DOCSLIB.ORG

Posttranscriptional Regulation of Human Endogenous Retroviruses by RNA-Binding Motif Protein 4, RBM4

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Posttranscriptional Regulation of Human Endogenous Retroviruses by RNA-Binding Motif Protein 4, RBM4 Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4 Amir K. Foroushania, Bryan Chima,1, Madeline Wonga,1, Andre Rastegara,1, Patrick T. Smitha, Saifeng Wanga, Kent Barbianb, Craig Martensb, Markus Hafnerc,2, and Stefan A. Muljoa,2 aLaboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; bResearch Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840; and cLaboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892 Edited by Akiko Iwasaki, Yale University, New Haven, CT, and approved August 17, 2020 (received for review April 2, 2020) The human genome encodes for over 1,500 RNA-binding proteins threat to genome and transcriptome integrity (19). Recently, (RBPs), which coordinate regulatory events on RNA transcripts. Most epigenetic silencing by TRIM28 and HDAC1 to suppress ERV studies of RBPs have concentrated on their action on host protein- expression at the transcriptional level was identified as a crucial encoding mRNAs, which constitute a minority of the transcriptome. mechanism to control HERVs (20–23). Interestingly, the RNA- A widely neglected subset of our transcriptome derives from inte- binding proteins (RBPs) such as TARDBP/TDP-43 and Spen grated retroviral elements, termed endogenous retroviruses (ERVs), were found to bind and modulate ERV transcripts in flies, mice, that comprise ∼8% of the human genome. Some ERVs have been and humans (24–27), suggesting that RBPs may play an under- shown to be transcribed under physiological and pathological con- appreciated role in their regulation. The human genome encodes ditions, suggesting that sophisticated regulatory mechanisms to co- around 1,500 RBPs that bind and regulate localization, stability, ordinate and prevent their ectopic expression exist. However, it is adenylation, and splicing patterns of coding and noncoding RNAs unknown how broadly RBPs and ERV transcripts directly interact to in a sequence- or structure-dependent manner (28). A recent study provide a posttranscriptional layer of regulation. Here, we imple- showed that many RBPs bind and repress evolutionarily young mented a computational pipeline to determine the correlation of ex- mobile repetitive elements, including intronic long interspersed pression between individual RBPs and ERVs from single-cell or bulk nuclear elements (LINEs) to prevent them from interfering with RNA-sequencing data. One of our top candidates for an RBP nega- cellular gene expression (29, 30). By analogy, RBPs seem like at- tively regulating ERV expression was RNA-binding motif protein 4 tractive candidates for broad regulation of HERV transcripts (31). SYSTEMS BIOLOGY (RBM4). We used photoactivatable ribonucleoside-enhanced cross- Until recently, systematic studies of expression patterns of linking and immunoprecipitation to demonstrate that RBM4 indeed HERVs have been hampered by the lack of adequate bioinformatic bound ERV transcripts at CGG consensus elements. Loss of RBM4 tools. In 2015, the Hammell group released TEToolkit (32), which resulted in an elevated transcript level of bound ERVs of the HERV- enables family-wise quantification of HERVs and other classes of K and -H families, as well as increased expression of HERV-K envelope transposable elements (TEs) from RNA-sequencing (RNA-seq) protein. We pinpointed RBM4 regulation of HERV-K to a CGG- data. In 2018, the Iwasaki and Vincent groups released ERVmap containing element that is conserved in the LTRs of HERV-K-10, -K- and hervQuant, respectively (33, 34), which enable high-resolution 11, and -K-20, and validated the functionality of this site using re- porter assays. In summary, we systematically identified RBPs that Significance may regulate ERV function and demonstrate a role for RBM4 in controlling ERV expression. The expression of endogenous retroviruses (ERVs) appears to have broad impact on human biology. Nevertheless, only a RNA-binding proteins | PAR-CLIP | RNA sequencing | posttranscriptional handful of transcriptional or posttranscriptional regulators of regulation | endogenous retroviruses ERV expression are known. We implemented a computational pipeline that allowed us to identify RNA-binding proteins uman endogenous retroviruses (HERVs) are the remnants of (RBPs) that modulate ERV expression levels. Experimental val- Hseveral ancient retroviral germline infections that have ac- idation of one of the prime candidates we identified, RNA- cumulated over the past 60 million y (1). Today, they account for binding motif protein 4 (RBM4), showed that it indeed bound ∼8% of our genome (2). Consequently, as a class, ERVs are RNAs made from ERVs and negatively regulated the levels of perpetual members of our virome, the compendium of viruses that those RNAs. We hereby identify a layer of ERV regulation by exist in or on an organism (3). As life-long residents of all human RBPs. We suspect that this work on RBM4 is only the beginning cells, these sequences of viral origin likely continue to have a in recognizing a broader set among the >1,500 human RBPs considerable impact on our biology, yet they are not fully under- that act on transcripts derived from endogenous and exogenous stood. Many of the integrated viral DNA sequences contain viruses. transcription-factor (TF) binding sites and have been exapted as genomic coordinators of a wide range of important processes, Author contributions: A.K.F., B.C., M.W., A.R., P.T.S., S.W., C.M., M.H., and S.A.M. de- including the expression of IFN-γ–responsive transcripts (4). At signed research; A.K.F., M.W., A.R., P.T.S., S.W., K.B., and C.M. performed research; A.K.F. and A.R. contributed new reagents/analytic tools; A.K.F., B.C., M.W., A.R., C.M., the transcriptomic level, HERVs seem largely silent in healthy M.H., and S.A.M. analyzed data; and A.K.F., B.C., M.W., A.R., M.H., and S.A.M. wrote adult cells and tissues. However, they are highly active in embry- the paper. onic cells at the earliest stages of human development, and in The authors declare no competing interest. induced pluripotent stem cells (iPSCs), where they seem indis- This article is a PNAS Direct Submission. pensable but need to be tightly regulated for successful differen- Published under the PNAS license. – tiation (5 12). HERV expression is also elevated in a wide range 1B.C., M.W., and A.R. contributed equally to this work. of diseases, among others systemic lupus erythematosus (SLE) 2To whom correspondence may be addressed. Email: [email protected] or stefan. (13, 14), various cancers (15–17), and multiple sclerosis (18). [email protected]. Despite their strong association with fundamental biological This article contains supporting information online at https://www.pnas.org/lookup/suppl/ processes, little is known about if and how these integral parts of doi:10.1073/pnas.2005237117/-/DCSupplemental. our genome and “virome” are regulated to avoid a potential www.pnas.org/cgi/doi/10.1073/pnas.2005237117 PNAS Latest Articles | 1of11 Downloaded by guest on September 25, 2021 mapping of sequencing reads to a curated set of ∼3,200 HERV Analysis of our previous (39) and two new rounds of RNA-seq proviral loci. These pioneering resources enabled us to develop a data (SI Appendix,TableS1) comparing RBM4-deficient cells hybrid computational pipeline to test the hypothesis that RBPs act versus WT controls supported our hypothesis that RBM4 silences as regulators of HERV expression. Running our pipeline on two HERVs. In the absence of RBM4, a range of HERV transcripts different single-cell and one bulk cell population RNA-seq datasets were differentially expressed in the HAP1 model system (Fig. 2A from the public domain yielded lists of RBPs with correlated or and Dataset S3). Although, expression of some HERVs were anticorrelated expression to that of HERVs, which represent pos- decreased in RBM4-deficient cells, they were either of lower sible positive regulators or suppressors of HERV function. Among statistical confidence or of much lower baseline abundance. As the top-candidates for HERV-repressing RBPs, we identified one example, in the absence of RBM4, reads mapping to ERV- RNA-binding protein motif 4 (RBM4). Follow-up experiments in map ID# 4452, an HERV-K13 (HML4) family member, was the human HAP1 cell line demonstrated that RBM4 directly bound dramatically decreased in abundance. (Fig. 2 B). However, its proviral transcripts of members of the HERV-K and HERV-H baseline expression is around 10-fold lower level than that of the families and that loss of RBM4 resulted in an increased abundance HERV-K (HML2) members (K-10/1.q22, 6272/22.q11.23, K-9/ of these HERV transcripts, as well as increased expression of its 6.q14.1, K-21/1.q23.3, K-11/5.q33.3, 1045/3.q12.3, K-7/8.p23.1) envelope (env) protein. In summary, we nominate RBPs that might that were all differentially up-regulated (Dataset S3). Interest- act as posttranscriptional suppressors of ERVs and identify a role ingly, there are also HERVs that are expressed but not signifi- for RBM4 in regulating HERV-K and -H proviral transcripts. cantly affected by RBM4 including, but not limited to, K-14 (Fig. 2C). K-14 is interesting for a reason to be discussed later. Results Overall, more HERV transcripts were elevated in the absence of Besides TARDBP and Spen (24–27), no RBP has been dem- RBM4 and thus we focused on them. By cross-referencing the onstrated to act directly on HERV transcripts. We hypothesized significantly changed HERVs to the TEToolkit’s (32) repeat- that RBPs represent prime candidates to regulate HERVs masker annotations, we realized that most HERVs negatively reg- posttranscriptionally. To identify which ones might, we imple- ulated by RBM4 belonged to the HERV-H and HERV-K (HML2) mented a computational pipeline to systematically analyze the families (42).
Load more

Recommended publications
  • The Expression of Human Endogenous Retroviruses Is Modulated by the Tat Protein of HIV‐1
    The Expression of Human Endogenous Retroviruses is modulated by the Tat protein of HIV‐1 by Marta Jeannette Gonzalez‐Hernandez A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Immunology) in The University of Michigan 2012 Doctoral Committee Professor David M. Markovitz, Chair Professor Gary Huffnagle Professor Michael J. Imperiale Associate Professor David J. Miller Assistant Professor Akira Ono Assistant Professor Christiane E. Wobus © Marta Jeannette Gonzalez‐Hernandez 2012 For my family and friends, the most fantastic teachers I have ever had. ii Acknowledgements First, and foremost, I would like to thank David Markovitz for his patience and his scientific and mentoring endeavor. My time in the laboratory has been an honor and a pleasure. Special thanks are also due to all the members of the Markovitz laboratory, past and present. It has been a privilege, and a lot of fun, to work near such excellent scientists and friends. You all have a special place in my heart. I would like to thank all the members of my thesis committee for all the valuable advice, help and jokes whenever needed. Our collaborators from the Bioinformatics Core, particularly James Cavalcoli, Fan Meng, Manhong Dai, Maureen Sartor and Gil Omenn gave generous support, technical expertise and scientific insight to a very important part of this project. Thank you. Thanks also go to Mariana Kaplan’s and Akira Ono’s laboratory for help with experimental designs and for being especially generous with time and reagents. iii Table of Contents Dedication ............................................................................................................................ ii Acknowledgements ............................................................................................................. iii List of Figures ...................................................................................................................
    [Show full text]
  • Detection of HERV‑K6 and HERV‑K11 Transpositions in the Human Genome
    BIOMEDICAL REPORTS 9: 53-59, 2018 Detection of HERV‑K6 and HERV‑K11 transpositions in the human genome BUKET CAKMAK GUNER1, ELIF KARLIK2, SEVGI MARAKLI1 and NERMIN GOZUKIRMIZI1 1Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, 34134 Istanbul; 2Department of Biotechnology, Institution of Science, Istanbul University, 34134 Istanbul, Turkey Received November 19, 2017; Accepted April 24, 2018 DOI: 10.3892/br.2018.1096 Abstract. Mobile genetic elements classed as transposons analysed HERV‑K movements among individuals. This is the comprise an estimated 45% of the human genome, and 8% of first report to investigate HERV‑K6 and HERV‑K11 retrotrans- these elements are human endogenous retroviruses (HERVs). poson polymorphisms between the genders and different age Endogenous retroviruses are retrotransposons, containing 5' groups. and 3' long terminal repeat sequences and encoding envelope, group‑specific antigen and DNA polymerase proteins. The Introduction aim of the present study was to analyse genome integration polymorphisms of HERV type K member 6 (HERV‑K6) and Human endogenous retroviruses (HERVs) belonging to the HERV‑K11 by using the retrotransposon based molecular superfamily of transposable and retrotransposable genetic marker technique, inter‑retrotransposon amplified polymor- elements represent ~8% of the human genome (1). HERV phism (IRAP). For this purpose, blood samples of 18 healthy type K (HERV‑K) is the sole group of endogenous retroviruses individuals within the age range of 10‑79 years (10 females that is established to contain human‑specific members. Group and 8 males) were collected, genomic DNAs were isolated HERV‑K (also known as human mouse mammary tumour and IRAP‑polymerase chain reaction (PCR) was performed.
    [Show full text]
  • Ervmap Analysis Reveals Genome-Wide Transcription of INAUGURAL ARTICLE Human Endogenous Retroviruses
    ERVmap analysis reveals genome-wide transcription of INAUGURAL ARTICLE human endogenous retroviruses Maria Tokuyamaa, Yong Konga, Eric Songa, Teshika Jayewickremea, Insoo Kangb, and Akiko Iwasakia,c,1 aDepartment of Immunobiology, Yale School of Medicine, New Haven, CT 06520; bDepartment of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520; and cHoward Hughes Medical Institute, Chevy Chase, MD 20815 This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected in 2018. Contributed by Akiko Iwasaki, October 23, 2018 (sent for review August 24, 2018; reviewed by Stephen P. Goff and Nir Hacohen) Endogenous retroviruses (ERVs) are integrated retroviral elements regulates expression of IFN-γ–responsive genes, such as AIM2, that make up 8% of the human genome. However, the impact of APOL1, IFI6, and SECTM1 (16). ERV elements can drive ERVs on human health and disease is not well understood. While transcription of genes, generate chimeric transcripts with protein- select ERVs have been implicated in diseases, including autoim- coding genes in cancer, serve as splice donors or acceptors mune disease and cancer, the lack of tools to analyze genome- for neighboring genes, and be targets of recombination and in- wide, locus-specific expression of proviral autonomous ERVs has crease genomic diversity (17, 18). ERVs that are elevated in hampered the progress in the field. Here we describe a method breast cancer tissues correlate with the expression of granzyme called ERVmap, consisting of an annotated database of 3,220 hu- and perforin levels, implying a possible role of ERVs in immune man proviral ERVs and a pipeline that allows for locus-specific surveillance of tumors (19).
    [Show full text]
  • (Hervs) and Mammalian Apparent Ltrs Retrotransposons (Malrs) Are Dynamically Modulated in Different Stages of Immunity
    biology Article Human Endogenous Retroviruses (HERVs) and Mammalian Apparent LTRs Retrotransposons (MaLRs) Are Dynamically Modulated in Different Stages of Immunity Maria Paola Pisano , Nicole Grandi and Enzo Tramontano * Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; [email protected] (M.P.P.); [email protected] (N.G.) * Correspondence: [email protected]; Tel.: +39-070-6754-538 Simple Summary: Human Endogenous retroviruses (HERVs) and Mammalian Apparent LTRs Retrotransposons (MaLRs) are remnants of ancient retroviral infections that make up about 8% of the human genome. HERV and MaLR expression is regulated in immunity, and, in particular, is known for their up-regulation after innate immune activation. In this work, we analyzed the differential expression of HERVs and MaLRs in different stages of immunity, triggered by the administration of an inactivated vaccine. Abstract: Human Endogenous retroviruses (HERVs) and Mammalian Apparent LTRs Retrotrans- posons (MaLRs) are remnants of ancient retroviral infections that represent a large fraction of our genome. The HERV and MaLR transcriptional activity is regulated in developmental stages, adult tissues, and pathological conditions. In this work, we used a bioinformatics approach based on Citation: Pisano, M.P.; Grandi, N.; RNA-sequencing (RNA-seq) to study the expression and modulation of HERVs and MaLR in a Tramontano, E. Human Endogenous scenario of activation of the immune response. We analyzed transcriptome data from subjects before Retroviruses (HERVs) and Mammalian Apparent LTRs and after the administration of an inactivated vaccine against the Hantaan orthohantavirus, the Retrotransposons (MaLRs) Are causative agent of Korean hemorrhagic fever, to investigate the HERV and MaLR expression and Dynamically Modulated in Different differential expression in response to the administration of the vaccine.
    [Show full text]
  • Human Endogenous Retrovirus Reactivation: Implications for Cancer Immunotherapy
    cancers Review Human Endogenous Retrovirus Reactivation: Implications for Cancer Immunotherapy Annacarmen Petrizzo *, Concetta Ragone, Beatrice Cavalluzzo, Angela Mauriello, Carmen Manolio, Maria Tagliamonte and Luigi Buonaguro * Laboratory of Innovative Immunological Models, Istituto Nazionale per lo Studio e la Cura dei Tumori, “Fondazione Pascale”-IRCCS, 80131 Naples, Italy; [email protected] (C.R.); [email protected] (B.C.); [email protected] (A.M.); [email protected] (C.M.); [email protected] (M.T.) * Correspondence: [email protected] (A.P.); [email protected] (L.B.); Tel.: +39-081-5903273 Simple Summary: Endogenous viruses are “ancient” viruses that have coevolved with their host species for millions of years, developing strategies to maintain an equilibrium state with their host. In particular, human endogenous retroviruses (HERVs) are permanently integrated and make up over 8% of our genome. Recent studies have shown that the equilibrium between these endogenous retroviruses and our cells can be broken in several conditions, including cancer. HERV reactivation in cancer cells may result in (a) the activation of a viral defense response against cancer, (b) the production of viral proteins that can be recognized as targets by our immune system and (c) the expression of viral transcripts that can be used as therapeutic targets or markers for prognosis. Overall, this may positively impact on cancer immunotherapy strategies. Citation: Petrizzo, A.; Ragone, C.; Abstract: Human endogenous retroviruses (HERVs) derive from ancestral exogenous retroviruses Cavalluzzo, B.; Mauriello, A.; whose genetic material has been integrated in our germline DNA. Several lines of evidence indicate Manolio, C.; Tagliamonte, M.; Buonaguro, L.
    [Show full text]
  • Full Text (PDF)
    Published OnlineFirst February 12, 2018; DOI: 10.1158/0008-5472.CAN-17-1861 Cancer Tumor Biology and Immunology Research A Distinct Oncogenerative Multinucleated Cancer Cell Serves as a Source of Stemness and Tumor Heterogeneity David Díaz-Carballo1, Sahitya Saka1, Jacqueline Klein1, Tobias Rennkamp1, Ali H. Acikelli1, Sascha Malak1, Holger Jastrow2, Gunther Wennemuth2, Clemens Tempfer3, Inge Schmitz4, Andrea Tannapfel4, and Dirk Strumberg1 Abstract The effects of anticancer treatments on cell heterogeneity and new mechanism used by tumor cells to invade surrounding tissues their proliferative potential play an important role in tumor and ensure life cycles. In contrast to the pregnant P1 cells with low persistence and metastasis. However, little is known about de- expression of stem cell markers despite their physiologic stem- polyploidization, cell fate, and physiologic stemness of the result- ness, the first offspring generations of daughter G1 cells expressed ing cell populations. Here, we describe a distinctive cell type high levels of ovarian cancer stem cell markers. Furthermore, termed "pregnant" P1 cells found within chemotherapy-refracto- both P1 and Gn cells overexpressed multiple human endogenous ry ovarian tumors, which generate and gestate daughter genera- retroviral envelope proteins. Moreover, programmed death- tion Gn cells intracytoplasmically. Release of Gn cells occurred by ligand 1 and the immunosuppressive domain of the retroviral ejection through crevices in the P1 cell membrane by body envelope proteins were also overexpressed in P1 cells, suggesting contractions or using a funiculus-like structure. These events effective protection against the host immune system. Together, characterized a not yet described mechanism of cell segregation. our data suggest that P1 oncogenerative cancer cells exhibit a not Maternal P1 cells were principally capable of surviving parturition yet described cell biological mechanism of persistence and trans- events and continued to breed and nurture Gn progenies.
    [Show full text]
  • Dsrna Sequencing for RNA Virus Surveillance Using Human Clinical Samples
    viruses Article DsRNA Sequencing for RNA Virus Surveillance Using Human Clinical Samples Takuma Izumi 1,2,†, Yuhei Morioka 1,†, Syun-ichi Urayama 3 , Daisuke Motooka 4, Tomokazu Tamura 1 , Takahiro Kawagishi 5, Yuta Kanai 5, Takeshi Kobayashi 5, Chikako Ono 1, Akinari Morinaga 2, Takahiro Tomiyama 2 , Norifumi Iseda 2, Yukiko Kosai 2, Shoichi Inokuchi 2, Shota Nakamura 4, Tomohisa Tanaka 6 , Kohji Moriishi 6 , Hiroaki Kariwa 7, Tomoharu Yoshizumi 2, Masaki Mori 2, Yoshiharu Matsuura 1,* and Takasuke Fukuhara 8,* 1 Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; [email protected] (T.I.); [email protected] (Y.M.); [email protected] (T.T.); [email protected] (C.O.) 2 Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 814-0180, Japan; [email protected] (A.M.); [email protected] (T.T.); [email protected] (N.I.); [email protected] (Y.K.); [email protected] (S.I.); [email protected] (T.Y.); [email protected] (M.M.) 3 Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8577, Japan; [email protected] 4 Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; [email protected] (D.M.); [email protected]
    [Show full text]
  • Demystified . . . Human Endogenous Retroviruses
    11 REVIEW Mol Path: first published as 10.1136/mp.56.1.11 on 1 February 2003. Downloaded from Demystified...Human endogenous retroviruses P N Nelson, P R Carnegie, J Martin, H Davari Ejtehadi, P Hooley, D Roden, S Rowland-Jones, P Warren, J Astley, P G Murray ............................................................................................................................. J Clin Pathol: Mol Pathol 2003;56:11–18 Human endogenous retroviruses (HERVs) are a family of viruses within our genome with similarities to present indeed, to produce viral-like particles. Further- more, some HERVs have been implicated in day exogenous retroviruses. HERVs have been inherited certain autoimmune diseases and cancers4–7 and by successive generations and it is possible that some might have a role in the aetiology and pathology have conferred biological benefits. However, several of disease. However, many HERVs have been present in our genome for a considerable period of HERVs have been implicated in certain cancers and time so that their presence may also be of benefit autoimmune diseases. This article demystifies these to the human host. retroviruses by providing an insight into HERVs, their means of classification, and a synopsis of HERVs MOLECULAR BIOLOGY AND HERVS The focus of the human genome project is to implicated in cancer and autoimmunity. Furthermore, the sequence the 3 billion DNA bases that compose biological roles of HERVs are explored. our human genome.8 Interestingly, only a small .......................................................................... proportion (about 3%) appears to constitute the estimated 24 179 to 87 720 genes that are translated into the proteins necessary to life. The uman endogenous retroviruses (HERVs) function of non-coding DNA (maligned as “junk represent footprints of previous retroviral DNA”) is not readily obvious and it may have Hinfection and have been termed “fossil important roles in packaging and influencing viruses”.
    [Show full text]
  • Reconstitution and Characterization of Human Endogenous Retrovirus-K Young Nam Lee
    Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2010 Reconstitution and Characterization of Human Endogenous Retrovirus-K Young Nam Lee Follow this and additional works at: http://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons Recommended Citation Lee, Young Nam, "Reconstitution and Characterization of Human Endogenous Retrovirus-K" (2010). Student Theses and Dissertations. Paper 78. This Thesis is brought to you for free and open access by Digital Commons @ RU. It has been accepted for inclusion in Student Theses and Dissertations by an authorized administrator of Digital Commons @ RU. For more information, please contact [email protected]. RECONSTITUTION AND CHARACTERIZATION OF HUMAN ENDOGENOUS RETROVIRUS-K A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Young Nam Lee June 2010 © Copyright by Young Nam Lee 2010 RECONSTITUTION AND CHARACTERIZATION OF HUMAN ENDOGENOUS RETROVIRUS-K Young Nam Lee, Ph.D. The Rockefeller University 2010 Retroviruses are a family of clinically significant and scientifically fascinating viruses that infect a wide array of organisms from all vertebrate classes. The two hallmark events in the life cycle of retroviruses are the reverse transcription of the single stranded RNA (ssRNA) genome generating a double stranded DNA (dsDNA) and the integration of this dsDNA into the host genome. Because integration is irreversible and the infected cells are usually difficult to target for elimination in the host, the infection is generally permanent. HIV-1, the most important and well-studied member of all retroviruses, is the causative agent of acquired immune deficiency syndrome (AIDS) for which no vaccine or cure is known.
    [Show full text]
  • Silencing and Transcriptional Regulation of Endogenous Retroviruses: an Overview
    viruses Review Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview Franziska K. Geis 1,2,3 and Stephen P. Goff 1,2,3,* 1 Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA; [email protected] 2 Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA 3 Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA * Correspondence: [email protected]; Tel.: +1-212-305-3794 Received: 23 June 2020; Accepted: 11 August 2020; Published: 13 August 2020 Abstract: Almost half of the human genome is made up of transposable elements (TEs), and about 8% consists of endogenous retroviruses (ERVs). ERVs are remnants of ancient exogenous retrovirus infections of the germ line. Most TEs are inactive and not detrimental to the host. They are tightly regulated to ensure genomic stability of the host and avoid deregulation of nearby gene loci. Histone-based posttranslational modifications such as H3K9 trimethylation are one of the main silencing mechanisms. Trim28 is one of the identified master regulators of silencing, which recruits most prominently the H3K9 methyltransferase Setdb1, among other factors. Sumoylation and ATP-dependent chromatin remodeling factors seem to contribute to proper localization of Trim28 to ERV sequences and promote Trim28 interaction with Setdb1. Additionally, DNA methylation as well as RNA-mediated targeting of TEs such as piRNA-based silencing play important roles in ERV regulation. Despite the involvement of ERV overexpression in several cancer types, autoimmune diseases, and viral pathologies, ERVs are now also appreciated for their potential positive role in evolution.
    [Show full text]
  • Functions and Regulation of Endogenous Retrovirus Elements During Zygotic Genome Activation: Implications for Improving Somatic Cell Nuclear Transfer Efficiency
    biomolecules Review Functions and Regulation of Endogenous Retrovirus Elements during Zygotic Genome Activation: Implications for Improving Somatic Cell Nuclear Transfer Efficiency Bo Fu 1,2,† , Hong Ma 1,2,† and Di Liu 1,2,* 1 Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; [email protected] (B.F.); [email protected] (H.M.) 2 Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China * Correspondence: [email protected] † These authors contributed equally to this work. Abstract: Endogenous retroviruses (ERVs), previously viewed as deleterious relics of ancestral retro- virus infections, are silenced in the vast majority of cells to minimize the risk of retrotransposition. Counterintuitively, bursts of ERV transcription usually occur during maternal-to-zygotic transition (MZT) in preimplantation embryos; this is regarded as a major landmark event in the zygotic genome activation (ZGA) process, indicating that ERVs play an active part in ZGA. Evolutionarily, the inter- action between ERVs and hosts is mutually beneficial. The endogenization of retrovirus sequences rewires the gene regulatory network during ZGA, and ERV repression may lower germline fitness. Unfortunately, owing to various limitations of somatic cell nuclear transfer (SCNT) technology, both developmental arrest and ZGA abnormalities occur in a high percentage of cloned embryos, accom- Citation: Fu, B.; Ma, H.; Liu, D. panied by ERV silencing, which may be caused by the activation failure of upstream ERV inducers. Functions and Regulation of In this review, we discuss the functions and regulation of ERVs during the ZGA process and the Endogenous Retrovirus Elements feasibility of temporal control over ERVs in cloned embryos via exogenous double homeobox (DUX).
    [Show full text]
  • A Human Endogenous Retrovirus Encoded Protease Potentially Cleaves Numerous Cellular Proteins Giuseppe Rigogliuso1, Martin L
    Rigogliuso et al. Mobile DNA (2019) 10:36 https://doi.org/10.1186/s13100-019-0178-z RESEARCH Open Access A human endogenous retrovirus encoded protease potentially cleaves numerous cellular proteins Giuseppe Rigogliuso1, Martin L. Biniossek2, John L. Goodier3, Bettina Mayer2, Gavin C. Pereira3, Oliver Schilling4,5, Eckart Meese1 and Jens Mayer1* Abstract Background: A considerable portion of the human genome derives from retroviruses inherited over millions of years. Human endogenous retroviruses (HERVs) are usually severely mutated, yet some coding-competent HERVs exist. The HERV-K(HML-2) group includes evolutionarily young proviruses that encode typical retroviral proteins. HERV-K(HML-2) has been implicated in various human diseases because transcription is often upregulated and some of its encoded proteins are known to affect cell biology. HERV-K(HML-2) Protease (Pro) has received little attention so far, although it is expressed in some disease contexts and other retroviral proteases are known to process cellular proteins. Results: We set out to identify human cellular proteins that are substrates of HERV-K(HML-2) Pro employing a modified Terminal Amine Isotopic Labeling of Substrates (TAILS) procedure. Thousands of human proteins were identified by this assay as significantly processed by HERV-K(HML-2) Pro at both acidic and neutral pH. We confirmed cleavage of a majority of selected human proteins in vitro and in co-expression experiments in vivo. Sizes of processing products observed for some of the tested proteins coincided with product sizes predicted by TAILS. Processed proteins locate to various cellular compartments and participate in diverse, often disease-relevant cellular processes.
    [Show full text]