1
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Lim GM, Maharajan N, Cho GW. How calorie restriction slows aging: an epigenetic perspective. J Mol Med (Berl) 2024; 102:629-640. [PMID: 38456926 DOI: 10.1007/s00109-024-02430-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 01/14/2024] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
Genomic instability and epigenetic alterations are some of the prominent factors affecting aging. Age-related heterochromatin loss and decreased whole-genome DNA methylation are associated with abnormal gene expression, leading to diseases and genomic instability. Modulation of these epigenetic changes is crucial for preserving genomic integrity and controlling cellular identity is important for slowing the aging process. Numerous studies have shown that caloric restriction is the gold standard for promoting longevity and healthy aging in various species ranging from rodents to primates. It can be inferred that delaying of aging through the main effector such as calorie restriction is involved in cellular identity and epigenetic modification. Thus, an understanding of aging through calorie restriction may seek a more in-depth understanding. In this review, we discuss how caloric restriction promotes longevity and healthy aging through genomic stability and epigenetic alterations. We have also highlighted how the effectors of caloric restriction are involved in modulating the chromatin-based barriers.
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Affiliation(s)
- Gyeong Min Lim
- Department of Biological Science, College of Natural Science, Chosun University, 309 Pilmun-Daero, Dong-Gu, Gwangju, 61452, Republic of Korea
- BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Department of Integrative Biological Science, Chosun University, Gwangju, 61452, Republic of Korea
| | - Nagarajan Maharajan
- The Department of Obstetrics & Gynecology and Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Gwang-Won Cho
- Department of Biological Science, College of Natural Science, Chosun University, 309 Pilmun-Daero, Dong-Gu, Gwangju, 61452, Republic of Korea.
- BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Department of Integrative Biological Science, Chosun University, Gwangju, 61452, Republic of Korea.
- The Basic Science Institute of Chosun University, Chosun University, Gwangju, 61452, Republic of Korea.
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2
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Yang D, Geng T, Harrison AG, Cahoon JG, Xing J, Jiao B, Wang M, Cheng C, Hill RE, Wang H, Vella AT, Cheng G, Wang Y, Wang P. UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors. Nat Commun 2024; 15:780. [PMID: 38278841 PMCID: PMC10817939 DOI: 10.1038/s41467-024-45141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
The Retinoic acid-Inducible Gene I (RIG-I) like receptors (RLRs) are the major viral RNA sensors essential for the initiation of antiviral immune responses. RLRs are subjected to stringent transcriptional and posttranslational regulations, of which ubiquitination is one of the most important. However, the role of ubiquitination in RLR transcription is unknown. Here, we screen 375 definite ubiquitin ligase knockout cell lines and identify Ubiquitin Protein Ligase E3 Component N-Recognin 5 (UBR5) as a positive regulator of RLR transcription. UBR5 deficiency reduces antiviral immune responses to RNA viruses, while increases viral replication in primary cells and mice. Ubr5 knockout mice are more susceptible to lethal RNA virus infection than wild type littermates. Mechanistically, UBR5 mediates the Lysine 63-linked ubiquitination of Tripartite Motif Protein 28 (TRIM28), an epigenetic repressor of RLRs. This modification prevents intramolecular SUMOylation of TRIM28, thus disengages the TRIM28-imposed brake on RLR transcription. In sum, UBR5 enables rapid upregulation of RLR expression to boost antiviral immune responses by ubiquitinating and de-SUMOylating TRIM28.
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Affiliation(s)
- Duomeng Yang
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA.
| | - Tingting Geng
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Andrew G Harrison
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Jason G Cahoon
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Jian Xing
- Department of Neuroscience, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Baihai Jiao
- Department of Medicine, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Mark Wang
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Robert E Hill
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, EH4, 2XU, UK
| | - Huadong Wang
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine of the People's Republic of China, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Anthony T Vella
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Gong Cheng
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Yanlin Wang
- Department of Medicine, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Penghua Wang
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA.
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3
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Roy A, Ghosh A. Epigenetic Restriction Factors (eRFs) in Virus Infection. Viruses 2024; 16:183. [PMID: 38399958 PMCID: PMC10892949 DOI: 10.3390/v16020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The ongoing arms race between viruses and their hosts is constantly evolving. One of the ways in which cells defend themselves against invading viruses is by using restriction factors (RFs), which are cell-intrinsic antiviral mechanisms that block viral replication and transcription. Recent research has identified a specific group of RFs that belong to the cellular epigenetic machinery and are able to restrict the gene expression of certain viruses. These RFs can be referred to as epigenetic restriction factors or eRFs. In this review, eRFs have been classified into two categories. The first category includes eRFs that target viral chromatin. So far, the identified eRFs in this category include the PML-NBs, the KRAB/KAP1 complex, IFI16, and the HUSH complex. The second category includes eRFs that target viral RNA or, more specifically, the viral epitranscriptome. These epitranscriptomic eRFs have been further classified into two types: those that edit RNA bases-adenosine deaminase acting on RNA (ADAR) and pseudouridine synthases (PUS), and those that covalently modify viral RNA-the N6-methyladenosine (m6A) writers, readers, and erasers. We delve into the molecular machinery of eRFs, their role in limiting various viruses, and the mechanisms by which viruses have evolved to counteract them. We also examine the crosstalk between different eRFs, including the common effectors that connect them. Finally, we explore the potential for new discoveries in the realm of epigenetic networks that restrict viral gene expression, as well as the future research directions in this area.
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Affiliation(s)
- Arunava Roy
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
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4
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Randolph K, Hyder U, Challa A, Perez E, D’Orso I. Functional Analysis of KAP1/TRIM28 Requirements for HIV-1 Transcription Activation. Viruses 2024; 16:116. [PMID: 38257816 PMCID: PMC10819576 DOI: 10.3390/v16010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
HIV-1 latency maintenance and reactivation are regulated by several viral and host factors. One such factor is Krüppel-associated box (KRAB)-associated protein 1 (KAP1: also named TRIM28 or TIF1β). While initial studies have revealed KAP1 to be a positive regulator of latency reversal in transformed and primary CD4+ T cells, subsequent studies have proposed KAP1 to be a repressor required for latency maintenance. Given this discrepancy, in this study, we re-examine KAP1 transcription regulatory functions using a chemical genetics strategy to acutely deplete KAP1 expression to avoid the accumulation of indirect effects. Notably, KAP1 acute loss partially decreased HIV-1 promoter activity in response to activating signals, a function that can be restored upon complementation with exogenous KAP1, thus revealing that KAP1-mediated activation is on target. By combining comprehensive KAP1 domain deletion and mutagenesis in a cell-based reporter assay, we genetically defined the RING finger domain and an Intrinsically Disordered Region as key activating features. Together, our study solidifies the notion that KAP1 activates HIV-1 transcription by exploiting its multi-domain protein arrangement via previously unknown domains and functions.
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Affiliation(s)
| | | | | | | | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (K.R.); (U.H.)
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5
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Xu H, Akinyemi IA, Haley J, McIntosh MT, Bhaduri-McIntosh S. ATM, KAP1 and the Epstein-Barr virus polymerase processivity factor direct traffic at the intersection of transcription and replication. Nucleic Acids Res 2023; 51:11104-11122. [PMID: 37852757 PMCID: PMC10639065 DOI: 10.1093/nar/gkad823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/09/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023] Open
Abstract
The timing of transcription and replication must be carefully regulated for heavily-transcribed genomes of double-stranded DNA viruses: transcription of immediate early/early genes must decline as replication ramps up from the same genome-ensuring efficient and timely replication of viral genomes followed by their packaging by structural proteins. To understand how the prototypic DNA virus Epstein-Barr virus tackles the logistical challenge of switching from transcription to DNA replication, we examined the proteome at viral replication forks. Specifically, to transition from transcription, the viral DNA polymerase-processivity factor EA-D is SUMOylated by the epigenetic regulator and E3 SUMO-ligase KAP1/TRIM28. KAP1's SUMO2-ligase function is triggered by phosphorylation via the PI3K-related kinase ATM and the RNA polymerase II-associated helicase RECQ5 at the transcription machinery. SUMO2-EA-D then recruits the histone loader CAF1 and the methyltransferase SETDB1 to silence the parental genome via H3K9 methylation, prioritizing replication. Thus, a key viral protein and host DNA repair, epigenetic and transcription-replication interference pathways orchestrate the handover from transcription-to-replication, a fundamental feature of DNA viruses.
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Affiliation(s)
- Huanzhou Xu
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - Ibukun A Akinyemi
- Child Health Research Institute, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - John Haley
- Department of Pathology and Stony Brook Proteomics Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael T McIntosh
- Child Health Research Institute, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Sumita Bhaduri-McIntosh
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
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6
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Hussain S, Sadouni N, van Essen D, Dao LTM, Ferré Q, Charbonnier G, Torres M, Gallardo F, Lecellier CH, Sexton T, Saccani S, Spicuglia S. Short tandem repeats are important contributors to silencer elements in T cells. Nucleic Acids Res 2023; 51:4845-4866. [PMID: 36929452 PMCID: PMC10250210 DOI: 10.1093/nar/gkad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/26/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
The action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements.
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Affiliation(s)
- Saadat Hussain
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Nori Sadouni
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Dominic van Essen
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Lan T M Dao
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Quentin Ferré
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Magali Torres
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Frederic Gallardo
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Charles-Henri Lecellier
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- LIRMM, University of Montpellier, CNRS, Montpellier, France
| | - Tom Sexton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire – IGBMC (CNRS UMR 7104, INSERM U1258, Université de Strasbourg), 67404 Illkirch, France
| | - Simona Saccani
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
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7
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Carnie CJ, Armstrong L, Sebesta M, Ariza A, Wang X, Graham E, Zhu K, Ahel D. ERCC6L2 mitigates replication stress and promotes centromere stability. Cell Rep 2023; 42:112329. [PMID: 37014751 DOI: 10.1016/j.celrep.2023.112329] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 01/26/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism behind centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here, we define ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes deposition of core centromeric factors. Interestingly, ERCC6L2-/- cells show unrestrained replication of centromeric DNA, likely caused by the erosion of centromeric chromatin. Beyond centromeres, ERCC6L2 facilitates replication at genomic repeats and non-canonical DNA structures. Notably, ERCC6L2 interacts with the DNA-clamp PCNA through an atypical peptide, presented here in a co-crystal structure. Finally, ERCC6L2 also restricts DNA end resection, acting independently of the 53BP1-REV7-Shieldin complex. We propose a mechanistic model, which reconciles seemingly distinct functions of ERCC6L2 in DNA repair and DNA replication. These findings provide a molecular context for studies linking ERCC6L2 to human disease.
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Affiliation(s)
| | - Lucy Armstrong
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Marek Sebesta
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Xiaomeng Wang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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8
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Zhang W, Tang M, Wang L, Zhou H, Gao J, Chen Z, Zhao B, Zheng P. Lnc956-TRIM28-HSP90B1 complex on replication forks promotes CMG helicase retention to ensure stem cell genomic stability and embryogenesis. SCIENCE ADVANCES 2023; 9:eadf6277. [PMID: 36706191 PMCID: PMC9882984 DOI: 10.1126/sciadv.adf6277] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Replication stress is a major source of endogenous DNA damage. Despite the identification of numerous proteins on replication forks to modulate fork or replication machinery activities, it remains unexplored whether noncoding RNAs can localize on stalled forks and play critical regulatory roles. Here, we identify an uncharacterized long noncoding RNA NONMMUT028956 (Lnc956 for short) predominantly expressed in mouse embryonic stem cells. Lnc956 is accumulated on replication forks to prevent fork collapse and preserve genomic stability and is essential for mouse embryogenesis. Mechanistically, it drives assembly of the Lnc956-TRIM28-HSP90B1 complex on stalled forks in an interdependent manner downstream of ataxia telangiectasia and Rad3-related (ATR) signaling. Lnc956-TRIM28-HSP90B1 complex physically associates with minichromosome maintenance proteins 2 (MCM2) to minichromosome maintenance proteins 7 (MCM7) hexamer via TRIM28 and directly regulates the CDC45-MCM-GINS (CMG) helicase retention on chromatin. The regulation of Lnc956-TRIM28-HSP90B1 on CMG retention is mediated by HSP90B1's chaperoning function. These findings reveal a player that actively regulates replisome retention to prevent fork collapse.
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Affiliation(s)
- Weidao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Min Tang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhongliang Chen
- Key Laboratory of Adult Stem Cell Translational Research (Chinese Academy of Medical Sciences), Guizhou Medical University, Guiyang, China
- National Joint Local Engineering Laboratory for Cell Engineering and Biomedicine Technique, Guizhou Medical University, Guiyang, China
| | - Bo Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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9
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Dufour D, Dumontet T, Sahut-Barnola I, Carusi A, Onzon M, Pussard E, Wilmouth JJ, Olabe J, Lucas C, Levasseur A, Damon-Soubeyrand C, Pointud JC, Roucher-Boulez F, Tauveron I, Bossis G, Yeh ET, Breault DT, Val P, Lefrançois-Martinez AM, Martinez A. Loss of SUMO-specific protease 2 causes isolated glucocorticoid deficiency by blocking adrenal cortex zonal transdifferentiation in mice. Nat Commun 2022; 13:7858. [PMID: 36543805 PMCID: PMC9772323 DOI: 10.1038/s41467-022-35526-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
SUMOylation is a dynamic posttranslational modification, that provides fine-tuning of protein function involved in the cellular response to stress, differentiation, and tissue development. In the adrenal cortex, an emblematic endocrine organ that mediates adaptation to physiological demands, the SUMOylation gradient is inversely correlated with the gradient of cellular differentiation raising important questions about its role in functional zonation and the response to stress. Considering that SUMO-specific protease 2 (SENP2), a deSUMOylating enzyme, is upregulated by Adrenocorticotropic Hormone (ACTH)/cAMP-dependent Protein Kinase (PKA) signalling within the zona fasciculata, we generated mice with adrenal-specific Senp2 loss to address these questions. Disruption of SENP2 activity in steroidogenic cells leads to specific hypoplasia of the zona fasciculata, a blunted reponse to ACTH and isolated glucocorticoid deficiency. Mechanistically, overSUMOylation resulting from SENP2 loss shifts the balance between ACTH/PKA and WNT/β-catenin signalling leading to repression of PKA activity and ectopic activation of β-catenin. At the cellular level, this blocks transdifferentiation of β-catenin-positive zona glomerulosa cells into fasciculata cells and sensitises them to premature apoptosis. Our findings indicate that the SUMO pathway is critical for adrenal homeostasis and stress responsiveness.
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Affiliation(s)
- Damien Dufour
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
| | - Typhanie Dumontet
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France ,grid.214458.e0000000086837370Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI USA ,grid.214458.e0000000086837370Training Program in Organogenesis, Center for Cell Plasticity and Organ Design, University of Michigan, Ann Arbor, MI USA
| | - Isabelle Sahut-Barnola
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
| | - Aude Carusi
- grid.4444.00000 0001 2112 9282IGMM, Université de Montpellier, CNRS, Montpellier, France
| | - Méline Onzon
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
| | - Eric Pussard
- grid.460789.40000 0004 4910 6535Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpital de Bicêtre, Assistance Publique-Hôpitaux de Paris (APHP), Physiologie et Physiopathologie Endocriniennes, INSERM, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - James Jr Wilmouth
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
| | - Julie Olabe
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
| | - Cécily Lucas
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France ,grid.7849.20000 0001 2150 7757Endocrinologie Moléculaire et Maladies Rares, Centre Hospitalier Universitaire, Université Claude Bernard Lyon 1, Bron, France
| | - Adrien Levasseur
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
| | - Christelle Damon-Soubeyrand
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
| | - Jean-Christophe Pointud
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
| | - Florence Roucher-Boulez
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France ,grid.7849.20000 0001 2150 7757Endocrinologie Moléculaire et Maladies Rares, Centre Hospitalier Universitaire, Université Claude Bernard Lyon 1, Bron, France
| | - Igor Tauveron
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France ,grid.494717.80000000115480420Service d’Endocrinologie, Centre Hospitalier Universitaire Gabriel Montpied, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Guillaume Bossis
- grid.4444.00000 0001 2112 9282IGMM, Université de Montpellier, CNRS, Montpellier, France
| | - Edward T. Yeh
- grid.241054.60000 0004 4687 1637Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR USA
| | - David T. Breault
- grid.38142.3c000000041936754XDivision of Endocrinology, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Stem Cell Institute, Harvard University, Cambridge, MA USA
| | - Pierre Val
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
| | - Anne-Marie Lefrançois-Martinez
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
| | - Antoine Martinez
- grid.494717.80000000115480420institut Génétique, Reproduction & Développement (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont–Ferrand, F-63000 France
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10
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Stoll GA, Pandiloski N, Douse CH, Modis Y. Structure and functional mapping of the KRAB-KAP1 repressor complex. EMBO J 2022; 41:e111179. [PMID: 36341546 PMCID: PMC9753469 DOI: 10.15252/embj.2022111179] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is lost genome-wide in cells expressing a KAP1 variant with mutations that abolish KRAB binding. Our work identifies and functionally validates the KRAB-KAP1 molecular interface, which is critical for a central transcriptional control axis in vertebrates. In addition, the structure-based prediction of KAP1 recruitment efficiency will enable optimization of KRABs used in CRISPRi.
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Affiliation(s)
- Guido A Stoll
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUK,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)University of Cambridge School of Clinical MedicineCambridgeUK
| | - Ninoslav Pandiloski
- Department of Experimental Medical Science, Lund Stem Cell CenterLund UniversityLundSweden
| | - Christopher H Douse
- Department of Experimental Medical Science, Lund Stem Cell CenterLund UniversityLundSweden
| | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUK,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)University of Cambridge School of Clinical MedicineCambridgeUK
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11
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Acurzio B, Cecere F, Giaccari C, Verma A, Russo R, Valletta M, Hay Mele B, Angelini C, Chambery A, Riccio A. The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex. Epigenetics Chromatin 2022; 15:27. [PMID: 35918739 PMCID: PMC9344765 DOI: 10.1186/s13072-022-00462-7] [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: 06/13/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022] Open
Abstract
Background Imprinting Control Regions (ICRs) are CpG-rich sequences acquiring differential methylation in the female and male germline and maintaining it in a parental origin-specific manner in somatic cells. Despite their expected high mutation rate due to spontaneous deamination of methylated cytosines, ICRs show conservation of CpG-richness and CpG-containing transcription factor binding sites in mammalian species. However, little is known about the mechanisms contributing to the maintenance of a high density of methyl CpGs at these loci. Results To gain functional insights into the mechanisms for maintaining CpG methylation, we sought to identify the proteins binding the methylated allele of the ICRs by determining the interactors of ZFP57 that recognizes a methylated hexanucleotide motif of these DNA regions in mouse ESCs. By using a tagged approach coupled to LC–MS/MS analysis, we identified several proteins, including factors involved in mRNA processing/splicing, chromosome organization, transcription and DNA repair processes. The presence of the post-replicative mismatch-repair (MMR) complex components MSH2 and MSH6 among the identified ZFP57 interactors prompted us to investigate their DNA binding profile by chromatin immunoprecipitation and sequencing. We demonstrated that MSH2 was enriched at gene promoters overlapping unmethylated CpG islands and at repeats. We also found that both MSH2 and MSH6 interacted with the methylated allele of the ICRs, where their binding to DNA was mediated by the ZFP57/KAP1 complex. Conclusions Our findings show that the MMR complex is concentrated on gene promoters and repeats in mouse ESCs, suggesting that maintaining the integrity of these regions is a primary function of highly proliferating cells. Furthermore, the demonstration that MSH2/MSH6 are recruited to the methylated allele of the ICRs through interaction with ZFP57/KAP1 suggests a role of the MMR complex in the maintenance of the integrity of these regulatory regions and evolution of genomic imprinting in mammalian species. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00462-7.
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Affiliation(s)
- Basilia Acurzio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Carlo Giaccari
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Rosita Russo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Mariangela Valletta
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Bruno Hay Mele
- Department of Biology, Università Degli Studi Di Napoli "Federico II", 80126, Naples, Italy
| | - Claudia Angelini
- Istituto Per Le Applicazioni del Calcolo "Mauro Picone" (IAC), CNR, 80131, Naples, Italy
| | - Angela Chambery
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy. .,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy.
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12
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Wang W, Yan T, Guo X, Cai H, Liang C, Huang L, Wang Y, Ma P, Qi S. KAP1 phosphorylation promotes the survival of neural stem cells after ischemia/reperfusion by maintaining the stability of PCNA. Stem Cell Res Ther 2022; 13:290. [PMID: 35799276 PMCID: PMC9264526 DOI: 10.1186/s13287-022-02962-5] [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: 12/07/2021] [Accepted: 04/17/2022] [Indexed: 11/28/2022] Open
Abstract
Aims To explore the function of phosphorylation of KAP1 (p-KAP1) at the serine-824 site (S824) in the proliferation and apoptosis of endogenous neural stem cells (NSCs) after cerebral ischemic/reperfusion (I/R). Methods The apoptosis and proliferation of C17.2 cells transfected with the p-KAP1-expression plasmids and the expression of proliferation cell nuclear antigen (PCNA) and p-KAP1 were detected by immunofluorescence and Western blotting after the Oxygen Glucose deprivation/reperfusion model (OGD/R). The interaction of p-KAP1 and CUL4A with PCNA was analyzed by immunoprecipitation. In the rats MCAO model, we performed the adeno-associated virus (AAV) 2/9 gene delivery of p-KAP1 mutants to verify the proliferation of endogenous NSCs and the colocalization of PCNA and CUL4A by immunofluorescence. Results The level of p-KAP1 was significantly down-regulated in the stroke model in vivo and in vitro. Simulated p-KAP1(S824) significantly increased the proliferation of C17.2 cells and the expression of PCNA after OGD/R. Simulated p-KAP1(S824) enhanced the binding of p-KAP1 and PCNA and decreased the interaction between PCNA and CUL4A in C17.2 cells subjected to OGD/R. The AAV2/9-mediated p-KAP1(S824) increased endogenous NSCs proliferation, PCNA expression, p-KAP1 binding to PCNA, and improved neurological function in the rat MCAO model. Conclusions Our findings confirmed that simulated p-KAP1(S824) improved the survival and proliferation of endogenous NSCs. The underlying mechanism is that highly expressed p-KAP1(S824) promotes binding to PCNA, and inhibits the binding of CUL4A to PCNA. This reduced CUL4A-mediated ubiquitination degradation to increase the stability of PCNA and promote the survival and proliferation of NSCs. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02962-5.
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Affiliation(s)
- Wan Wang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Tianqing Yan
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xinjian Guo
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Heng Cai
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Chang Liang
- School of Basic Medical Science, Xuzhou Medical University, Xuzhou, 221004, China
| | - Linyan Huang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yanling Wang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ping Ma
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
| | - Suhua Qi
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China. .,Pharmacology College, Xuzhou Medical University, Xuzhou, 221004, China.
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13
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Tsai MS, Chen SH, Chang CP, Hsiao YL, Wang LC. Integrin-Linked Kinase Reduces H3K9 Trimethylation to Enhance Herpes Simplex Virus 1 Replication. Front Cell Infect Microbiol 2022; 12:814307. [PMID: 35350437 PMCID: PMC8957879 DOI: 10.3389/fcimb.2022.814307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Histone modifications control the lytic gene expression of herpes simplex virus 1 (HSV-1). The heterochromatin mark, trimethylation of histone H3 on lysine (K) 9 (H3K9me3), is detected on HSV-1 genomes at early phases of infection to repress viral gene transcription. However, the components and mechanisms involved in the process are mostly unknown. Integrin-linked kinase (ILK) is activated by PI3K to phosphorylate Akt and promote several RNA virus infections. Akt has been shown to enhance HSV-1 infection, suggesting a pro-viral role of ILK in HSV-1 infection that has not been addressed before. Here, we reveal that ILK enhances HSV-1 replication in an Akt-independent manner. ILK reduces the accumulation of H3K9me3 on viral promoters and replication compartments. Notably, ILK reduces H3K9me3 in a manner independent of ICP0. Instead, we show an increased binding of H3K9 methyltransferase SUV39H1 and corepressor TRIM28 on viral promoters in ILK knockdown cells. Knocking down SUV39H1 or TRIM28 increases HSV-1 lytic gene transcription in ILK knockdown cells. These results show that ILK antagonizes SVU39H1- and TRIM28-mediated repression on lytic gene transcription. We further demonstrate that ILK knockdown reduces TRIM28 phosphorylation on serine 473 and 824 in HSV-1-infected cells, suggesting that ILK facilitates TRIM28 phosphorylation to abrogate its inhibition on lytic gene transcription. OSU-T315, an ILK inhibitor, suppresses HSV-1 replication in cells and mice. In conclusion, we demonstrate that ILK decreases H3K9me3 on HSV-1 DNA by reducing SUV39H1 and TRIM28 binding. Moreover, our results suggest that targeting ILK could be a broad-spectrum antiviral strategy for DNA and RNA virus infections, especially for DNA viruses controlled by histone modifications.
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Affiliation(s)
- Meng-Shan Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shun-Hua Chen
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Peng Chang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ling Hsiao
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Li-Chiu Wang
- School of Medicine, I-Shou University, Kaohsiung, Taiwan
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14
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TOP2B's contributions to transcription. Biochem Soc Trans 2021; 49:2483-2493. [PMID: 34747992 DOI: 10.1042/bst20200454] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/23/2022]
Abstract
Transcription is regulated and mediated by multiprotein complexes in a chromatin context. Transcription causes changes in DNA topology which is modulated by DNA topoisomerases, enzymes that catalyse changes in DNA topology via transient breaking and re-joining of one or both strands of the phosphodiester backbone. Mammals have six DNA topoisomerases, this review focuses on one, DNA topoisomerase II beta (TOP2B). In the absence of TOP2B transcription of many developmentally regulated genes is altered. Long genes seem particularly susceptible to the lack of TOP2B. Biochemical studies of the role of TOP2B in transcription regulated by ligands such as nuclear hormones, growth factors and insulin has revealed PARP1 associated with TOP2B and also PRKDC, XRCC5 and XRCC6. Analysis of publicly available databases of protein interactions confirms these interactions and illustrates interactions with other key transcriptional regulators including TRIM28. TOP2B has been shown to interact with proteins involved in chromosome organisation including CTCF and RAD21. Comparison of publicly available Chip-seq datasets reveals the location at which these proteins interact with genes. The availability of resources such as large datasets of protein-protein interactions, e.g. BioGrid and IntAct and protein-DNA interactions such as Chip-seq in GEO enables scientists to extend models and propose new hypotheses.
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15
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Beyond the Double-Strand Breaks: The Role of DNA Repair Proteins in Cancer Stem-Cell Regulation. Cancers (Basel) 2021; 13:cancers13194818. [PMID: 34638302 PMCID: PMC8508278 DOI: 10.3390/cancers13194818] [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: 09/01/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cancer stem cells (CSCs) are a tumor cell population maintaining tumor growth and promoting tumor relapse if not wholly eradicated during treatment. CSCs are often equipped with molecular mechanisms making them resistant to conventional anti-cancer therapies whose curative potential depends on DNA damage-induced cell death. An elevated expression of some key DNA repair proteins is one of such defense mechanisms. However, new research reveals that the role of critical DNA repair proteins is extending far beyond the DNA repair mechanisms. This review discusses the diverse biological functions of DNA repair proteins in CSC maintenance and the adaptation to replication and oxidative stress, anti-cancer immune response, epigenetic reprogramming, and intracellular signaling mechanisms. It also provides an overview of their potential therapeutic targeting. Abstract Cancer stem cells (CSCs) are pluripotent and highly tumorigenic cells that can re-populate a tumor and cause relapses even after initially successful therapy. As with tissue stem cells, CSCs possess enhanced DNA repair mechanisms. An active DNA damage response alleviates the increased oxidative and replicative stress and leads to therapy resistance. On the other hand, mutations in DNA repair genes cause genomic instability, therefore driving tumor evolution and developing highly aggressive CSC phenotypes. However, the role of DNA repair proteins in CSCs extends beyond the level of DNA damage. In recent years, more and more studies have reported the unexpected role of DNA repair proteins in the regulation of transcription, CSC signaling pathways, intracellular levels of reactive oxygen species (ROS), and epithelial–mesenchymal transition (EMT). Moreover, DNA damage signaling plays an essential role in the immune response towards tumor cells. Due to its high importance for the CSC phenotype and treatment resistance, the DNA damage response is a promising target for individualized therapies. Furthermore, understanding the dependence of CSC on DNA repair pathways can be therapeutically exploited to induce synthetic lethality and sensitize CSCs to anti-cancer therapies. This review discusses the different roles of DNA repair proteins in CSC maintenance and their potential as therapeutic targets.
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16
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Abstract
Plant intra-individual and inter-individual variation can be determined by the epigenome, a set of covalent modifications of DNA and chromatin that can alter genome structure and activity without changes to the genome sequence. The epigenome of plant cells is plastic, that is, it can change in response to internal or external cues, such as during development or due to environmental changes, to create a memory of such events. Ongoing advances in technologies to read and write epigenomic patterns with increasing resolution, scale and precision are enabling the extent of plant epigenome variation to be more extensively characterized and functionally interrogated. In this Review, we discuss epigenome dynamics and variation within plants during development and in response to environmental changes, including stress, as well as between plants. We review known or potential functions of such plasticity and emphasize the importance of investigating the causality of epigenomic changes. Finally, we discuss emerging technologies that may underpin future research into plant epigenome plasticity.
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Affiliation(s)
- James P B Lloyd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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17
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Frey TR, Akinyemi IA, Burton EM, Bhaduri-McIntosh S, McIntosh MT. An Ancestral Retrovirus Envelope Protein Regulates Persistent Gammaherpesvirus Lifecycles. Front Microbiol 2021; 12:708404. [PMID: 34434177 PMCID: PMC8381357 DOI: 10.3389/fmicb.2021.708404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) persist as life-long infections alternating between latency and lytic replication. Human endogenous retroviruses (HERVs), via integration into the host genome, represent genetic remnants of ancient retroviral infections. Both show similar epigenetic silencing while dormant, but can reactivate in response to cell signaling cues or triggers that, for gammaherpesviruses, result in productive lytic replication. Given their co-existence with humans and shared epigenetic silencing, we asked if HERV expression might be linked to lytic activation of human gammaherpesviruses. We found ERVW-1 mRNA, encoding the functional HERV-W envelope protein Syncytin-1, along with other repeat class elements, to be elevated upon lytic activation of EBV. Knockdown/knockout of ERVW-1 reduced lytic activation of EBV and KSHV in response to various lytic cycle triggers. In this regard, reduced expression of immediate early proteins ZEBRA and RTA for EBV and KSHV, respectively, places Syncytin-1's influence on lytic activation mechanistically upstream of the latent-to-lytic switch. Conversely, overexpression of Syncytin-1 enhanced lytic activation of EBV and KSHV in response to lytic triggers, though this was not sufficient to induce lytic activation in the absence of such triggers. Syncytin-1 is expressed in replicating B cell blasts and lymphoma-derived B cell lines where it appears to contribute to cell cycle progression. Together, human gammaherpesviruses and B cells appear to have adapted a dependency on Syncytin-1 that facilitates the ability of EBV and KSHV to activate lytic replication from latency, while promoting viral persistence during latency by contributing to B cell proliferation.
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Affiliation(s)
- Tiffany R. Frey
- Department of Pediatrics, Child Health Research Institute, University of Florida, Gainesville, FL, United States
| | - Ibukun A. Akinyemi
- Department of Pediatrics, Child Health Research Institute, University of Florida, Gainesville, FL, United States
| | - Eric M. Burton
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL, United States
| | - Sumita Bhaduri-McIntosh
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL, United States
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, United States
| | - Michael T. McIntosh
- Department of Pediatrics, Child Health Research Institute, University of Florida, Gainesville, FL, United States
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, United States
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18
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Wong X, Cutler JA, Hoskins VE, Gordon M, Madugundu AK, Pandey A, Reddy KL. Mapping the micro-proteome of the nuclear lamina and lamina-associated domains. Life Sci Alliance 2021; 4:e202000774. [PMID: 33758005 PMCID: PMC8008952 DOI: 10.26508/lsa.202000774] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 01/13/2023] Open
Abstract
The nuclear lamina is a proteinaceous network of filaments that provide both structural and gene regulatory functions by tethering proteins and large domains of DNA, the so-called lamina-associated domains (LADs), to the periphery of the nucleus. LADs are a large fraction of the mammalian genome that are repressed, in part, by their association to the nuclear periphery. The genesis and maintenance of LADs is poorly understood as are the proteins that participate in these functions. In an effort to identify proteins that reside at the nuclear periphery and potentially interact with LADs, we have taken a two-pronged approach. First, we have undertaken an interactome analysis of the inner nuclear membrane bound LAP2β to further characterize the nuclear lamina proteome. To accomplish this, we have leveraged the BioID system, which previously has been successfully used to characterize the nuclear lamina proteome. Second, we have established a system to identify proteins that bind to LADs by developing a chromatin-directed BioID system. We combined the BioID system with the m6A-tracer system which binds to LADs in live cells to identify both LAD proximal and nuclear lamina proteins. In combining these datasets, we have further characterized the protein network at the nuclear lamina, identified putative LAD proximal proteins and found several proteins that appear to interface with both micro-proteomes. Importantly, several proteins essential for LAD function, including heterochromatin regulating proteins related to H3K9 methylation, were identified in this study.
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Affiliation(s)
- Xianrong Wong
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Developmental and Regenerative Biology, Institute of Medical Biology, Agency for Science, Technology and Research (A∗STAR), Immunos, Singapore
| | - Jevon A Cutler
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Victoria E Hoskins
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Molly Gordon
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anil K Madugundu
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHNS), Bangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Akhilesh Pandey
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHNS), Bangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen L Reddy
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Cancer Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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19
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Burton EM, Akinyemi IA, Frey TR, Xu H, Li X, Su LJ, Zhi J, McIntosh MT, Bhaduri-McIntosh S. A heterochromatin inducing protein differentially recognizes self versus foreign genomes. PLoS Pathog 2021; 17:e1009447. [PMID: 33730092 PMCID: PMC8007004 DOI: 10.1371/journal.ppat.1009447] [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: 10/30/2020] [Revised: 03/29/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022] Open
Abstract
Krüppel-associated box-domain zinc finger protein (KRAB-ZFP) transcriptional repressors recruit TRIM28/KAP1 to heterochromatinize the mammalian genome while also guarding the host by silencing invading foreign genomes. However, how a KRAB-ZFP recognizes target sequences in the natural context of its own or foreign genomes is unclear. Our studies on B-lymphocytes permanently harboring the cancer-causing Epstein-Barr virus (EBV) have shown that SZF1, a KRAB-ZFP, binds to several lytic/replicative phase genes to silence them, thereby promoting the latent/quiescent phase of the virus. As a result, unless SZF1 and its binding partners are displaced from target regions on the viral genome, EBV remains dormant, i.e. refractory to lytic phase-inducing triggers. As SZF1 also heterochromatinizes the cellular genome, we performed in situ footprint mapping on both viral and host genomes in physically separated B-lymphocytes bearing latent or replicative/active EBV genomes. By analyzing footprints, we learned that SZF1 recognizes the host genome through a repeat sequence-bearing motif near centromeres. Remarkably, SZF1 does not use this motif to recognize the EBV genome. Instead, it uses distinct binding sites that lack obvious similarities to each other or the above motif, to silence the viral genome. Virus mutagenesis studies show that these distinct binding sites are not only key to maintaining the established latent phase but also silencing the lytic phase in newly-infected cells, thus enabling the virus to establish latency and transform cells. Notably, these binding sites on the viral genome, when also present on the human genome, are not used by SZF1 to silence host genes during latency. This differential approach towards target site recognition may reflect a strategy by which the host silences and regulates genomes of persistent invaders without jeopardizing its own homeostasis. Heterochromatin marks silenced portions of the human genome. Heterochromatin also serves as a defense strategy to silence foreign genomes. Yet, how the heterochromatin inducing KRAB-ZFP-TRIM28 machinery recognizes target sites on the native genome, whether self or foreign, is unclear. Using Epstein-Barr virus-infected cells in which a KRAB-ZFP, SZF1, silences lytic/replicative-phase genes of the virus, we performed in situ mapping of ZFP-footprints on cell and viral genomes. We find that while the ZFP uses a repeat sequence-bearing motif to target pericentromeric regions, it uses non-consensus sites to target viral genes. These findings point towards i) a mechanism for directing constitutive heterochromatin and ii) a strategy that allows the host to use the same heterochromatin machinery to regulate an invader without deregulating itself.
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Affiliation(s)
- Eric M. Burton
- Dept. of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, United States of America
| | - Ibukun A. Akinyemi
- Child Health Research Institute, Dept. of Pediatrics, University of Florida, Gainesville, Florida, United States of America
| | - Tiffany R. Frey
- Child Health Research Institute, Dept. of Pediatrics, University of Florida, Gainesville, Florida, United States of America
| | - Huanzhou Xu
- Division of Infectious Disease, Dept. of Pediatrics, University of Florida, Gainesville, Florida, United States of America
| | - Xiaofan Li
- Division of Infectious Disease, Dept. of Pediatrics, University of Florida, Gainesville, Florida, United States of America
| | - Lai Jing Su
- Child Health Research Institute, Dept. of Pediatrics, University of Florida, Gainesville, Florida, United States of America
| | - Jizu Zhi
- Dept of Pathology, Stony Brook University, Stony Brook, New York, United States of America
| | - Michael T. McIntosh
- Child Health Research Institute, Depts. of Pediatrics and of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (MTM); (SB-M)
| | - Sumita Bhaduri-McIntosh
- Division of Infectious Disease, Depts. of Pediatrics and of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (MTM); (SB-M)
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20
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Studies on the Regulatory Roles and Related Mechanisms of lncRNAs in the Nervous System. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6657944. [PMID: 33791072 PMCID: PMC7984887 DOI: 10.1155/2021/6657944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/19/2020] [Accepted: 02/15/2021] [Indexed: 11/25/2022]
Abstract
Long noncoding RNAs (lncRNAs) have attracted extensive attention due to their regulatory role in various cellular processes. Emerging studies have indicated that lncRNAs are expressed to varying degrees after the growth and development of the nervous system as well as injury and degeneration, thus affecting various physiological processes of the nervous system. In this review, we have compiled various reported lncRNAs related to the growth and development of central and peripheral nerves and pathophysiology (including advanced nerve centers, spinal cord, and peripheral nervous system) and explained how these lncRNAs play regulatory roles through their interactions with target-coding genes. We believe that a full understanding of the regulatory function of lncRNAs in the nervous system will contribute to understand the molecular mechanism of changes after nerve injury and will contribute to discover new diagnostic markers and therapeutic targets for nerve injury diseases.
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21
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Chikuma S, Yamanaka S, Nakagawa S, Ueda MT, Hayabuchi H, Tokifuji Y, Kanayama M, Okamura T, Arase H, Yoshimura A. TRIM28 Expression on Dendritic Cells Prevents Excessive T Cell Priming by Silencing Endogenous Retrovirus. THE JOURNAL OF IMMUNOLOGY 2021; 206:1528-1539. [PMID: 33619215 DOI: 10.4049/jimmunol.2001003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/12/2021] [Indexed: 11/19/2022]
Abstract
Acquired immune reaction is initiated by dendritic cells (DCs), which present Ags to a few naive Ag-specific T cells. Deregulation of gene expression in DCs may alter the outcome of the immune response toward immunodeficiency and/or autoimmune diseases. Expression of TRIM28, a nuclear protein that mediates gene silencing through heterochromatin, decreased in DCs from old mice, suggesting alteration of gene regulation. Mice specifically lacking TRIM28 in DCs show increased DC population in the spleen and enhanced T cell priming toward inflammatory effector T cells, leading to acceleration and exacerbation in experimental autoimmune encephalomyelitis. TRIM28-deficient DCs were found to ectopically transcribe endogenous retrovirus (ERV) elements. Combined genome-wide analysis revealed a strong colocalization among the decreased repressive histone mark H3K9me3-transcribed ERV elements and the derepressed host genes that were related to inflammation in TRIM28-deficient DCs. This suggests that TRIM28 occupancy of ERV elements critically represses expression of proximal inflammatory genes on the genome. We propose that gene silencing through repressive histone modification by TRIM28 plays a role in maintaining the integrity of precise gene regulation in DCs, which prevents aberrant T cell priming to inflammatory effector T cells.
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Affiliation(s)
- Shunsuke Chikuma
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan;
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan.,Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hodaka Hayabuchi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yukiko Tokifuji
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masashi Kanayama
- Department of Biodefense Research, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan.,Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Disease, Osaka University, Osaka 565-0871, Japan; and.,Laboratory of Immunochemistry, World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
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22
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Yadav RP, Mäkelä JA, Hyssälä H, Cisneros-Montalvo S, Kotaja N. DICER regulates the expression of major satellite repeat transcripts and meiotic chromosome segregation during spermatogenesis. Nucleic Acids Res 2020; 48:7135-7153. [PMID: 32484548 PMCID: PMC7367195 DOI: 10.1093/nar/gkaa460] [Citation(s) in RCA: 12] [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: 02/20/2020] [Revised: 04/23/2020] [Accepted: 05/22/2020] [Indexed: 12/16/2022] Open
Abstract
Constitutive heterochromatin at the pericentric regions of chromosomes undergoes dynamic changes in its epigenetic and spatial organization during spermatogenesis. Accurate control of pericentric heterochromatin is required for meiotic cell divisions and production of fertile and epigenetically intact spermatozoa. In this study, we demonstrate that pericentric heterochromatin is expressed during mouse spermatogenesis to produce major satellite repeat (MSR) transcripts. We show that the endonuclease DICER localizes to the pericentric heterochromatin in the testis. Furthermore, DICER forms complexes with MSR transcripts, and their processing into small RNAs is compromised in Dicer1 knockout mice leading to an elevated level of MSR transcripts in meiotic cells. We also show that defective MSR forward transcript processing in Dicer1 cKO germ cells is accompanied with reduced recruitment of SUV39H2 and H3K9me3 to the pericentric heterochromatin and meiotic chromosome missegregation. Altogether, our results indicate that the physiological role of DICER in maintenance of male fertility extends to the regulation of pericentric heterochromatin through direct targeting of MSR transcripts.
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Affiliation(s)
- Ram Prakash Yadav
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Finland
| | - Juho-Antti Mäkelä
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Finland
| | - Hanna Hyssälä
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Finland
| | - Sheyla Cisneros-Montalvo
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Finland
| | - Noora Kotaja
- To whom correspondence should be addressed. Tel: +358 44 2539225;
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23
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TRIM28 functions as the SUMO E3 ligase for PCNA in prevention of transcription induced DNA breaks. Proc Natl Acad Sci U S A 2020; 117:23588-23596. [PMID: 32900933 DOI: 10.1073/pnas.2004122117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In human cells, the DNA replication factor proliferating cell nuclear antigen (PCNA) can be conjugated to either the small ubiquitinlike modifier SUMO1 or SUMO2, but only SUMO2-conjugated PCNA is induced by transcription to facilitate resolution of transcription-replication conflict (TRC). To date, the SUMO E3 ligase that provides substrate specificity for SUMO2-PCNA conjugation in response to TRC remains unknown. Using a proteomic approach, we identified TRIM28 as the E3 ligase that catalyzes SUMO2-PCNA conjugation. In vitro, TRIM28, together with the RNA polymerase II (RNAPII)-interacting protein RECQ5, promotes SUMO2-PCNA conjugation but inhibits SUMO1-PCNA formation. This activity requires a PCNA-interacting protein (PIP) motif located within the bromodomain of TRIM28. In cells, TRIM28 interaction with PCNA on human chromatin is dependent on both transcription and RECQ5, and SUMO2-PCNA level correlates with TRIM28 expression. As a consequence, TRIM28 depletion led to RNAPII accumulation at TRC sites, and expression of a TRIM28 PIP mutant failed to suppress TRC-induced DNA breaks.
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24
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Kauzlaric A, Jang SM, Morchikh M, Cassano M, Planet E, Benkirane M, Trono D. KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190334. [PMID: 32068487 PMCID: PMC7061982 DOI: 10.1098/rstb.2019.0334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation, notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
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Affiliation(s)
- Annamaria Kauzlaric
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Suk Min Jang
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Mehdi Morchikh
- Laboratory of Molecular Virology, Institute of Human Genetics, CNRS UPR1142, MGX-Montpellier GenomiX, 141 rue de la Cardonille, 34396 Montpellier, France.,Institute of Molecular Genetics of Montpellier, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Marco Cassano
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Monsef Benkirane
- Laboratory of Molecular Virology, Institute of Human Genetics, CNRS UPR1142, MGX-Montpellier GenomiX, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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25
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SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells. Nat Commun 2019; 10:1335. [PMID: 30902974 PMCID: PMC6430823 DOI: 10.1038/s41467-019-09078-0] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
Endogenous retroviruses (ERVs) can confer benefits to their host but present a threat to genome integrity if not regulated correctly. Here we identify the SWI/SNF-like remodeler SMARCAD1 as a key factor in the control of ERVs in embryonic stem cells. SMARCAD1 is enriched at ERV subfamilies class I and II, particularly at active intracisternal A-type particles (IAPs), where it preserves repressive histone methylation marks. Depletion of SMARCAD1 results in de-repression of IAPs and adjacent genes. Recruitment of SMARCAD1 to ERVs is dependent on KAP1, a central component of the silencing machinery. SMARCAD1 and KAP1 occupancy at ERVs is co-dependent and requires the ATPase function of SMARCAD1. Our findings uncover a role for the enzymatic activity of SMARCAD1 in cooperating with KAP1 to silence ERVs. This reveals ATP-dependent chromatin remodeling as an integral step in retrotransposon regulation in stem cells and advances our understanding of the mechanisms driving heterochromatin establishment. Tight regulation of retrotransposons such as endogenous retroviruses (ERVs) is essential for genome and transcriptome integrity. Here, the authors show that the ATPase function of the chromatin remodeler SMARCAD1 facilitates the binding of KAP1 to ERVs and is required for their repression in embryonic stem cells.
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