201
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Schumann T, Ramon SC, Schubert N, Mayo MA, Hega M, Maser KI, Ada SR, Sydow L, Hajikazemi M, Badstübner M, Müller P, Ge Y, Shakeri F, Buness A, Rupf B, Lienenklaus S, Utess B, Muhandes L, Haase M, Rupp L, Schmitz M, Gramberg T, Manel N, Hartmann G, Zillinger T, Kato H, Bauer S, Gerbaulet A, Paeschke K, Roers A, Behrendt R. Deficiency for SAMHD1 activates MDA5 in a cGAS/STING-dependent manner. J Exp Med 2022; 220:213670. [PMID: 36346347 PMCID: PMC9648672 DOI: 10.1084/jem.20220829] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/01/2022] [Accepted: 10/06/2022] [Indexed: 11/09/2022] Open
Abstract
Defects in nucleic acid metabolizing enzymes can lead to spontaneous but selective activation of either cGAS/STING or RIG-like receptor (RLR) signaling, causing type I interferon-driven inflammatory diseases. In these pathophysiological conditions, activation of the DNA sensor cGAS and IFN production are linked to spontaneous DNA damage. Physiological, or tonic, IFN signaling on the other hand is essential to functionally prime nucleic acid sensing pathways. Here, we show that low-level chronic DNA damage in mice lacking the Aicardi-Goutières syndrome gene SAMHD1 reduced tumor-free survival when crossed to a p53-deficient, but not to a DNA mismatch repair-deficient background. Increased DNA damage did not result in higher levels of type I interferon. Instead, we found that the chronic interferon response in SAMHD1-deficient mice was driven by the MDA5/MAVS pathway but required functional priming through the cGAS/STING pathway. Our work positions cGAS/STING upstream of tonic IFN signaling in Samhd1-deficient mice and highlights an important role of the pathway in physiological and pathophysiological innate immune priming.
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Affiliation(s)
- Tina Schumann
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Santiago Costas Ramon
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Nadja Schubert
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Mohamad Aref Mayo
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Melanie Hega
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Katharina Isabell Maser
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Servi-Remzi Ada
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Lukas Sydow
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Mona Hajikazemi
- Clinic of Internal Medicine III, Oncology, Hematology, Rheumatology and Clinical Immunology, University Hospital Bonn, Bonn, Germany
| | - Markus Badstübner
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Patrick Müller
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Yan Ge
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany,Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Farhad Shakeri
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany,Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Andreas Buness
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany,Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Benjamin Rupf
- Institute for Immunology, Philipps-University Marburg, Marburg, Germany
| | - Stefan Lienenklaus
- Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Barbara Utess
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Lina Muhandes
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany,Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Michael Haase
- Department of Pediatric Surgery, University Hospital Dresden, Dresden, Germany
| | - Luise Rupp
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Marc Schmitz
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany,National Center for Tumor Diseases, Partner Site Dresden, Dresden, Germany,German Cancer Consortium, Partner Site Dresden, and German Cancer Research Center, Heidelberg, Germany
| | - Thomas Gramberg
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Nicolas Manel
- Institut national de la santé et de la recherche médicale U932, Institut Curie, Paris Sciences et Lettres Research University, Paris, France
| | - Gunther Hartmann
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Thomas Zillinger
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, Bonn, Germany
| | - Stefan Bauer
- Institute for Immunology, Philipps-University Marburg, Marburg, Germany
| | - Alexander Gerbaulet
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Katrin Paeschke
- Clinic of Internal Medicine III, Oncology, Hematology, Rheumatology and Clinical Immunology, University Hospital Bonn, Bonn, Germany
| | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany,Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Rayk Behrendt
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany,Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany,Correspondence to Rayk Behrendt:
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202
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Hagelkruys A, Horrer M, Taubenschmid-Stowers J, Kavirayani A, Novatchkova M, Orthofer M, Pai TP, Cikes D, Zhuk S, Balmaña M, Esk C, Koglgruber R, Moeseneder P, Lazovic J, Zopf LM, Cronin SJ, Elling U, Knoblich JA, Penninger JM. The HUSH complex controls brain architecture and protocadherin fidelity. SCIENCE ADVANCES 2022; 8:eabo7247. [PMID: 36332029 PMCID: PMC9635835 DOI: 10.1126/sciadv.abo7247] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The HUSH (human silencing hub) complex contains the H3K9me3 binding protein M-phase phosphoprotein 8 (MPP8) and recruits the histone methyltransferase SETDB1 as well as Microrchidia CW-type zinc finger protein 2 (MORC2). Functional and mechanistic studies of the HUSH complex have hitherto been centered around SETDB1 while the in vivo functions of MPP8 and MORC2 remain elusive. Here, we show that genetic inactivation of Mphosph8 or Morc2a in the nervous system of mice leads to increased brain size, altered brain architecture, and behavioral changes. Mechanistically, in both mouse brains and human cerebral organoids, MPP8 and MORC2 suppress the repetitive-like protocadherin gene cluster in an H3K9me3-dependent manner. Our data identify MPP8 and MORC2, previously linked to silencing of repetitive elements via the HUSH complex, as key epigenetic regulators of protocadherin expression in the nervous system and thereby brain development and neuronal individuality in mice and humans.
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Affiliation(s)
- Astrid Hagelkruys
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Marion Horrer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | | | | | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Michael Orthofer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Tsung-Pin Pai
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Domagoj Cikes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Sergei Zhuk
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Meritxell Balmaña
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Christopher Esk
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Rubina Koglgruber
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Paul Moeseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Jelena Lazovic
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Lydia M. Zopf
- Vienna Biocenter Core Facilities (VBCF), Vienna, Austria
| | - Shane J.F. Cronin
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Jürgen A. Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Josef M. Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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203
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She J, Du M, Xu Z, Jin Y, Li Y, Zhang D, Tao C, Chen J, Wang J, Yang E. The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites. Genome Biol 2022; 23:231. [PMID: 36329469 PMCID: PMC9632151 DOI: 10.1186/s13059-022-02804-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Human endogenous retroviruses (HERVs), the remnants of ancient retroviruses, account for 8% of the human genome, but most have lost their transcriptional abilities under physiological conditions. However, mounting evidence shows that several expressed HERVs do exert biological functions. Here, we systematically characterize physiologically expressed HERVs and examine whether they may give insight into the molecular fundamentals of human development and disease. RESULTS We systematically identify 13,889 expressed HERVs across normal body sites and demonstrate that they are expressed in body site-specific patterns and also by sex, ethnicity, and age. Analyzing cis-ERV-related quantitative trait loci, we find that 5435 hervRNAs are regulated by genetic variants. Combining this with a genome-wide association study, we elucidate that the dysregulation of expressed HERVs might be associated with various complex diseases, particularly neurodegenerative and psychiatric diseases. We further find that physiologically activated hervRNAs are associated with histone modifications rather than DNA demethylation. CONCLUSIONS Our results present a locus-specific landscape of physiologically expressed hervRNAs, which represent a hidden layer of genetic architecture in development and disease.
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Affiliation(s)
- Jianqi She
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Minghao Du
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zhanzhan Xu
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yueqi Jin
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yu Li
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Daoning Zhang
- Peking University First Hospital, Beijing, 100034, China
| | - Changyu Tao
- Department of Human Anatomy, Histology & Embryology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jian Chen
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ence Yang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China.
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Chinese Institute for Brain Research, Beijing, 102206, China.
- Taizhou Medical New & Hi-tech Industrial Development Zone, Jiangsu, 225326, China.
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204
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Ichino L, Picard CL, Yun J, Chotai M, Wang S, Lin EK, Papareddy RK, Xue Y, Jacobsen SE. Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing in the vegetative cell of developing pollen. Cell Rep 2022; 41:111699. [DOI: 10.1016/j.celrep.2022.111699] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/28/2022] [Accepted: 10/28/2022] [Indexed: 11/23/2022] Open
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205
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Wang J, Ren M, Yu J, Hu M, Wang X, Ma W, Jiang X, Cui J. Single-cell RNA sequencing highlights the functional role of human endogenous retroviruses in gallbladder cancer. EBioMedicine 2022; 85:104319. [PMID: 36374772 PMCID: PMC9626538 DOI: 10.1016/j.ebiom.2022.104319] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/05/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
Background Gallbladder cancer (GBC), the most common malignancy of the biliary tract, shows late diagnosis and low survival rate and requires continued search for new diagnostic biomarkers and therapeutic targets. Human endogenous retroviruses (HERVs) are specifically prone to be reactivated in diverse cancers and are implicated in cancer progression and immunotherapy. Methods Single-cell RNA sequencing was performed on tumor tissues and paired adjacent tissues from 4 GBC patients. Dual-luciferase reporter assay was applied to measure enhancer activity of HERV sequences. Findings We dissected the cellular diversity and described the HERV transcriptomic landscape for GBC. We found that HERVs were transcribed in a cell type-specific manner and different HERV families were associated with diverse biological effects. HERVs could function as enhancers, presumably causing altered expression of neighboring genes. The transcription level of HERVH was gradually elevated with the malignant transformation of epithelial cells, suggesting HERVH may be a potential early diagnostic biomarker of GBC. HHLA2, a newly emerging immune checkpoint, was derived by HERVH, exhibited an expressional correlation with HERVH, and was identified as a promising target for immunotherapy. Interpretation Exploring the transcriptional landscape and potential functional impact of HERVs highlights the important role of HERVs in GBC and provides a fresh perspective on managing GBC. Funding This study was supported by the National Natural Science Foundation of China (31970176, 81972256) and the research grants from the Innovation Capacity Building Project of Jiangsu province (BM2020019).
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Key Words
- gallbladder cancer
- single-cell rna sequencing
- human endogenous retrovirus
- enhancer
- immune checkpoint
- hervh
- gbc, gallbladder cancer
- herv, human endogenous retrovirus
- scrna-seq, single-cell rna sequencing
- tme, tumor microenvironment
- wta, whole transcriptome analysis
- deg, differentially expressed gene
- cnv, copy number variation
- go, gene ontology
- nk cell, natural killer cell
- nkt cell, natural killer t cell
- dc, dendritic cell
- ics, intermediate cell state
- hhla2, human endogenous retrovirus-h long terminal repeat-associating 2
- cd4+ th cell, cd4+ t helper cell
- igg, immunoglobulin g
- cdc, conventional dc
- mo-dc, monocyte-derived dc
- caf, cancer-associated fibroblast
- ecm, extracellular matrix
- icaf, inflammatory caf
- myocaf, myo-cancer-associated fibroblast
- te, transposable element
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Affiliation(s)
- Jinghan Wang
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Meng Ren
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China,Nanjing Advanced Academy of Life and Health, Nanjing 211135, China
| | - Jundan Yu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingtai Hu
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Xiaojing Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wencong Ma
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Xiaoqing Jiang
- Department of Biliary Tract Surgery I, the Third Hospital of Naval Medical University, Shanghai 200438, China,Corresponding author.
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China,Nanjing Advanced Academy of Life and Health, Nanjing 211135, China,Corresponding author.
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206
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Fernandes LP, Enriquez-Gasca R, Gould PA, Holt JH, Conde L, Ecco G, Herrero J, Gifford R, Trono D, Kassiotis G, Rowe HM. A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819. SCIENCE ADVANCES 2022; 8:eabp8085. [PMID: 36306355 PMCID: PMC9616502 DOI: 10.1126/sciadv.abp8085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 09/08/2022] [Indexed: 06/11/2023]
Abstract
Mammalian genomes are a battleground for genetic conflict between repetitive elements and KRAB-zinc finger proteins (KZFPs). We asked whether KZFPs can regulate cell fate by using ZFP819, which targets a satellite DNA array, ZP3AR. ZP3AR coats megabase regions of chromosome 7 encompassing genes encoding ZSCAN4, a master transcription factor of totipotency. Depleting ZFP819 in mouse embryonic stem cells (mESCs) causes them to transition to a 2-cell (2C)-like state, whereby the ZP3AR array switches from a poised to an active enhancer state. This is accompanied by a global erosion of heterochromatin roadblocks, which we link to decreased SETDB1 stability. These events result in transcription of active LINE-1 elements and impaired differentiation. In summary, ZFP819 and TRIM28 partner up to close chromatin across Zscan4, to promote exit from totipotency. We propose that satellite DNAs may control developmental fate transitions by barcoding and switching off master transcription factor genes.
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Affiliation(s)
- Liane P. Fernandes
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Rocio Enriquez-Gasca
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Poppy A. Gould
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - James H. Holt
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK
| | - Gabriela Ecco
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK
| | - Robert Gifford
- MRC–University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Helen M. Rowe
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
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207
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Savytska N, Heutink P, Bansal V. Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level. Front Genet 2022; 13:1026847. [PMID: 36338986 PMCID: PMC9633680 DOI: 10.3389/fgene.2022.1026847] [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: 08/24/2022] [Accepted: 10/11/2022] [Indexed: 08/31/2023] Open
Abstract
The transcriptional activity of Transposable Elements (TEs) has been involved in numerous pathological processes, including neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. The TE expression analysis from short-read sequencing technologies is, however, challenging due to the multitude of similar sequences derived from singular TEs subfamilies and the exaptation of TEs within longer coding or non-coding RNAs. Specialised tools have been developed to quantify the expression of TEs that either relies on probabilistic re-distribution of multimapper count fractions or allow for discarding multimappers altogether. Until now, the benchmarking across those tools was largely limited to aggregated expression estimates over whole TEs subfamilies. Here, we compared the performance of recently published tools (SQuIRE, TElocal, SalmonTE) with simplistic quantification strategies (featureCounts in unique, fraction and random modes) at the individual loci level. Using simulated datasets, we examined the false discovery rate and the primary driver of those false positive hits in the optimal quantification strategy. Our findings suggest a high false discovery number that exceeds the total number of correctly recovered active loci for all the quantification strategies, including the best performing tool TElocal. As a remedy, filtering based on the minimum number of read counts or baseMean expression improves the F1 score and decreases the number of false positives. Finally, we demonstrate that additional profiling of Transcription Start Site mapping statistics (using a k-means clustering approach) significantly improves the performance of TElocal while reporting a reliable set of detected and differentially expressed TEs in human simulated RNA-seq data.
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Affiliation(s)
| | | | - Vikas Bansal
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
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208
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Rodríguez-Quiroz R, Valdebenito-Maturana B. SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression. Commun Biol 2022; 5:1063. [PMID: 36202992 PMCID: PMC9537157 DOI: 10.1038/s42003-022-04020-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022] Open
Abstract
Transposable Elements (TEs) contribute to the repetitive fraction in almost every eukaryotic genome known to date, and their transcriptional activation can influence the expression of neighboring genes in healthy and disease states. Single cell RNA-Seq (scRNA-Seq) is a technical advance that allows the study of gene expression on a cell-by-cell basis. Although a current computational approach is available for the single cell analysis of TE expression, it omits their genomic location. Here we show SoloTE, a pipeline that outperforms the previous approach in terms of computational resources and by allowing the inclusion of locus-specific TE activity in scRNA-Seq expression matrixes. We then apply SoloTE to several datasets to reveal the repertoire of TEs that become transcriptionally active in different cell groups, and based on their genomic location, we predict their potential impact on gene expression. As our tool takes as input the resulting files from standard scRNA-Seq processing pipelines, we expect it to be widely adopted in single cell studies to help researchers discover patterns of cellular diversity associated with TE expression.
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Affiliation(s)
- Rocío Rodríguez-Quiroz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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209
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Exploration of nuclear body-enhanced sumoylation reveals that PML represses 2-cell features of embryonic stem cells. Nat Commun 2022; 13:5726. [PMID: 36175410 PMCID: PMC9522831 DOI: 10.1038/s41467-022-33147-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/05/2022] [Indexed: 01/12/2023] Open
Abstract
Membrane-less organelles are condensates formed by phase separation whose functions often remain enigmatic. Upon oxidative stress, PML scaffolds Nuclear Bodies (NBs) to regulate senescence or metabolic adaptation. PML NBs recruit many partner proteins, but the actual biochemical mechanism underlying their pleiotropic functions remains elusive. Similarly, PML role in embryonic stem cell (ESC) and retro-element biology is unsettled. Here we demonstrate that PML is essential for oxidative stress-driven partner SUMO2/3 conjugation in mouse ESCs (mESCs) or leukemia, a process often followed by their poly-ubiquitination and degradation. Functionally, PML is required for stress responses in mESCs. Differential proteomics unravel the KAP1 complex as a PML NB-dependent SUMO2-target in arsenic-treated APL mice or mESCs. PML-driven KAP1 sumoylation enables activation of this key epigenetic repressor implicated in retro-element silencing. Accordingly, Pml-/- mESCs re-express transposable elements and display 2-Cell-Like features, the latter enforced by PML-controlled SUMO2-conjugation of DPPA2. Thus, PML orchestrates mESC state by coordinating SUMO2-conjugation of different transcriptional regulators, raising new hypotheses about PML roles in cancer.
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210
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Pasquesi GIM, Kelly CJ, Ordonez AD, Chuong EB. Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells. Mob DNA 2022; 13:22. [PMID: 36068622 PMCID: PMC9446614 DOI: 10.1186/s13100-022-00277-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/09/2022] [Indexed: 12/02/2022] Open
Abstract
Background Bats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adaptations affecting interferon (IFN) signaling and IFN-stimulated genes (ISGs), but we still have a limited understanding of the genetic mechanisms that have shaped the evolution of bat immunity. Here we investigated the transcriptional and epigenetic dynamics of transposable elements (TEs) during the type I IFN response in little brown bat (Myotis lucifugus) primary embryonic fibroblast cells, using RNA-seq and CUT&RUN. Results We found multiple bat-specific TEs that undergo both locus-specific and family-level transcriptional induction in response to IFN. Our transcriptome reassembly identified multiple ISGs that have acquired novel exons from bat-specific TEs, including NLRC5, SLNF5 and a previously unannotated isoform of the IFITM2 gene. We also identified examples of TE-derived regulatory elements, but did not find strong evidence supporting genome-wide epigenetic activation of TEs in response to IFN. Conclusion Collectively, our study uncovers numerous TE-derived transcripts, proteins, and alternative isoforms that are induced by IFN in Myotis lucifugus cells, highlighting candidate loci that may contribute to bat-specific immune function. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00277-z.
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Affiliation(s)
- Giulia Irene Maria Pasquesi
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
| | - Conor J Kelly
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
| | - Andrea D Ordonez
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
| | - Edward B Chuong
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA.
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211
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Modzelewski AJ, Gan Chong J, Wang T, He L. Mammalian genome innovation through transposon domestication. Nat Cell Biol 2022; 24:1332-1340. [PMID: 36008480 PMCID: PMC9729749 DOI: 10.1038/s41556-022-00970-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/27/2022] [Indexed: 01/13/2023]
Abstract
Since the discovery of transposons, their sheer abundance in host genomes has puzzled many. While historically viewed as largely harmless 'parasitic' DNAs during evolution, transposons are not a mere record of ancient genome invasion. Instead, nearly every element of transposon biology has been integrated into host biology. Here we review how host genome sequences introduced by transposon activities provide raw material for genome innovation and document the distinct evolutionary path of each species.
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Affiliation(s)
- Andrew J Modzelewski
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, CA, USA
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Johnny Gan Chong
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, CA, USA
| | - Ting Wang
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Lin He
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, CA, USA.
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212
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Detailed Analysis of Dorsal-Ventral Gradients of Gene Expression in the Hippocampus of Adult Rats. Int J Mol Sci 2022; 23:ijms23179948. [PMID: 36077346 PMCID: PMC9456131 DOI: 10.3390/ijms23179948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
We performed RNA sequencing of the dorsal and ventral parts of the hippocampus and compared it with previously published data to determine the differences in the dorsoventral gradients of gene expression that may result from biological or technical variability. Our data suggest that the dorsal and ventral parts of the hippocampus differ in the expression of genes related to signaling pathways mediated by classical neurotransmitters (glutamate, GABA, monoamines, etc.) as well as peptide and Wnt ligands. These hippocampal parts also diverge in the expression of axon-guiding molecules (both receptors and ligands) and splice isoforms of genes associated with intercellular signaling and cell adhesion. Furthermore, analysis of differential expressions of genes specific for astrocytes, microglia, oligodendrocytes, and vascular cells suggests that non-neuronal cells may also differ in the characteristics between hippocampal parts. Analysis of expression of transposable elements showed that depletion of ribosomal RNA strongly increased the representation of transposable elements in the RNA libraries and helped to detect a weak predominance of expression of these elements in the ventral hippocampus. Our data revealed new molecular dimensions of functional differences between the dorsal and ventral hippocampus and points to possible cascades that may be involved in the longitudinal organization of the hippocampus.
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213
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Sasaki E, Gunis J, Reichardt-Gomez I, Nizhynska V, Nordborg M. Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes. PLoS Genet 2022; 18:e1010345. [PMID: 36084135 PMCID: PMC9491579 DOI: 10.1371/journal.pgen.1010345] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/21/2022] [Accepted: 07/16/2022] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have revealed that the striking natural variation for DNA CHH-methylation (mCHH; H is A, T, or C) of transposons has oligogenic architecture involving major alleles at a handful of known methylation regulators. Here we use a conditional GWAS approach to show that CHG-methylation (mCHG) has a similar genetic architecture-once mCHH is statistically controlled for. We identify five key trans-regulators that appear to modulate mCHG levels, and show that they interact with a previously identified modifier of mCHH in regulating natural transposon mobilization.
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Affiliation(s)
- Eriko Sasaki
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Joanna Gunis
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Ilka Reichardt-Gomez
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Viktoria Nizhynska
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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214
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Carter JA, Strömich L, Peacey M, Chapin SR, Velten L, Steinmetz LM, Brors B, Pinto S, Meyer HV. Transcriptomic diversity in human medullary thymic epithelial cells. Nat Commun 2022; 13:4296. [PMID: 35918316 PMCID: PMC9345899 DOI: 10.1038/s41467-022-31750-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
The induction of central T cell tolerance in the thymus depends on the presentation of peripheral self-epitopes by medullary thymic epithelial cells (mTECs). This promiscuous gene expression (pGE) drives mTEC transcriptomic diversity, with non-canonical transcript initiation, alternative splicing, and expression of endogenous retroelements (EREs) representing important but incompletely understood contributors. Here we map the expression of genome-wide transcripts in immature and mature human mTECs using high-throughput 5' cap and RNA sequencing. Both mTEC populations show high splicing entropy, potentially driven by the expression of peripheral splicing factors. During mTEC maturation, rates of global transcript mis-initiation increase and EREs enriched in long terminal repeat retrotransposons are up-regulated, the latter often found in proximity to differentially expressed genes. As a resource, we provide an interactive public interface for exploring mTEC transcriptomic diversity. Our findings therefore help construct a map of transcriptomic diversity in the healthy human thymus and may ultimately facilitate the identification of those epitopes which contribute to autoimmunity and immune recognition of tumor antigens.
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Affiliation(s)
- Jason A. Carter
- grid.225279.90000 0004 0387 3667Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA ,grid.36425.360000 0001 2216 9681Medical Scientist Training Program, Stony Brook University, Stony Brook, NY USA ,grid.34477.330000000122986657Department of Surgery, University of Washington, Seattle, WA USA
| | - Léonie Strömich
- grid.7497.d0000 0004 0492 0584German Cancer Research Center, Heidelberg, Germany ,grid.7445.20000 0001 2113 8111Present Address: Imperial College London, London, UK
| | - Matthew Peacey
- grid.225279.90000 0004 0387 3667School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Sarah R. Chapin
- grid.225279.90000 0004 0387 3667Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Lars Velten
- grid.473715.30000 0004 6475 7299Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lars M. Steinmetz
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Stanford Genome Technology Center, Palo Alto, CA USA
| | - Benedikt Brors
- grid.7497.d0000 0004 0492 0584German Cancer Research Center, Heidelberg, Germany
| | - Sheena Pinto
- grid.7497.d0000 0004 0492 0584German Cancer Research Center, Heidelberg, Germany
| | - Hannah V. Meyer
- grid.225279.90000 0004 0387 3667Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
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215
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Stolz P, Mantero AS, Tvardovskiy A, Ugur E, Wange LE, Mulholland CB, Cheng Y, Wierer M, Enard W, Schneider R, Bartke T, Leonhardt H, Elsässer SJ, Bultmann S. TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation. Nucleic Acids Res 2022; 50:8491-8511. [PMID: 35904814 PMCID: PMC9410877 DOI: 10.1093/nar/gkac642] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/25/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation (5-methylcytosine (5mC)) is critical for genome stability and transcriptional regulation in mammals. The discovery that ten-eleven translocation (TET) proteins catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) revolutionized our perspective on the complexity and regulation of DNA modifications. However, to what extent the regulatory functions of TET1 can be attributed to its catalytic activity remains unclear. Here, we use genome engineering and quantitative multi-omics approaches to dissect the precise catalytic vs. non-catalytic functions of TET1 in murine embryonic stem cells (mESCs). Our study identifies TET1 as an essential interaction hub for multiple chromatin modifying complexes and a global regulator of histone modifications. Strikingly, we find that the majority of transcriptional regulation depends on non-catalytic functions of TET1. In particular, we show that TET1 is critical for the establishment of H3K9me3 and H4K20me3 at endogenous retroviral elements (ERVs) and their silencing that is independent of its canonical role in DNA demethylation. Furthermore, we provide evidence that this repression of ERVs depends on the interaction between TET1 and SIN3A. In summary, we demonstrate that the non-catalytic functions of TET1 are critical for regulation of gene expression and the silencing of endogenous retroviruses in mESCs.
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Affiliation(s)
- Paul Stolz
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Angelo Salazar Mantero
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Enes Ugur
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Lucas E Wange
- Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany
| | - Christopher B Mulholland
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Yuying Cheng
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Wolfgang Enard
- Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Till Bartke
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Heinrich Leonhardt
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Sebastian Bultmann
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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216
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Ansaloni F, Gualandi N, Esposito M, Gustincich S, Sanges R. TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments. Bioinformatics 2022; 38:4430-4433. [PMID: 35876845 PMCID: PMC9477521 DOI: 10.1093/bioinformatics/btac526] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY Transposable elements (TEs) play key roles in crucial biological pathways. Therefore, several tools enabling the quantification of their expression were recently developed. However, many of the existing tools lack the capability to distinguish between the transcription of autonomously expressed TEs and TE fragments embedded in canonical coding/non-coding non-TE transcripts. Consequently, an apparent change in the expression of a given TE may simply reflect the variation in the expression of the transcripts containing TE-derived sequences. To overcome this issue, we have developed TEspeX, a pipeline for the quantification of TE expression at the consensus level. TEspeX uses Illumina RNA-seq short reads to quantify TE expression avoiding counting reads deriving from inactive TE fragments embedded in canonical transcripts. AVAILABILITY AND IMPLEMENTATION The tool is implemented in python3, distributed under the GNU General Public License (GPL) and available on Github at https://github.com/fansalon/TEspeX (Zenodo URL: https://doi.org/10.5281/zenodo.6800331). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Federico Ansaloni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy,Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Nicolò Gualandi
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy
| | - Mauro Esposito
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy
| | | | - Remo Sanges
- To whom correspondence should be addressed. or
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217
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Billon V, Sanchez-Luque FJ, Rasmussen J, Bodea GO, Gerhardt DJ, Gerdes P, Cheetham SW, Schauer SN, Ajjikuttira P, Meyer TJ, Layman CE, Nevonen KA, Jansz N, Garcia-Perez JL, Richardson SR, Ewing AD, Carbone L, Faulkner GJ. Somatic retrotransposition in the developing rhesus macaque brain. Genome Res 2022; 32:1298-1314. [PMID: 35728967 PMCID: PMC9341517 DOI: 10.1101/gr.276451.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022]
Abstract
The retrotransposon LINE-1 (L1) is central to the recent evolutionary history of the human genome and continues to drive genetic diversity and germline pathogenesis. However, the spatiotemporal extent and biological significance of somatic L1 activity are poorly defined and are virtually unexplored in other primates. From a single L1 lineage active at the divergence of apes and Old World monkeys, successive L1 subfamilies have emerged in each descendant primate germline. As revealed by case studies, the presently active human L1 subfamily can also mobilize during embryonic and brain development in vivo. It is unknown whether nonhuman primate L1s can similarly generate somatic insertions in the brain. Here we applied approximately 40× single-cell whole-genome sequencing (scWGS), as well as retrotransposon capture sequencing (RC-seq), to 20 hippocampal neurons from two rhesus macaques (Macaca mulatta). In one animal, we detected and PCR-validated a somatic L1 insertion that generated target site duplications, carried a short 5' transduction, and was present in ∼7% of hippocampal neurons but absent from cerebellum and nonbrain tissues. The corresponding donor L1 allele was exceptionally mobile in vitro and was embedded in PRDM4, a gene expressed throughout development and in neural stem cells. Nanopore long-read methylome and RNA-seq transcriptome analyses indicated young retrotransposon subfamily activation in the early embryo, followed by repression in adult tissues. These data highlight endogenous macaque L1 retrotransposition potential, provide prototypical evidence of L1-mediated somatic mosaicism in a nonhuman primate, and allude to L1 mobility in the brain over the past 30 million years of human evolution.
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Affiliation(s)
- Victor Billon
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
- Biology Department, École Normale Supérieure Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Francisco J Sanchez-Luque
- GENYO. Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
- Institute of Parasitology and Biomedicine "Lopez-Neyra"-Spanish National Research Council, PTS Granada 18016, Spain
| | - Jay Rasmussen
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Gabriela O Bodea
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Daniel J Gerhardt
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Patricia Gerdes
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Seth W Cheetham
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Stephanie N Schauer
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Prabha Ajjikuttira
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Thomas J Meyer
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Cora E Layman
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Natasha Jansz
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Jose L Garcia-Perez
- GENYO. Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Sandra R Richardson
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Lucia Carbone
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Geoffrey J Faulkner
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
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218
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Lee HJ, Hou Y, Maeng JH, Shah NM, Chen Y, Lawson HA, Yang H, Yue F, Wang T. Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish. Genome Res 2022; 32:1424-1436. [PMID: 35649578 PMCID: PMC9341505 DOI: 10.1101/gr.276052.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 05/27/2022] [Indexed: 12/04/2022]
Abstract
Transposable elements (TEs) encode regulatory elements that impact gene expression in multiple species, yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE-derived transcriptional units expressed across tissues. Finally, we show that novel TE-derived promoters can initiate tissue-specific transcription of alternate gene isoforms. This work provides a comprehensive profile of TE activity across normal zebrafish tissues, shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.
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Affiliation(s)
- Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Yiran Hou
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Ju Heon Maeng
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Nakul M Shah
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois 60611, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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219
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Li W, Pandya D, Pasternack N, Garcia-Montojo M, Henderson L, Kozak CA, Nath A. Retroviral Elements in Pathophysiology and as Therapeutic Targets for Amyotrophic Lateral Sclerosis. Neurotherapeutics 2022; 19:1085-1101. [PMID: 35415778 PMCID: PMC9587200 DOI: 10.1007/s13311-022-01233-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2022] [Indexed: 10/18/2022] Open
Abstract
The study of the role of retroviruses in amyotrophic lateral sclerosis (ALS) dates back to the 1960s shortly after transposable elements themselves were first discovered. It was quickly realized that in wild mice both horizontal and vertical transmissions of retroviral elements were key to the development of an ALS-like syndrome leading to the postulate that endogenous retroviruses (ERVs) contribute significantly to the pathogenicity of this disease. Subsequent studies identified retroviral reverse transcriptase activity in brains of individuals with ALS from Guam. However, except for a single study from the former Soviet Union, ALS could not be transmitted to rhesus macaques. The discovery of an ALS-like syndrome in human immunodeficiency virus (HIV) and human T cell leukemia virus infected individuals led to renewed interest in the field and reverse transcriptase activity was found in the blood and cerebrospinal fluid of individuals with sporadic ALS. However, exogenous retroviruses could not be found in individuals with ALS which further reinforced the possibility of involvement of a human ERV (HERV). The first demonstration of the involvement of a HERV was the discovery of the activation of human endogenous retrovirus-K subtype HML-2 in the brains of individuals with ALS. The envelope protein of HML-2 is neurotoxic and transgenic animals expressing the envelope protein develop an ALS-like syndrome. Activation of HML-2 occurs in the context of generalized transposable element activation and is not specific for ALS. Individuals with HIV-associated ALS show a remarkable response to antiretroviral therapy; however, antiretroviral trials in ALS down-regulate HML-2 without ameliorating the disease. This highlights the need for specific drugs to be developed against HML-2 as a novel therapeutic target for ALS. Other approaches might include antisense oligonucleotides, shRNA targeted against the envelope gene or antibodies that can target the extracellular envelope protein. Future clinical trials in ALS should consider combination therapies to control these ERVs.
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Affiliation(s)
- Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Darshan Pandya
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Nicholas Pasternack
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Marta Garcia-Montojo
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Lisa Henderson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Christine A Kozak
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
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220
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Chang NC, Rovira Q, Wells J, Feschotte C, Vaquerizas JM. Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression. Genome Res 2022; 32:1408-1423. [PMID: 34987056 PMCID: PMC9341512 DOI: 10.1101/gr.275655.121] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/30/2021] [Indexed: 12/02/2022]
Abstract
There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos and by the relative scarcity of active TEs in these organisms. The zebrafish is an outstanding model for the study of vertebrate development, and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whereas short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. Although two-thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage- and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched among transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides a valuable resource for using zebrafish as a model to study the impact of TEs on vertebrate development.
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Affiliation(s)
- Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Quirze Rovira
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
| | - Jonathan Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
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221
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Yu X, Liang S, Chen M, Yu H, Li R, Qu Y, Kong X, Guo R, Zheng R, Izsvák Z, Sun C, Yang M, Wang J. Recapitulating early human development with 8C-like cells. Cell Rep 2022; 39:110994. [PMID: 35732112 DOI: 10.1016/j.celrep.2022.110994] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/21/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
In human embryos, major zygotic genome activation (ZGA) initiates at the eight-cell (8C) stage. Abnormal ZGA leads to developmental defects and even contributes to the failure of human blastocyst formation or implantation. An in vitro cell model mimicking human 8C blastomeres would be invaluable to understanding the mechanisms regulating key biological events during early human development. Using the non-canonical promoter of LEUTX that putatively regulates human ZGA, we developed an 8C::mCherry reporter, which specifically marks the 8C state, to isolate rare 8C-like cells (8CLCs) from human preimplantation epiblast-like stem cells. The 8CLCs express a panel of human ZGA genes and have a unique transcriptome resembling that of the human 8C embryo. Using the 8C::mCherry reporter, we further optimize the chemical-based culture condition to increase and maintain the 8CLC population. Functionally, 8CLCs can self-organize to form blastocyst-like structures. The discovery and maintenance of 8CLCs provide an opportunity to recapitulate early human development.
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Affiliation(s)
- Xiu Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Shiqi Liang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Manqi Chen
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Hanwen Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Ruiqi Li
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yuliang Qu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Xuhui Kong
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Ruirui Guo
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Rongyan Zheng
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China.
| | - Mingzhu Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
| | - Jichang Wang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China.
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222
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Suleiman M, Kounosu A, Murcott B, Dayi M, Pawluk R, Yoshida A, Viney M, Kikuchi T, Hunt VL. piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode. Sci Rep 2022; 12:10156. [PMID: 35710810 PMCID: PMC9203780 DOI: 10.1038/s41598-022-14247-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/03/2022] [Indexed: 12/02/2022] Open
Abstract
The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the C. elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway. Here, we investigated the role of sRNAs in the Clade IV parasitic nematode Strongyloides ratti by comparing two genetically identical adult stages (the parasitic female and free-living female). We identified putative small-interfering RNAs, microRNAs and tRNA-derived sRNA fragments that are differentially expressed between the two adult stages. Two classes of sRNAs were predicted to regulate TE activity including (i) a parasite-associated class of 21-22 nt long sRNAs with a 5' uridine (21-22Us) and a 5' monophosphate, and (ii) 27 nt long sRNAs with a 5' guanine/adenine (27GAs) and a 5' modification. The 21-22Us show striking resemblance to the 21U PIWI-interacting RNAs found in C. elegans, including an AT rich upstream sequence, overlapping loci and physical clustering in the genome. Overall, we have shown that an alternative class of sRNAs compensate for the loss of piRNAs and regulate TE activity in nematodes outside of Clade V.
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Affiliation(s)
- Mona Suleiman
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Asuka Kounosu
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Ben Murcott
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Mehmet Dayi
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
- Forestry Vocational School, Duzce University, 81620, Duzce, Turkey
| | - Rebecca Pawluk
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Akemi Yoshida
- Laboratory of Genomics, Frontier Science Research Center, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Taisei Kikuchi
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan.
| | - Vicky L Hunt
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
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223
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Bonté PE, Arribas YA, Merlotti A, Carrascal M, Zhang JV, Zueva E, Binder ZA, Alanio C, Goudot C, Amigorena S. Single-cell RNA-seq-based proteogenomics identifies glioblastoma-specific transposable elements encoding HLA-I-presented peptides. Cell Rep 2022; 39:110916. [PMID: 35675780 DOI: 10.1016/j.celrep.2022.110916] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/22/2022] [Accepted: 05/12/2022] [Indexed: 11/03/2022] Open
Abstract
We analyze transposable elements (TEs) in glioblastoma (GBM) patients using a proteogenomic pipeline that combines single-cell transcriptomics, bulk RNA sequencing (RNA-seq) samples from tumors and healthy-tissue cohorts, and immunopeptidomic samples. We thus identify 370 human leukocyte antigen (HLA)-I-bound peptides encoded by TEs differentially expressed in GBM. Some of the peptides are encoded by repeat sequences from intact open reading frames (ORFs) present in up to several hundred TEs from recent long interspersed nuclear element (LINE)-1, long terminal repeat (LTR), and SVA subfamilies. Other HLA-I-bound peptides are encoded by single copies of TEs from old subfamilies that are expressed recurrently in GBM tumors and not expressed, or very infrequently and at low levels, in healthy tissues (including brain). These peptide-coding, GBM-specific, highly recurrent TEs represent potential tumor-specific targets for cancer immunotherapies.
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Affiliation(s)
- Pierre-Emmanuel Bonté
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Yago A Arribas
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Antonela Merlotti
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona-CSIC, IDIBAPS, Roselló 161, 6a planta, 08036 Barcelona, Spain
| | - Jiasi Vicky Zhang
- GBM Translational Center of Excellence, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elina Zueva
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Zev A Binder
- GBM Translational Center of Excellence, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cécile Alanio
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France; Laboratoire d'Immunologie Clinique, Institut Curie, Paris 75005, France; Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Christel Goudot
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France.
| | - Sebastian Amigorena
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France.
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224
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Dang Y, Li S, Zhao P, Xiao L, Wang L, Shi Y, Luo L, Wang S, Wang H, Zhang K. The lysine deacetylase activity of histone deacetylases 1 and 2 is required to safeguard zygotic genome activation in mice and cattle. Development 2022; 149:275603. [PMID: 35575026 DOI: 10.1242/dev.200854] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/03/2022] [Indexed: 12/15/2022]
Abstract
The genome is transcriptionally inert at fertilization and must be activated through a remarkable developmental process called zygotic genome activation (ZGA). Epigenetic reprogramming contributes significantly to the dynamic gene expression during ZGA; however, the mechanism has yet to be resolved. Here, we find histone deacetylases 1 and 2 (HDAC1/2) can regulate ZGA through lysine deacetylase activity. Notably, in mouse embryos, overexpression of a HDAC1/2 dominant-negative mutant leads to developmental arrest at the two-cell stage. RNA-seq reveals that 64% of downregulated genes are ZGA genes and 49% of upregulated genes are developmental genes. Inhibition of the deacetylase activity of HDAC1/2 causes a failure of histone deacetylation at multiple sites, including H4K5, H4K16, H3K14, H3K18 and H3K27. ChIP-seq analysis exhibits an increase and decrease of H3K27ac enrichment at promoters of up- and downregulated genes, respectively. Moreover, HDAC1 mutants prohibit the removal of H3K4me3 by impeding expression of Kdm5 genes. Importantly, the developmental block can be greatly rescued by Kdm5b injection and by partially correcting the expression of the majority of dysregulated genes. Similar functional significance of HDAC1/2 is conserved in bovine embryos. Overall, we propose that HDAC1/2 are indispensable for ZGA by creating correct transcriptional repressive and active states in mouse and bovine embryos.
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Affiliation(s)
- Yanna Dang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuang Li
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Panpan Zhao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lieying Xiao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lefeng Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Department of Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Shi
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Luo
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohua Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huanan Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Department of Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
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225
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Alam SS, Kumar S, Beauchamp MC, Bareke E, Boucher A, Nzirorera N, Dong Y, Padilla R, Zhang SJ, Majewski J, Jerome-Majewska LA. Snrpb is required in murine neural crest cells for proper splicing and craniofacial morphogenesis. Dis Model Mech 2022; 15:275486. [PMID: 35593225 PMCID: PMC9235875 DOI: 10.1242/dmm.049544] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/05/2022] [Indexed: 12/18/2022] Open
Abstract
Heterozygous mutations in SNRPB, an essential core component of the five small ribonucleoprotein particles of the spliceosome, are responsible for cerebrocostomandibular syndrome (CCMS). We show that Snrpb heterozygous mouse embryos arrest shortly after implantation. Additionally, heterozygous deletion of Snrpb in the developing brain and neural crest cells models craniofacial malformations found in CCMS, and results in death shortly after birth. RNAseq analysis of mutant heads prior to morphological defects revealed increased exon skipping and intron retention in association with increased 5′ splice site strength. We found increased exon skipping in negative regulators of the P53 pathway, along with increased levels of nuclear P53 and P53 target genes. However, removing Trp53 in Snrpb heterozygous mutant neural crest cells did not completely rescue craniofacial development. We also found a small but significant increase in exon skipping of several transcripts required for head and midface development, including Smad2 and Rere. Furthermore, mutant embryos exhibited ectopic or missing expression of Fgf8 and Shh, which are required to coordinate face and brain development. Thus, we propose that mis-splicing of transcripts that regulate P53 activity and craniofacial-specific genes contributes to craniofacial malformations. This article has an associated First Person interview with the first author of the paper. Summary: We report the first mouse model for cerebrocostomandibular syndrome, showing that mis-splicing of transcripts that regulate P53 activity and craniofacial-specific genes contributes to craniofacial malformations.
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Affiliation(s)
- Sabrina Shameen Alam
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada.,Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Shruti Kumar
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada.,Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Marie-Claude Beauchamp
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada
| | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Alexia Boucher
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B2, Canada
| | - Nadine Nzirorera
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada.,Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Yanchen Dong
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada.,Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Reinnier Padilla
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Si Jing Zhang
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Loydie A Jerome-Majewska
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada.,Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B2, Canada.,Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada
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226
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Meng Q, Stoyko D, Andrews CM, Konstantinidou P, Genzor P, O T, Elchert AR, Benner L, Sobti S, Katz EY, Haase AD. Functional editing of endogenous genes through rapid selection of cell pools (Rapid generation of endogenously tagged genes in Drosophila ovarian somatic sheath cells). Nucleic Acids Res 2022; 50:e90. [PMID: 35639929 DOI: 10.1093/nar/gkac448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
The combination of genome-editing and epitope tagging provides a powerful strategy to study proteins with high affinity and specificity while preserving their physiological expression patterns. However, stably modifying endogenous genes in cells that do not allow for clonal selection has been challenging. Here, we present a simple and fast strategy to generate stable, endogenously tagged alleles in a non-transformed cell culture model. At the example of piwi in Drosophila ovarian somatic sheath cells, we show that this strategy enables the generation of an N-terminally tagged protein that emulates the expression level and subcellular localization of the wild type protein and forms functional Piwi-piRNA complexes. We further present a concise workflow to establish endogenously N-terminally and C-terminally tagged proteins, and knockout alleles through rapid selection of cell pools in fly and human models.
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Affiliation(s)
- Qingcai Meng
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Stoyko
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Celine Marlin Andrews
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Parthena Konstantinidou
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Pavol Genzor
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy O
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alexandra R Elchert
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leif Benner
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sushil Sobti
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Esther Y Katz
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Astrid D Haase
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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227
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Femenias MM, Santos JC, Sites JW, Avila LJ, Morando M. ExplorATE: A new pipeline to explore active transposable elements from RNA-seq data. Bioinformatics 2022; 38:3361-3366. [PMID: 35608310 DOI: 10.1093/bioinformatics/btac354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 05/03/2022] [Accepted: 05/19/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Transposable elements (TEs) are ubiquitous in genomes and many remain active. TEs comprise an important fraction of the transcriptomes with potential effects on the host genome, either by generating deleterious mutations or promoting evolutionary novelties. However, their functional study is limited by the difficulty in their identification and quantification, particularly in non-model organisms. RESULTS We developed a new pipeline (ExplorATE or Explore Active Transposable Elements) implemented in R and bash that allows the quantification of active TEs in both model and non-model organisms. ExplorATE creates TE-specific indexes and uses the Selective Alignment (SA) to filter out co-transcribed transposons within genes based on alignment scores. Moreover, our software incorporates a Wicker-like criteria to refine a set of target TEs and avoid spurious mapping. Based on simulated and real data, we show that the SA strategy adopted by ExplorATE achieved better estimates of non-co-transcribed elements than other available alignment-based or mapping-based software. ExplorATE results showed high congruence with alignment-based tools with and without a reference genome, yet ExplorATE required less execution time. Likewise, ExplorATE expands and complements most previous TE analyses by incorporating the co-transcription and multi-mapping effects during quantification, and provides a seamless integration with other downstream tools within the R environment. AVAILABILITY Source code is available at https://github.com/FemeniasM/ExplorATEproject and https://github.com/FemeniasM/ExplorATE_shell_script. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martin M Femenias
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
| | - Juan C Santos
- Department of Biological Sciences, St. John's University, Queens, NY, 11439, USA
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University (BYU), Provo, UT, 84602, USA
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
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228
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Chen TH, Winefield C. Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants. Mob DNA 2022; 13:16. [PMID: 35549762 PMCID: PMC9097378 DOI: 10.1186/s13100-022-00271-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/13/2022] [Indexed: 11/29/2022] Open
Abstract
Background Transposable element (TE) transcription is a precursor to its mobilisation in host genomes. However, the characteristics of expressed TE loci, the identification of self-competent transposon loci contributing to new insertions, and the genomic conditions permitting their mobilisation remain largely unknown. Results Using Vitis vinifera embryogenic callus, we explored the impact of biotic stressors on transposon transcription through the exposure of the callus to live cultures of an endemic grapevine yeast, Hanseniaspora uvarum. We found that only 1.7–2.5% of total annotated TE loci were transcribed, of which 5–10% of these were full-length, and the expressed TE loci exhibited a strong location bias towards expressed genes. These trends in transposon transcription were also observed in RNA-seq data from Arabidopsis thaliana wild-type plants but not in epigenetically compromised Arabidopsis ddm1 mutants. Moreover, differentially expressed TE loci in the grapevine tended to share expression patterns with co-localised differentially expressed genes. Utilising nanopore cDNA sequencing, we found a strong correlation between the inclusion of intronic TEs in gene transcripts and the presence of premature termination codons in these transcripts. Finally, we identified low levels of full-length transcripts deriving from structurally intact TE loci in the grapevine model. Conclusion Our observations in two disparate plant models representing clonally and seed propagated plant species reveal a closely connected transcriptional relationship between TEs and co-localised genes, particularly when epigenetic silencing is not compromised. We found that the stress treatment alone was insufficient to induce large-scale full-length transcription from structurally intact TE loci, a necessity for non-autonomous and autonomous mobilisation. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00271-5.
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Affiliation(s)
- Ting-Hsuan Chen
- Department of Wine, Food, and Molecular Biosciences, Lincoln University, Lincoln, 7647, New Zealand.,Present address: The New Zealand Institute for Plant and Food Research Ltd, Lincoln, 7608, New Zealand
| | - Christopher Winefield
- Department of Wine, Food, and Molecular Biosciences, Lincoln University, Lincoln, 7647, New Zealand.
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229
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Nguyen A, Wang W, Chong E, Chatla K, Bachtrog D. Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila. Genome Res 2022; 32:1074-1088. [PMID: 35501131 DOI: 10.1101/gr.275996.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 04/15/2022] [Indexed: 11/24/2022]
Abstract
Y Chromosomes of many species are gene poor and show low levels of nucleotide variation, yet often display high amounts of structural diversity. Dobzhansky cataloged several morphologically distinct Y Chromosomes in Drosophila pseudoobscura that differ in size and shape, but the molecular causes of their dramatic size differences are unclear. Here we use cytogenetics and long-read sequencing to study the sequence content of polymorphic Y Chromosomes in D. pseudoobscura We show that Y Chromosomes differ almost 2-fold in size, ranging from 30 to 60 Mb. Most of this size difference is caused by a handful of active transposable elements (TEs) that have recently expanded on the largest Y Chromosome, with different elements being responsible for Y expansion on differently sized D. pseudoobscura Y's. We show that Y Chromosomes differ in their heterochromatin enrichment, expression of Y-enriched TEs, and also influence expression of dozens of autosomal and X-linked genes. The same helitron element that showed the most drastic amplification on the largest Y in D. pseudoobscura independently amplified on a polymorphic large Y Chromosome in D. affinis, suggesting that some TEs are inherently more prone to become deregulated on Y Chromosomes.
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230
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Taylor D, Lowe R, Philippe C, Cheng KCL, Grant OA, Zabet NR, Cristofari G, Branco MR. Locus-specific chromatin profiling of evolutionarily young transposable elements. Nucleic Acids Res 2022; 50:e33. [PMID: 34908129 PMCID: PMC8989514 DOI: 10.1093/nar/gkab1232] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 01/13/2023] Open
Abstract
Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of HiChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we reveal previously unappreciated variation in the epigenetic profiles of young TE loci in mouse and human cells. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.
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Affiliation(s)
- Darren Taylor
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Robert Lowe
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | | | - Kevin C L Cheng
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Olivia A Grant
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Nicolae Radu Zabet
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | | | - Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
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231
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scTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Sci Rep 2022; 12:5776. [PMID: 35388081 PMCID: PMC8986802 DOI: 10.1038/s41598-022-09765-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/28/2022] [Indexed: 12/11/2022] Open
Abstract
Global changes in DNA methylation are observed in development and disease, and single-cell analyses are highlighting the heterogeneous regulation of these processes. However, technical challenges associated with single-cell analysis of DNA methylation limit these studies. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of average DNA methylation levels. By targeting high-copy SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of loci covered in each scTEM-seq library. Parallel transcriptome analysis is also performed to link global DNA methylation estimates with gene expression. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary AML cells. Our method reveals global DNA methylation heterogeneity induced by decitabine treatment of KG1a cells associated with altered expression of immune process genes. We also compare global DNA methylation estimates to expression of transposable elements and find a predominance of negative correlations. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated cells. By linking global DNA methylation heterogeneity with transcription, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond.
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232
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Vandewege MW, Patt RN, Merriman DK, Ray DA, Hoffmann FG. The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements. RNA (NEW YORK, N.Y.) 2022; 28:609-621. [PMID: 35064043 PMCID: PMC8925971 DOI: 10.1261/rna.078862.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Transposable elements (TEs) are genomic parasites that can propagate throughout host genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and germline mobilization is a challenge to genome integrity. There are defenses against TE proliferation and the PIWI/piRNA defense is among the most well understood. However, the PIWI/piRNA system has been investigated largely in animals with actively mobilizing TEs and it is unclear how the PIWI/piRNA system functions in the absence of mobilizing TEs. The 13-lined ground squirrel provides the opportunity to examine PIWI/piRNA and TE dynamics within the context of minimal, and possibly nonexistent, TE accumulation. To do so, we compared the PIWI/piRNA dynamics in squirrels to observations from the rabbit and mouse. Despite a lack of young insertions in squirrels, TEs were still actively transcribed at higher levels compared to mouse and rabbit. All three Piwi genes were not expressed, prior to P8 in squirrel testis, and there was little TE expression change with the onset of Piwi expression. We also demonstrated there was not a major expression change in the young squirrel LINE families in the transition from juvenile to adult testis in contrast to young mouse and rabbit LINE families. These observations lead us to conclude that PIWI suppression, was weaker for squirrel LINEs and SINEs and did not strongly reduce their transcription. We speculate that, although the PIWI/piRNA system is adaptable to novel TE threats, transcripts from TEs that are no longer threatening receive less attention from PIWI proteins.
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Affiliation(s)
- Michael W Vandewege
- Department of Biology, Eastern New Mexico University, Portales, New Mexico 88130, USA
| | - Roy N Patt
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas 78245-0549, USA
| | - Dana K Merriman
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, Wisconsin 54901, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, USA
- Institute of Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi 39762, USA
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Garland W, Müller I, Wu M, Schmid M, Imamura K, Rib L, Sandelin A, Helin K, Jensen TH. Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression. Mol Cell 2022; 82:1691-1707.e8. [PMID: 35349793 PMCID: PMC9433625 DOI: 10.1016/j.molcel.2022.03.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) are widespread genetic parasites known to be kept under tight transcriptional control. Here, we describe a functional connection between the mouse-orthologous “nuclear exosome targeting” (NEXT) and “human silencing hub” (HUSH) complexes, involved in nuclear RNA decay and the epigenetic silencing of TEs, respectively. Knocking out the NEXT component ZCCHC8 in embryonic stem cells results in elevated TE RNA levels. We identify a physical interaction between ZCCHC8 and the MPP8 protein of HUSH and establish that HUSH recruits NEXT to chromatin at MPP8-bound TE loci. However, while NEXT and HUSH both dampen TE RNA expression, their activities predominantly affect shorter non-polyadenylated and full-length polyadenylated transcripts, respectively. Indeed, our data suggest that the repressive action of HUSH promotes a condition favoring NEXT RNA decay activity. In this way, transcriptional and post-transcriptional machineries synergize to suppress the genotoxic potential of TE RNAs. Garland et al. report a physical and functional connection between the NEXT complex, involved in RNA decay, and the HUSH complex, involved in chromatin regulation. Together, NEXT and HUSH cooperate to control transposable element (TE) RNA expression in embryonic stem cells, suppressing pA− and pA+ transcripts, respectively.
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Affiliation(s)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iris Müller
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mengjun Wu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Leonor Rib
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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234
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Hansen AM, Ge Y, Schuster MB, Pundhir S, Jakobsen JS, Kalvisa A, Tapia MC, Gordon S, Ambri F, Bagger FO, Pandey D, Helin K, Porse BT. H3K9 dimethylation safeguards cancer cells against activation of the interferon pathway. SCIENCE ADVANCES 2022; 8:eabf8627. [PMID: 35302840 PMCID: PMC8932663 DOI: 10.1126/sciadv.abf8627] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Activation of interferon genes constitutes an important anticancer pathway able to restrict proliferation of cancer cells. Here, we demonstrate that the H3K9me3 histone methyltransferase (HMT) suppressor of variegation 3-9 homolog 1 (SUV39H1) is required for the proliferation of acute myeloid leukemia (AML) and find that its loss leads to activation of the interferon pathway. Mechanistically, we show that this occurs via destabilization of a complex composed of SUV39H1 and the two H3K9me2 HMTs, G9A and GLP. Indeed, loss of H3K9me2 correlated with the activation of key interferon pathway genes, and interference with the activities of G9A/GLP largely phenocopied loss of SUV39H1. Last, we demonstrate that inhibition of G9A/GLP synergized with DNA demethylating agents and that SUV39H1 constitutes a potential biomarker for the response to hypomethylation treatment. Collectively, we uncovered a clinically relevant role for H3K9me2 in safeguarding cancer cells against activation of the interferon pathway.
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Affiliation(s)
- Anne Meldgaard Hansen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ying Ge
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mikkel Bruhn Schuster
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sachin Pundhir
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Janus Schou Jakobsen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Adrija Kalvisa
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Marta Cecylia Tapia
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sandra Gordon
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Francesca Ambri
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Frederik Otzen Bagger
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Deo Pandey
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Microbiology, Oslo University Hospital, NO-0373 Oslo, Norway
| | - Kristian Helin
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Center, New York, NY 10065, USA
- The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Bo Torben Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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235
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LncRNA Biomarkers of Inflammation and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:121-145. [PMID: 35220568 DOI: 10.1007/978-3-030-92034-0_7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are promising candidates as biomarkers of inflammation and cancer. LncRNAs have several properties that make them well-suited as molecular markers of disease: (1) many lncRNAs are expressed in a tissue-specific manner, (2) distinct lncRNAs are upregulated based on different inflammatory or oncogenic stimuli, (3) lncRNAs released from cells are packaged and protected in extracellular vesicles, and (4) circulating lncRNAs in the blood are detectable using various RNA sequencing approaches. Here we focus on the potential for lncRNA biomarkers to detect inflammation and cancer, highlighting key biological, technological, and analytical considerations that will help advance the development of lncRNA-based liquid biopsies.
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236
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Sin JH, Kashyap S, Acenas D, Cortez JT, Lee J, Marson A, Matloubian M, Waterfield MR. ATF7ip Targets Transposable Elements for H3K9me3 Deposition to Modify CD8 + T Cell Effector and Memory Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1155-1169. [PMID: 35110421 PMCID: PMC8881383 DOI: 10.4049/jimmunol.2100996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/18/2021] [Indexed: 11/19/2022]
Abstract
CD8+ T cells are critical for the immune response to pathogens and tumors, and CD8+ T cell memory protects against repeat infections. In this study, we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of CD8+ T cell immune responses. Mice with a T cell-specific deletion of ATF7ip have a CD8+ T cell-intrinsic enhancement of Il7r expression and Il2 expression leading to enhanced effector and memory responses. Chromatin immunoprecipitation sequencing studies identified ATF7ip as a repressor of Il7r and Il2 gene expression through the deposition of the repressive histone mark H3K9me3 at the Il7r gene and Il2-Il21 intergenic region. Interestingly, ATF7ip targeted transposable elements for H3K9me3 deposition at both the IL7r locus and the Il2-Il21 intergenic region, indicating that ATF7ip silencing of transposable elements is important for regulating CD8+ T cell function. These results demonstrate a new epigenetic pathway by which IL-7R and IL-2 production are constrained in CD8+ T cells, and this may open up new avenues for modulating their production.
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Affiliation(s)
- Jun Hyung Sin
- Division of Pediatric Rheumatology, University of California San Francisco, San Francisco, CA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA
| | - Sujit Kashyap
- Division of Pediatric Rheumatology, University of California San Francisco, San Francisco, CA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - Dante Acenas
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Jessica T Cortez
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - James Lee
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA
- Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Alexander Marson
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- J. David Gladstone Institutes, San Francisco, CA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA; and
| | - Mehrdad Matloubian
- Department of Medicine, University of California San Francisco, San Francisco, CA
- Division of Rheumatology, University of California San Francisco, San Francisco, CA
| | - Michael R Waterfield
- Division of Pediatric Rheumatology, University of California San Francisco, San Francisco, CA;
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA
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237
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Dicer promotes genome stability via the bromodomain transcriptional co-activator BRD4. Nat Commun 2022; 13:1001. [PMID: 35194019 PMCID: PMC8863982 DOI: 10.1038/s41467-022-28554-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
RNA interference is required for post-transcriptional silencing, but also has additional roles in transcriptional silencing of centromeres and genome stability. However, these roles have been controversial in mammals. Strikingly, we found that Dicer-deficient embryonic stem cells have strong proliferation and chromosome segregation defects as well as increased transcription of centromeric satellite repeats, which triggers the interferon response. We conducted a CRISPR-Cas9 genetic screen to restore viability and identified transcriptional activators, histone H3K9 methyltransferases, and chromosome segregation factors as suppressors, resembling Dicer suppressors identified in independent screens in fission yeast. The strongest suppressors were mutations in the transcriptional co-activator Brd4, which reversed the strand-specific transcription of major satellite repeats suppressing the interferon response, and in the histone acetyltransferase Elp3. We show that identical mutations in the second bromodomain of Brd4 rescue Dicer-dependent silencing and chromosome segregation defects in both mammalian cells and fission yeast. This remarkable conservation demonstrates that RNA interference has an ancient role in transcriptional silencing and in particular of satellite repeats, which is essential for cell cycle progression and proper chromosome segregation. Our results have pharmacological implications for cancer and autoimmune diseases characterized by unregulated transcription of satellite repeats. While RNA interference is conserved across species, small RNA pathways are very diverse. In this study, Gutbrod et al. find that non-canonical roles of Dicer in genome stability are in fact deeply conserved from yeast to humans.
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238
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McGlacken-Byrne SM, Del Valle I, Le Quesne Stabej P, Bellutti L, Garcia-Alonso L, Ocaka LA, Ishida M, Suntharalingham JP, Gagunashvili A, Ogunbiyi OK, Mistry T, Buonocore F, Crespo B, Moreno N, Niola P, Brooks T, Brain CE, Dattani MT, Kelberman D, Vento-Tormo R, Lagos CF, Livera G, Conway GS, Achermann JC. Pathogenic variants in the human m6A reader YTHDC2 are associated with primary ovarian insufficiency. JCI Insight 2022; 7:154671. [PMID: 35138268 PMCID: PMC8983136 DOI: 10.1172/jci.insight.154671] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Primary ovarian insufficiency (POI) affects 1% of women and carries significant medical and psychosocial sequelae. Approximately 10% of POI has a defined genetic cause, with most implicated genes relating to biological processes involved in early fetal ovary development and function. Recently, Ythdc2, an RNA helicase and N6-methyladenosine (m6a) reader, has emerged as a novel regulator of meiosis in mice. Here, we describe homozygous pathogenic variants in YTHDC2 in three women with early-onset POI from two families: c. 2567C>G, p.P856R in the helicase-associated (HA2) domain; and c.1129G>T, p.E377*. We demonstrate that YTHDC2 is expressed in the developing human fetal ovary and is upregulated in meiotic germ cells, together with related meiosis-associated factors. The p.P856R variant results in a less flexible protein that likely disrupts downstream conformational kinetics of the HA2 domain, whereas the p.E377* variant truncates the helicase core. Taken together, our results reveal that YTHDC2 is a key new regulator of meiosis in humans and pathogenic variants within this gene are associated with POI.
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Affiliation(s)
- Sinead M McGlacken-Byrne
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ignacio Del Valle
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Polona Le Quesne Stabej
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Laura Bellutti
- Laboratory of Development of the Gonads, UMR E008, Université de Paris, Université Paris Saclay, CEA, Fontenay aux Roses, France
| | - Luz Garcia-Alonso
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Louise A Ocaka
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Miho Ishida
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Jenifer P Suntharalingham
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Andrey Gagunashvili
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Olumide K Ogunbiyi
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Talisa Mistry
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Federica Buonocore
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Berta Crespo
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child health, London, United Kingdom
| | - Nadjeda Moreno
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Paola Niola
- UCL Genomics, Zayed Centre for Research, London, United Kingdom
| | - Tony Brooks
- UCL Genomics, Zayed Centre for Research, London, United Kingdom
| | - Caroline E Brain
- Department of Paediatric Endocrinology, Great Ormond Street Hospital, London, United Kingdom
| | - Mehul T Dattani
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Daniel Kelberman
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Carlos F Lagos
- Chemical Biology & Drug Discovery Lab, Escuela de Química y Farmacia, Universidad San Sebastián, Santiago, Chile
| | - Gabriel Livera
- Laboratory of Development of the Gonads, UMR E008, Université de Paris, Université Paris Saclay, CEA, Fontenay aux Roses, France
| | - Gerard S Conway
- Institute for Women's Health, University College London, London, United Kingdom
| | - John C Achermann
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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239
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Freeman B, White T, Kaul T, Stow EC, Baddoo M, Ungerleider N, Morales M, Yang H, Deharo D, Deininger P, Belancio V. Analysis of epigenetic features characteristic of L1 loci expressed in human cells. Nucleic Acids Res 2022; 50:1888-1907. [PMID: 35100410 PMCID: PMC8887483 DOI: 10.1093/nar/gkac013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 12/27/2021] [Accepted: 01/24/2022] [Indexed: 12/26/2022] Open
Abstract
Only a select few L1 loci in the human genome are expressed in any given cell line or organ, likely to minimize damage done to the genome. The epigenetic features and requirements of expressed L1 loci are currently unknown. Using human cells and comprehensive epigenetic analysis of individual expressed and unexpressed L1 loci, we determined that endogenous L1 transcription depends on a combination of epigenetic factors, including open chromatin, activating histone modifications, and hypomethylation at the L1 promoter. We demonstrate that the L1 promoter seems to require interaction with enhancer elements for optimal function. We utilize epigenetic context to predict the expression status of L1Hs loci that are poorly mappable with RNA-Seq. Our analysis identified a population of ‘transitional’ L1 loci that likely have greater potential to be activated during the epigenetic dysregulation seen in tumors and during aging because they are the most responsive to targeted CRISPR-mediated delivery of trans-activating domains. We demonstrate that an engineered increase in endogenous L1 mRNA expression increases Alu mobilization. Overall, our findings present the first global and comprehensive analysis of epigenetic status of individual L1 loci based on their expression status and demonstrate the importance of epigenetic context for L1 expression heterogeneity.
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Affiliation(s)
- Benjamin Freeman
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Travis White
- Sloan Kettering Institute for Cancer Research, NY, NY 10065, USA
| | - Tiffany Kaul
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Emily C Stow
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Melody Baddoo
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Maria Morales
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Hanlin Yang
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Dawn Deharo
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Prescott Deininger
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- To whom correspondence should be addressed. Tel: +1 504 988 4506; Fax: +1 504 988 1687;
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240
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Xiang X, Tao Y, DiRusso J, Hsu FM, Zhang J, Xue Z, Pontis J, Trono D, Liu W, Clark AT. Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. Nat Commun 2022; 13:463. [PMID: 35075135 PMCID: PMC8786967 DOI: 10.1038/s41467-022-28105-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/16/2021] [Indexed: 12/26/2022] Open
Abstract
Germ cells are essential to pass DNA from one generation to the next. In human reproduction, germ cell development begins with the specification of primordial germ cells (PGCs) and a failure to specify PGCs leads to human infertility. Recent studies have revealed that the transcription factor network required for PGC specification has diverged in mammals, and this has a significant impact on our understanding of human reproduction. Here, we reveal that the Hominidae-specific Transposable Elements (TEs) LTR5Hs, may serve as TEENhancers (TE Embedded eNhancers) to facilitate PGC specification. LTR5Hs TEENhancers become transcriptionally active during PGC specification both in vivo and in vitro with epigenetic reprogramming leading to increased chromatin accessibility, localized DNA demethylation, enrichment of H3K27ac, and occupation of key hPGC transcription factors. Inactivation of LTR5Hs TEENhancers with KRAB mediated CRISPRi has a significant impact on germ cell specification. In summary, our data reveals the essential role of Hominidae-specific LTR5Hs TEENhancers in human germ cell development. The transcription factor network required for primordial germ cell (PGC) specification is known to diverge in mammals. Here the authors show that hominidae-specific transposable element (TE) LTR5Hs becomes transcriptionally active during PGC specification, and LTR5Hs inactivation abrogates human PGC specification
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Affiliation(s)
- Xinyu Xiang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Yu Tao
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jonathan DiRusso
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fei-Man Hsu
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jinchun Zhang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Ziwei Xue
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fe ́de ́rale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fe ́de ́rale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China. .,Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310029, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China. .,Alibaba-Zhejiang University Joint Research Center of Future DigitalHealthcare, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Amander T Clark
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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241
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Hwang T, Kim S, Chowdhury T, Yu HJ, Kim KM, Kang H, Won JK, Park SH, Shin JH, Park CK. Genome-wide perturbations of Alu expression and Alu-associated post-transcriptional regulations distinguish oligodendroglioma from other gliomas. Commun Biol 2022; 5:62. [PMID: 35042936 PMCID: PMC8766575 DOI: 10.1038/s42003-022-03011-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 12/27/2021] [Indexed: 01/09/2023] Open
Abstract
AbstractAlu is a primate-specific repeat element in the human genome and has been increasingly appreciated as a regulatory element in many biological processes. But the appreciation of Alu has been limited in tumorigenesis, especially for brain tumor. To investigate the relevance of Alu to the gliomagenesis, we studied Alu element-associated post-transcriptional processes and the RNA expression of the element by performing RNA-seq for a total of 41 pairs of neurotypical and diverse glioma brain tissues. We find that A-to-I editing and circular RNA levels, as well as Alu RNA expression, are decreased overall in gliomas, compared to normal tissue. Interestingly, grade 2 oligodendrogliomas are least affected in A-to-I editing and circular RNA levels among gliomas, whereas they have a higher proportion of down-regulated Alu subfamilies, compared to the other gliomas. These findings collectively imply a unique pattern of Alu-associated transcriptomes in grade 2 oligodendroglioma, providing an insight to gliomagenesis from the perspective of an evolutionary genetic element.
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242
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Wang C, Liang C. The insertion and dysregulation of transposable elements in osteosarcoma and their association with patient event-free survival. Sci Rep 2022; 12:377. [PMID: 35013466 PMCID: PMC8748539 DOI: 10.1038/s41598-021-04208-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022] Open
Abstract
The dysregulation of transposable elements (TEs) has been explored in a variety of cancers. However, TE activities in osteosarcoma (OS) have not been extensively studied yet. By integrative analysis of RNA-seq, whole-genome sequencing (WGS), and methylation data, we showed aberrant TE activities associated with dysregulations of TEs in OS tumors. Specifically, expression levels of LINE-1 and Alu of different evolutionary ages, as well as subfamilies of SVA and HERV-K, were significantly up-regulated in OS tumors, accompanied by enhanced DNA repair responses. We verified the characteristics of LINE-1 mediated TE insertions, including target site duplication (TSD) length (centered around 15 bp) and preferential insertions into intergenic and AT-rich regions as well as intronic regions of longer genes. By filtering polymorphic TE insertions reported in 1000 genome project (1KGP), besides 148 tumor-specific somatic TE insertions, we found most OS patient-specific TE insertions (3175 out of 3326) are germline insertions, which are associated with genes involved in neuronal processes or with transcription factors important for cancer development. In addition to 68 TE-affected cancer genes, we found recurrent germline TE insertions in 72 non-cancer genes with high frequencies among patients. We also found that +/− 500 bps flanking regions of transcription start sites (TSS) of LINE-1 (young) and Alu showed lower methylation levels in OS tumor samples than controls. Interestingly, by incorporating patient clinical data and focusing on TE activities in OS tumors, our data analysis suggested that higher TE insertions in OS tumors are associated with a longer event-free survival time.
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Affiliation(s)
- Chao Wang
- Department of Biology, Miami University, Oxford, Ohio, 45056, USA.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, Ohio, 45056, USA.
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243
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Matkovic R, Morel M, Lanciano S, Larrous P, Martin B, Bejjani F, Vauthier V, Hansen MMK, Emiliani S, Cristofari G, Gallois-Montbrun S, Margottin-Goguet F. TASOR epigenetic repressor cooperates with a CNOT1 RNA degradation pathway to repress HIV. Nat Commun 2022; 13:66. [PMID: 35013187 PMCID: PMC8748822 DOI: 10.1038/s41467-021-27650-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/30/2021] [Indexed: 12/17/2022] Open
Abstract
The Human Silencing Hub (HUSH) complex constituted of TASOR, MPP8 and Periphilin recruits the histone methyl-transferase SETDB1 to spread H3K9me3 repressive marks across genes and transgenes in an integration site-dependent manner. The deposition of these repressive marks leads to heterochromatin formation and inhibits gene expression, but the underlying mechanism is not fully understood. Here, we show that TASOR silencing or HIV-2 Vpx expression, which induces TASOR degradation, increases the accumulation of transcripts derived from the HIV-1 LTR promoter at a post-transcriptional level. Furthermore, using a yeast 2-hybrid screen, we identify new TASOR partners involved in RNA metabolism including the RNA deadenylase CCR4-NOT complex scaffold CNOT1. TASOR and CNOT1 synergistically repress HIV expression from its LTR. Similar to the RNA-induced transcriptional silencing complex found in fission yeast, we show that TASOR interacts with the RNA exosome and RNA Polymerase II, predominantly under its elongating state. Finally, we show that TASOR facilitates the association of RNA degradation proteins with RNA polymerase II and is detected at transcriptional centers. Altogether, we propose that HUSH operates at the transcriptional and post-transcriptional levels to repress HIV proviral expression.
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Affiliation(s)
- Roy Matkovic
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France.
| | - Marina Morel
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | | | - Pauline Larrous
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Benjamin Martin
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Fabienne Bejjani
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Virginie Vauthier
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, 6525 AM, Nijmegen, The Netherlands
| | - Stéphane Emiliani
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
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244
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Bakoulis S, Krautz R, Alcaraz N, Salvatore M, Andersson R. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2111-2127. [PMID: 35166831 PMCID: PMC8887488 DOI: 10.1093/nar/gkac088] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 01/22/2022] [Accepted: 01/27/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Nicolas Alcaraz
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Marco Salvatore
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Robin Andersson
- To whom correspondence should be addressed. Tel: +45 35330245;
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245
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Haase AD. An introduction to PIWI-interacting RNAs (piRNAs) in the context of metazoan small RNA silencing pathways. RNA Biol 2022; 19:1094-1102. [PMID: 36217279 PMCID: PMC9559041 DOI: 10.1080/15476286.2022.2132359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022] Open
Abstract
PIWI proteins and their associated PIWI-interacting RNAs (piRNAs) constitute a small RNA-based adaptive immune system that restricts the deleterious activity of mobile genetic elements to protect genome integrity. Self/nonself discrimination is at the very core of successful defence and relies on complementary base-pairing in RNA-guided immunity. How the millions of piRNA sequences faithfully discriminate between self and nonself and how they adapt to novel genomic invaders remain key outstanding questions in genome biology. This review aims to introduce principles of piRNA silencing in the context of metazoan small RNA pathways. A distinct feature of piRNAs is their origin from single-stranded instead of double-stranded RNA precursors, and piRNAs require a unique set of processing factors. Novel nucleases, helicases and RNA binding proteins have been identified in piRNA biology, and while we are starting to understand some mechanisms of piRNA biogenesis and function, this diverse and prolific class of small RNAs remains full of surprises.
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Affiliation(s)
- Astrid D. Haase
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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246
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Ramirez P, Zuniga G, Sun W, Beckmann A, Ochoa E, DeVos SL, Hyman B, Chiu G, Roy ER, Cao W, Orr M, Buggia-Prevot V, Ray WJ, Frost B. Pathogenic tau accelerates aging-associated activation of transposable elements in the mouse central nervous system. Prog Neurobiol 2022; 208:102181. [PMID: 34670118 PMCID: PMC8712387 DOI: 10.1016/j.pneurobio.2021.102181] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 01/03/2023]
Abstract
Transposable elements comprise almost half of the mammalian genome. A growing body of evidence suggests that transposable element dysregulation accompanies brain aging and neurodegenerative disorders, and that transposable element activation is neurotoxic. Recent studies have identified links between pathogenic forms of tau, a protein that accumulates in Alzheimer's disease and related "tauopathies," and transposable element-induced neurotoxicity. Starting with transcriptomic analyses, we find that age- and tau-induced transposable element activation occurs in the mouse brain. Among transposable elements that are activated at the RNA level in the context of brain aging and tauopathy, we find that the endogenous retrovirus (ERV) class of retrotransposons is particularly enriched. We show that protein encoded by Intracisternal A-particle, a highly active mouse ERV, is elevated in brains of tau transgenic mice. Using two complementary approaches, we find that brains of tau transgenic mice contain increased DNA copy number of transposable elements, raising the possibility that these elements actively retrotranspose in the context of tauopathy. Taken together, our study lays the groundwork for future mechanistic studies focused on transposable element regulation in the aging mouse brain and in mouse models of tauopathy and provides support for ongoing therapeutic efforts targeting transposable element activation in patients with Alzheimer's disease.
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Affiliation(s)
- Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Gabrielle Zuniga
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Wenyan Sun
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Adrian Beckmann
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Elizabeth Ochoa
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Sarah L. DeVos
- Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Bradley Hyman
- Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Gabriel Chiu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX
| | - Ethan R. Roy
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX
| | - Wei Cao
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX
| | - Miranda Orr
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC,WG Hefner VA Medical Center, Salisbury, NC
| | - Virginie Buggia-Prevot
- The Neurodegeneration Consortium, Therapeutics Discovery Division, University of Texas MD Anderson Cancer Center, Houston, TX
| | - William J. Ray
- The Neurodegeneration Consortium, Therapeutics Discovery Division, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas,Corresponding Author and Lead Contact: Bess Frost, Ph.D., Associate Professor, 4939 Charles Katz, Barshop Institute, rm 1041, University of Texas Health San Antonio, San Antonio, TX 78229, Phone: 210-562-5037,
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247
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Valdebenito-Maturana B, Guatimosim C, Carrasco MA, Tapia JC. Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE. Int J Mol Sci 2021; 22:ijms222413623. [PMID: 34948421 PMCID: PMC8708317 DOI: 10.3390/ijms222413623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Spatial transcriptomics (ST) is transforming the way we can study gene expression and its regulation through position-specific resolution within tissues. However, as in bulk RNA-Seq, transposable elements (TEs) are not being studied due to their highly repetitive nature. In recent years, TEs have been recognized as important regulators of gene expression, and thus, TE expression analysis in a spatially resolved manner could further help to understand their role in gene regulation within tissues. We present SpatialTE, a tool to analyze TE expression from ST datasets and show its application in somatic and diseased tissues. The results indicate that TEs have spatially regulated expression patterns and that their expression profiles are spatially altered in ALS disease, indicating that TEs might perform differential regulatory functions within tissue organs. We have made SpatialTE publicly available as open-source software under an MIT license.
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Affiliation(s)
- Braulio Valdebenito-Maturana
- Núcleo Científico Multidisciplinario, School of Medicine, Universidad de Talca, Campus Talca, Talca 3460000, Chile;
| | - Cristina Guatimosim
- Departamento de Morfologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
| | - Mónica Alejandra Carrasco
- School of Medicine, Universidad de Talca, Campus Talca, Talca 3460000, Chile
- Correspondence: (M.A.C.); (J.C.T.)
| | - Juan Carlos Tapia
- School of Medicine, Universidad de Talca, Campus Talca, Talca 3460000, Chile
- Correspondence: (M.A.C.); (J.C.T.)
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248
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Chen Z, Xie Z, Zhang Y. DPPA2 and DPPA4 are dispensable for mouse zygotic genome activation and pre-implantation development. Development 2021; 148:dev200178. [PMID: 34878123 PMCID: PMC8722388 DOI: 10.1242/dev.200178] [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] [Received: 09/08/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022]
Abstract
How maternal factors in oocytes initiate zygotic genome activation (ZGA) remains elusive in mammals, partly due to the challenge of de novo identification of key factors using scarce materials. Two-cell (2C)-like cells have been widely used as an in vitro model in order to understand mouse ZGA and totipotency because of their expression of a group of two-cell embryo-specific genes and their simplicity for genetic manipulation. Recent studies indicate that DPPA2 and DPPA4 are required for establishing the 2C-like state in mouse embryonic stem cells in a DUX-dependent manner. These results suggest that DPPA2 and DPPA4 are essential maternal factors that regulate Dux and ZGA in embryos. By analyzing maternal knockout and maternal-zygotic knockout embryos, we unexpectedly found that DPPA2 and DPPA4 are dispensable for Dux activation, ZGA and pre-implantation development. Our study suggests that 2C-like cells do not fully recapitulate two-cell embryos in terms of regulation of two-cell embryo-specific genes, and, therefore, caution should be taken when studying ZGA and totipotency using 2C-like cells as the model system.
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Affiliation(s)
- Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Zhenfei Xie
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Harvard Stem Cell Institute, WAB-149G, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
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Puri D, Koschorz B, Engist B, Onishi-Seebacher M, Ryan D, Soujanya M, Montavon T. Foxd3 controls heterochromatin-mediated repression of repeat elements and 2-cell state transcription. EMBO Rep 2021; 22:e53180. [PMID: 34605600 PMCID: PMC8647145 DOI: 10.15252/embr.202153180] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/18/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Repeat element transcription plays a vital role in early embryonic development. The expression of repeats such as MERVL characterises mouse embryos at the 2‐cell stage and defines a 2‐cell‐like cell (2CLC) population in a mouse embryonic stem cell culture. Repeat element sequences contain binding sites for numerous transcription factors. We identify the forkhead domain transcription factor FOXD3 as a regulator of major satellite repeats and MERVL transcription in mouse embryonic stem cells. FOXD3 binds to and recruits the histone methyltransferase SUV39H1 to MERVL and major satellite repeats, consequentially repressing the transcription of these repeats by the establishment of the H3K9me3 heterochromatin modification. Notably, depletion of FOXD3 leads to the de‐repression of MERVL and major satellite repeats as well as a subset of genes expressed in the 2‐cell state, shifting the balance between the stem cell and 2‐cell‐like population in culture. Thus, FOXD3 acts as a negative regulator of repeat transcription, ascribing a novel function to this transcription factor.
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Affiliation(s)
- Deepika Puri
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany.,National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Birgit Koschorz
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Bettina Engist
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Megumi Onishi-Seebacher
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Devon Ryan
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Thomas Montavon
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
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Dallaire A, Manley BF, Wilkens M, Bista I, Quan C, Evangelisti E, Bradshaw CR, Ramakrishna NB, Schornack S, Butter F, Paszkowski U, Miska EA. Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis. Genome Res 2021; 31:2290-2302. [PMID: 34772700 PMCID: PMC8647823 DOI: 10.1101/gr.275752.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/16/2021] [Indexed: 11/29/2022]
Abstract
Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species. AM fungi have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements for generating such genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families. Whole-genome epigenomic profiling of R. irregularis provides direct evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a model in which TE activity shapes the genome, while DNA methylation and small RNA-mediated silencing keep their overproliferation in check. We propose that a well-controlled TE activity directly contributes to genome evolution in AM fungi.
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Affiliation(s)
- Alexandra Dallaire
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Bethan F Manley
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Maya Wilkens
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Iliana Bista
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Clement Quan
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Edouard Evangelisti
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Charles R Bradshaw
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Navin B Ramakrishna
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sebastian Schornack
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Uta Paszkowski
- Crop Science Centre, University of Cambridge, Cambridge CB3 0LE, United Kingdom
| | - Eric A Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
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