE-1 mobilization but also has retrotransposition-independent consequences. We previously reported that in cancer, aberrantly active LINE-1 promoters can drive transcription of flanking unique sequences giving rise to LINE-1 chimeric transcripts (LCTs). Here, we show that one such LCT, LCT13, is a large transcript (>300 kb) running antisense to the metastasis-suppressor gene TFPI-2. We have modelled antisense RNA expression at TFPI-2 in transgenic mouse embryonic stem (ES) cells and demonstrate that antisense RNA induces silencing and deposition of repressive histone modifications implying a causal link. Consistent with this, LCT13 expression in breast and colon cancer cell lines is associated with silencing and repressive chromatin at TFPI-2. Furthermore, we detected LCT13 transcripts in 56% of colorectal tumours exhibiting reduced TFPI-2 expression. Our findings implicate activation of LINE-1 elements in subsequent epigenetic remodelling of surrounding genes, thus hinting a novel retrotransposition-independent role for LINE-1 elements in malignancy.
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Affiliation(s)
- Hazel A. Cruickshanks
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Natasha Vafadar-Isfahani
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Donncha S. Dunican
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Andy Lee
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Duncan Sproul
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Jonathan N. Lund
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Richard R. Meehan
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Cristina Tufarelli
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
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Britto-Kido SDA, Ferreira Neto JRC, Pandolfi V, Marcelino-Guimarães FC, Nepomuceno AL, Vilela Abdelnoor R, Benko-Iseppon AM, Kido EA. Natural antisense transcripts in plants: a review and identification in soybean infected with Phakopsora pachyrhizi SuperSAGE library. ScientificWorldJournal 2013; 2013:219798. [PMID: 23878522 PMCID: PMC3710604 DOI: 10.1155/2013/219798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/05/2013] [Indexed: 11/23/2022] Open
Abstract
Natural antisense ranscripts (NAT) are RNA molecules complementary to other endogenous RNAs. They are capable of regulating the expression of target genes at different levels (transcription, mRNA stability, translation, etc.). Such a property makes them ideal for interventions in organisms' metabolism. The present study reviewed plant NAT aspects, including features, availability and genesis, conservation and distribution, coding capacity, NAT pair expression, and functions. Besides, an in silico identification of NATs pairs was presented, using deepSuperSAGE libraries of soybean infected or not with Phakopsora pachyrhizi. Results showed that around 1/3 of the 77,903 predicted trans-NATs (by PlantsNATsDB database) detected had unitags mapped in both sequences of each pair. The same 1/3 of the 436 foreseen cis-NATs showed unitags anchored in both sequences of the related pairs. For those unitags mapped in NAT pairs, a modulation expression was assigned as upregulated, downregulated, or constitutive, based on the statistical analysis (P < 0.05). As a result, the infected treatment promoted the expression of 2,313 trans-NATs pairs comprising unitags exclusively from that library (1,326 pairs had unitags only found in the mock library). To understand the regulation of these NAT pairs could be a key aspect in the ASR plant response.
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Affiliation(s)
| | | | - Valesca Pandolfi
- Federal University of Pernambuco (UFPE), Department of Genetics, Recife, PE, Brazil
| | | | - Alexandre Lima Nepomuceno
- Embrapa Soybean, Rod. Carlos João Strass, Distrito de Warta, Caixa Postal 231, 86.001-970 Londrina, PR, Brazil
| | - Ricardo Vilela Abdelnoor
- Embrapa Soybean, Rod. Carlos João Strass, Distrito de Warta, Caixa Postal 231, 86.001-970 Londrina, PR, Brazil
| | | | - Ederson Akio Kido
- Federal University of Pernambuco (UFPE), Department of Genetics, Recife, PE, Brazil
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38
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Whiteside EJ, Seim I, Pauli JP, O'Keeffe AJ, Thomas PB, Carter SL, Walpole CM, Fung JNT, Josh P, Herington AC, Chopin LK. Identification of a long non-coding RNA gene, growth hormone secretagogue receptor opposite strand, which stimulates cell migration in non-small cell lung cancer cell lines. Int J Oncol 2013; 43:566-74. [PMID: 23722988 DOI: 10.3892/ijo.2013.1969] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 03/07/2013] [Indexed: 11/06/2022] Open
Abstract
The molecular mechanisms involved in non‑small cell lung cancer tumourigenesis are largely unknown; however, recent studies have suggested that long non-coding RNAs (lncRNAs) are likely to play a role. In this study, we used public databases to identify an mRNA-like, candidate long non-coding RNA, GHSROS (GHSR opposite strand), transcribed from the antisense strand of the ghrelin receptor gene, growth hormone secretagogue receptor (GHSR). Quantitative real-time RT-PCR revealed higher expression of GHSROS in lung cancer tissue compared to adjacent, non-tumour lung tissue. In common with many long non-coding RNAs, GHSROS is 5' capped and 3' polyadenylated (mRNA-like), lacks an extensive open reading frame and harbours a transposable element. Engineered overexpression of GHSROS stimulated cell migration in the A549 and NCI-H1299 non-small cell lung cancer cell lines, but suppressed cell migration in the Beas-2B normal lung-derived bronchoepithelial cell line. This suggests that GHSROS function may be dependent on the oncogenic context. The identification of GHSROS, which is expressed in lung cancer and stimulates cell migration in lung cancer cell lines, contributes to the growing number of non-coding RNAs that play a role in the regulation of tumourigenesis and metastatic cancer progression.
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Affiliation(s)
- Eliza J Whiteside
- Ghrelin Research Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
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39
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Hellen EH, Brookfield JF. Alu elements in primates are preferentially lost from areas of high GC content. PeerJ 2013; 1:e78. [PMID: 23717800 PMCID: PMC3661076 DOI: 10.7717/peerj.78] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/02/2013] [Indexed: 11/20/2022] Open
Abstract
The currently-accepted dogma when analysing human Alu transposable elements is that ‘young’ Alu elements are found in low GC regions and ‘old’ Alus in high GC regions. The correlation between high GC regions and high gene frequency regions make this observation particularly difficult to explain. Although a number of studies have tackled the problem, no analysis has definitively explained the reason for this trend. These observations have been made by relying on the subfamily as a proxy for age of an element. In this study, we suggest that this is a misleading assumption and instead analyse the relationship between the taxonomic distribution of an individual element and its surrounding GC environment. An analysis of 103906 Alu elements across 6 human chromosomes was carried out, using the presence of orthologous Alu elements in other primate species as a proxy for age. We show that the previously-reported effect of GC content correlating with subfamily age is not reflected by the ages of the individual elements. Instead, elements are preferentially lost from areas of high GC content over time. The correlation between GC content and subfamily may be due to a change in insertion bias in the young subfamilies. The link between Alu subfamily age and GC region was made due to an over-simplification of the data and is incorrect. We suggest that use of subfamilies as a proxy for age is inappropriate and that the analysis of ortholog presence in other primate species provides a deeper insight into the data.
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Affiliation(s)
- Elizabeth Hb Hellen
- Centre for Genetics and Genomics, School of Biology, University of Nottingham , University Park, Nottingham , UK
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40
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Dumesic PA, Natarajan P, Chen C, Drinnenberg IA, Schiller BJ, Thompson J, Moresco JJ, Yates JR, Bartel DP, Madhani HD. Stalled spliceosomes are a signal for RNAi-mediated genome defense. Cell 2013; 152:957-68. [PMID: 23415457 DOI: 10.1016/j.cell.2013.01.046] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 11/13/2012] [Accepted: 01/17/2013] [Indexed: 11/29/2022]
Abstract
Using the yeast Cryptococcus neoformans, we describe a mechanism by which transposons are initially targeted for RNAi-mediated genome defense. We show that intron-containing mRNA precursors template siRNA synthesis. We identify a Spliceosome-Coupled And Nuclear RNAi (SCANR) complex required for siRNA synthesis and demonstrate that it physically associates with the spliceosome. We find that RNAi target transcripts are distinguished by suboptimal introns and abnormally high occupancy on spliceosomes. Functional investigations demonstrate that the stalling of mRNA precursors on spliceosomes is required for siRNA accumulation. Lariat debranching enzyme is also necessary for siRNA production, suggesting a requirement for processing of stalled splicing intermediates. We propose that recognition of mRNA precursors by the SCANR complex is in kinetic competition with splicing, thereby promoting siRNA production from transposon transcripts stalled on spliceosomes. Disparity in the strength of expression signals encoded by transposons versus host genes offers an avenue for the evolution of genome defense.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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41
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Mandal AK, Pandey R, Jha V, Mukerji M. Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. Nucleic Acids Res 2013; 41:2121-37. [PMID: 23303787 PMCID: PMC3575813 DOI: 10.1093/nar/gks1457] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 12/13/2012] [Accepted: 12/13/2012] [Indexed: 12/18/2022] Open
Abstract
Non-coding RNAs from transposable elements of human genome are gaining prominence in modulating transcriptome dynamics. Alu elements, as exonized, edited and antisense components within same transcripts could create novel regulatory switches in response to different transcriptional cues. We provide the first evidence for co-occurrences of these events at transcriptome-wide scale through integrative analysis of data sets across diverse experimental platforms and tissues. This involved the following: (i) positional anchoring of Alu exonization events in the UTRs and CDS of 4663 transcript isoforms from RefSeq mRNAs and (ii) mapping on to them A→I editing events inferred from ∼7 million ESTs from dbEST and antisense transcripts identified from virtual serial analysis of gene expression tags represented in Cancer Genome Anatomy Project next-generation sequencing data sets across 20 tissues. We observed significant enrichment of these events in the 3'UTR as well as positional preference within the embedded Alus. More than 300 genes had co-occurrence of all these events at the exon level and were significantly enriched in apoptosis and lysosomal processes. Further, we demonstrate functional evidence of such dynamic interactions between Alu-mediated events in a time series data from Integrated Personal Omics Profiling during recovery from a viral infection. Such 'single transcript-multiple fate' opportunity facilitated by Alu elements may modulate transcriptional response, especially during stress.
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Affiliation(s)
- Amit K. Mandal
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Rajesh Pandey
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Vineet Jha
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Mitali Mukerji
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
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42
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HERV-E-mediated modulation of PLA2G4A transcription in urothelial carcinoma. PLoS One 2012; 7:e49341. [PMID: 23145155 PMCID: PMC3492278 DOI: 10.1371/journal.pone.0049341] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/09/2012] [Indexed: 12/30/2022] Open
Abstract
Human endogenous retroviruses (HERV) and related elements account for more than 8% of the human genome and significantly contribute to the human transcriptome by long terminal repeat (LTR) promoter activity. In this context, HERVs are thought to intervene in the expression of adjacent genes by providing regulatory sequences (cis-effect) or via noncoding RNA including natural antisense transcripts. To address the potential impact of HERV activity in urothelial carcinoma, we comparatively analyzed the HERV transcription profiles in paired samples of non-malignant urothelium and urothelial carcinoma derived from 13 patients with bladder cancer by means of a retrovirus-specific microarray (RetroArray). We established a characteristic HERV signature consisting of six ubiquitously active HERV subgroups (E4-1, HERV-Rb, ERV9, HERV-K-T47D, NMWV3, HERV-KC4). The transcription pattern is largely identical in human urothelial carcinoma, non-malignant urothelial tissue, four tumor-derived cell lines and in a non-malignant urothelial cell line (UROtsa). Quantitative reverse transcriptase PCR (qRT-PCR) of HERV-E4-1, HERV-K(HML-6) and HERV-T(S71-TK1) revealed a bias to lower HERV activity in carcinoma samples compared to non-malignant tissue. Determination of active HERV-E4-1 loci by cloning and sequencing revealed six HERV-E4-1 proviral loci that are differentially regulated in urothelial carcinoma cells and normal tissue. Two full-length HERV-E4-1 proviruses, HERV-Ec1 and HERV-Ec6, are located in antisense orientation in introns of the genes PLA2G4A and RNGTT, respectively. PLA2G4A encodes a cytosolic phospholipase A2 (cPLA2) that is dysregulated in many human tumors. PLA2G4A and HERV-Ec1 displayed reciprocal transcript levels in 7 of 11 urothelial carcinoma patients. Moreover, reciprocal shifts were observed after treatment of UROtsa cells with HERV-Ec1 and PLA2G4A-directed siRNAs or 5-aza-2′-deoxycytidine (aza-dC) pointing to an antagonistic regulation of PLA2G4A and HERV-Ec1 transcription in human urothelial cells. We suggest that transcription of HERV-Ec1 contributes to fine tuning of cPLA2 expression, thereby facilitating tumorigenesis.
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43
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Vieira C, Fablet M, Lerat E, Boulesteix M, Rebollo R, Burlet N, Akkouche A, Hubert B, Mortada H, Biémont C. A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2012; 113:83-86. [PMID: 22659421 DOI: 10.1016/j.jenvrad.2012.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/23/2012] [Accepted: 04/04/2012] [Indexed: 06/01/2023]
Abstract
Genes are important in defining genetic variability, but they do not constitute the largest component of genomes, which in most organisms contain large amounts of various repeated sequences including transposable elements (TEs), which have been shown to account for most of the genome size. TEs contribute to genetic diversity by their mutational potential as a result of their ability to insert into genes or gene regulator regions, to promote chromosomal rearrangements, and to interfere with gene networks. Also, TEs may be activated by environmental stresses (such as temperature or radiation) that interfere with epigenetic regulation systems, and makes them powerful mutation agents in nature. To understand the relationship between genotype and phenotype, we need to analyze the portions of the genome corresponding to TEs in great detail, and to decipher their relationships with the genes. For this purpose, we carried out comparative analyses of various natural populations of the closely-related species Drosophila melanogaster and Drosophila simulans, which differ with regard to their TE amounts as well as their ecology and population size.
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Affiliation(s)
- Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France.
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44
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Micale L, Loviglio MN, Manzoni M, Fusco C, Augello B, Migliavacca E, Cotugno G, Monti E, Borsani G, Reymond A, Merla G. A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish. PLoS One 2012; 7:e46642. [PMID: 23118857 PMCID: PMC3485254 DOI: 10.1371/journal.pone.0046642] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 09/03/2012] [Indexed: 12/04/2022] Open
Abstract
Transposable elements, as major components of most eukaryotic organisms' genomes, define their structural organization and plasticity. They supply host genomes with functional elements, for example, binding sites of the pleiotropic master transcription factor p53 were identified in LINE1, Alu and LTR repeats in the human genome. Similarly, in this report we reveal the role of zebrafish (Danio rerio) EnSpmN6_DR non-autonomous DNA transposon in shaping the repertoire of the p53 target genes. The multiple copies of EnSpmN6_DR and their embedded p53 responsive elements drive in several instances p53-dependent transcriptional modulation of the adjacent gene, whose human orthologs were frequently previously annotated as p53 targets. These transposons define predominantly a set of target genes whose human orthologs contribute to neuronal morphogenesis, axonogenesis, synaptic transmission and the regulation of programmed cell death. Consistent with these biological functions the orthologs of the EnSpmN6_DR-colonized loci are enriched for genes expressed in the amygdala, the hippocampus and the brain cortex. Our data pinpoint a remarkable example of convergent evolution: the exaptation of lineage-specific transposons to shape p53-regulated neuronal morphogenesis-related pathways in both a hominid and a teleost fish.
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Affiliation(s)
- Lucia Micale
- Medical Genetics Unit, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Maria Nicla Loviglio
- Medical Genetics Unit, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Marta Manzoni
- Department of Biomedical Science and Biotechnology, University of Brescia, Brescia, Italy
| | - Carmela Fusco
- Medical Genetics Unit, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Bartolomeo Augello
- Medical Genetics Unit, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Eugenia Migliavacca
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Grazia Cotugno
- Medical Genetics Unit, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Eugenio Monti
- Department of Biomedical Science and Biotechnology, University of Brescia, Brescia, Italy
| | - Giuseppe Borsani
- Department of Biomedical Science and Biotechnology, University of Brescia, Brescia, Italy
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Merla
- Medical Genetics Unit, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
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45
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Casa V, Gabellini D. A repetitive elements perspective in Polycomb epigenetics. Front Genet 2012; 3:199. [PMID: 23060903 PMCID: PMC3465993 DOI: 10.3389/fgene.2012.00199] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 09/17/2012] [Indexed: 01/10/2023] Open
Abstract
Repetitive elements comprise over two-thirds of the human genome. For a long time, these elements have received little attention since they were considered non-functional. On the contrary, recent evidence indicates that they play central roles in genome integrity, gene expression, and disease. Indeed, repeats display meiotic instability associated with disease and are located within common fragile sites, which are hotspots of chromosome re-arrangements in tumors. Moreover, a variety of diseases have been associated with aberrant transcription of repetitive elements. Overall this indicates that appropriate regulation of repetitive elements' activity is fundamental. Polycomb group (PcG) proteins are epigenetic regulators that are essential for the normal development of multicellular organisms. Mammalian PcG proteins are involved in fundamental processes, such as cellular memory, cell proliferation, genomic imprinting, X-inactivation, and cancer development. PcG proteins can convey their activity through long-distance interactions also on different chromosomes. This indicates that the 3D organization of PcG proteins contributes significantly to their function. However, it is still unclear how these complex mechanisms are orchestrated and which role PcG proteins play in the multi-level organization of gene regulation. Intriguingly, the greatest proportion of Polycomb-mediated chromatin modifications is located in genomic repeats and it has been suggested that they could provide a binding platform for Polycomb proteins. Here, these lines of evidence are woven together to discuss how repetitive elements could contribute to chromatin organization in the 3D nuclear space.
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Affiliation(s)
- Valentina Casa
- Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Dulbecco Telethon Institute and San Raffaele Scientific Institute Milano, Italy ; Università Vita-Salute San Raffaele Milano, Italy
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46
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Rebollo R, Romanish MT, Mager DL. Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet 2012; 46:21-42. [PMID: 22905872 DOI: 10.1146/annurev-genet-110711-155621] [Citation(s) in RCA: 352] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The fact that transposable elements (TEs) can influence host gene expression was first recognized more than 50 years ago. However, since that time, TEs have been widely regarded as harmful genetic parasites-selfish elements that are rarely co-opted by the genome to serve a beneficial role. Here, we survey recent findings that relate to TE impact on host genes and remind the reader that TEs, in contrast to other noncoding parts of the genome, are uniquely suited to gene regulatory functions. We review recent studies that demonstrate the role of TEs in establishing and rewiring gene regulatory networks and discuss the overall ubiquity of exaptation. We suggest that although individuals within a population can be harmed by the deleterious effects of new TE insertions, the presence of TE sequences in a genome is of overall benefit to the population.
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Affiliation(s)
- Rita Rebollo
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.
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47
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Naidoo N, Pawitan Y, Soong R, Cooper DN, Ku CS. Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics 2012; 5:577-622. [PMID: 22155605 PMCID: PMC3525251 DOI: 10.1186/1479-7364-5-6-577] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade.
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Affiliation(s)
- Nasheen Naidoo
- Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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48
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Conley AB, Jordan IK. Epigenetic regulation of human cis-natural antisense transcripts. Nucleic Acids Res 2012; 40:1438-45. [PMID: 22371288 PMCID: PMC3287164 DOI: 10.1093/nar/gkr1010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mammalian genomes encode numerous cis-natural antisense transcripts (cis-NATs). The extent to which these cis-NATs are actively regulated and ultimately functionally relevant, as opposed to transcriptional noise, remains a matter of debate. To address this issue, we analyzed the chromatin environment and RNA Pol II binding properties of human cis-NAT promoters genome-wide. Cap analysis of gene expression data were used to identify thousands of cis-NAT promoters, and profiles of nine histone modifications and RNA Pol II binding for these promoters in ENCODE cell types were analyzed using chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Active cis-NAT promoters are enriched with activating histone modifications and occupied by RNA Pol II, whereas weak cis-NAT promoters are depleted for both activating modifications and RNA Pol II. The enrichment levels of activating histone modifications and RNA Pol II binding show peaks centered around cis-NAT transcriptional start sites, and the levels of activating histone modifications at cis-NAT promoters are positively correlated with cis-NAT expression levels. Cis-NAT promoters also show highly tissue-specific patterns of expression. These results suggest that human cis-NATs are actively transcribed by the RNA Pol II and that their expression is epigenetically regulated, prerequisites for a functional potential for many of these non-coding RNAs.
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Affiliation(s)
- Andrew B Conley
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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49
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Ross JP, Rand KN, Molloy PL. Hypomethylation of repeated DNA sequences in cancer. Epigenomics 2012; 2:245-69. [PMID: 22121873 DOI: 10.2217/epi.10.2] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
An important feature of cancer development and progression is the change in DNA methylation patterns, characterized by the hypermethylation of specific genes concurrently with an overall decrease in the level of 5-methylcytosine. Hypomethylation of the genome can affect both single-copy genes, repeat DNA sequences and transposable elements, and is highly variable among and within cancer types. Here, we review our current understanding of genome hypomethylation in cancer, with a particular focus on hypomethylation of the different classes and families of repeat sequences. The emerging data provide insights into the importance of methylation of different repeat families in the maintenance of chromosome structural integrity and the fidelity of normal transcriptional regulation. We also consider the events underlying cancer-associated hypomethylation and the potential for the clinical use of characteristic DNA methylation changes in diagnosis, prognosis or classification of tumors.
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Affiliation(s)
- Jason P Ross
- Commonwealth Scientific & Industrial Research Organisation, Food & Nutritional Science, Preventative Health National Research Flagship, North Ryde, NSW 1670, Australia
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Feschotte C, Gilbert C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 2012; 13:283-96. [PMID: 22421730 DOI: 10.1038/nrg3199] [Citation(s) in RCA: 498] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent studies have uncovered myriad viral sequences that are integrated or 'endogenized' in the genomes of various eukaryotes. Surprisingly, it appears that not just retroviruses but almost all types of viruses can become endogenous. We review how these genomic 'fossils' offer fresh insights into the origin, evolutionary dynamics and structural evolution of viruses, which are giving rise to the burgeoning field of palaeovirology. We also examine the multitude of ways through which endogenous viruses have influenced, for better or worse, the biology of their hosts. We argue that the conflict between hosts and viruses has led to the invention and diversification of molecular arsenals, which, in turn, promote the cellular co-option of endogenous viruses.
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Affiliation(s)
- Cédric Feschotte
- Department of Biology, University of Texas, Arlington, Texas 76016, USA.
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