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Trovato M, Bunina D, Yildiz U, Fernandez-Novel Marx N, Uckelmann M, Levina V, Perez Y, Janeva A, Garcia BA, Davidovich C, Zaugg JB, Noh KM. Histone H3.3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters. Nat Commun 2024; 15:7557. [PMID: 39214979 PMCID: PMC11364623 DOI: 10.1038/s41467-024-51785-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Histone modifications are associated with distinct transcriptional states, but it is unclear whether they instruct gene expression. To investigate this, we mutate histone H3.3 K9 and K27 residues in mouse embryonic stem cells (mESCs). Here, we find that H3.3K9 is essential for controlling specific distal intergenic regions and for proper H3K27me3 deposition at promoters. The H3.3K9A mutation resulted in decreased H3K9me3 at regions encompassing endogenous retroviruses and induced a gain of H3K27ac and nascent transcription. These changes in the chromatin environment unleash cryptic enhancers, resulting in the activation of distinctive transcriptional programs and culminating in protein expression normally restricted to specialized immune cell types. The H3.3K27A mutant disrupts the deposition and spreading of the repressive H3K27me3 mark, particularly impacting bivalent genes with higher basal levels of H3.3 at promoters. Therefore, H3.3K9 and K27 crucially orchestrate repressive chromatin states at cis-regulatory elements and bivalent promoters, respectively, and instruct proper transcription in mESCs.
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Affiliation(s)
- Matteo Trovato
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Daria Bunina
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Umut Yildiz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | | | - Michael Uckelmann
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, and EMBL-Australia, Clayton, VIC, Australia
| | - Vita Levina
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, and EMBL-Australia, Clayton, VIC, Australia
| | - Yekaterina Perez
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ana Janeva
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, and EMBL-Australia, Clayton, VIC, Australia
| | - Judith B Zaugg
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Kyung-Min Noh
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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Tal A, Aguilera JD, Bren I, Strauss C, Schlesinger S. Differential effect of histone H3.3 depletion on retroviral repression in embryonic stem cells. Clin Epigenetics 2023; 15:83. [PMID: 37170146 PMCID: PMC10176700 DOI: 10.1186/s13148-023-01499-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Integration of retroviruses into the host genome can impair the genomic and epigenomic integrity of the cell. As a defense mechanism, epigenetic modifications on the proviral DNA repress retroviral sequences in mouse embryonic stem cells (ESC). Here, we focus on the histone 3 variant H3.3, which is abundant in active transcription zones, as well as centromeres and heterochromatinized repeat elements, e.g., endogenous retroviruses (ERV). RESULTS To understand the involvement of H3.3 in the epigenetic silencing of retroviral sequences in ESC, we depleted the H3.3 genes in ESC and transduced the cells with GFP-labeled MLV pseudovirus. This led to altered retroviral repression and reduced Trim28 recruitment, which consequently led to a loss of heterochromatinization in proviral sequences. Interestingly, we show that H3.3 depletion has a differential effect depending on which of the two genes coding for H3.3, H3f3a or H3f3b, are knocked out. Depletion of H3f3a resulted in a transient upregulation of incoming retroviral expression and ERVs, while the depletion of H3f3b did not have the same effect and repression was maintained. However, the depletion of both genes resulted in a stable activation of the retroviral promoter. These findings suggest that H3.3 is important for regulating retroviral gene expression in mouse ESC and provide evidence for a distinct function of the two H3.3 genes in this regulation. Furthermore, we show that Trim28 is needed for depositing H3.3 in retroviral sequences, suggesting a functional interaction between Trim28 recruitment and H3.3 loading. CONCLUSIONS Identifying the molecular mechanisms by which H3.3 and Trim28 interact and regulate retroviral gene expression could provide a deeper understanding of the fundamental processes involved in retroviral silencing and the general regulation of gene expression, thus providing new answers to a central question of stem cell biology.
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Affiliation(s)
- Ayellet Tal
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jose David Aguilera
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Igor Bren
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Carmit Strauss
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sharon Schlesinger
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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Torres-Arciga K, Flores-León M, Ruiz-Pérez S, Trujillo-Pineda M, González-Barrios R, Herrera LA. Histones and their chaperones: Adaptive remodelers of an ever-changing chromatinic landscape. Front Genet 2022; 13:1057846. [PMID: 36468032 PMCID: PMC9709290 DOI: 10.3389/fgene.2022.1057846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/02/2022] [Indexed: 07/29/2023] Open
Abstract
Chromatin maintenance and remodeling are processes that take place alongside DNA repair, replication, or transcription to ensure the survival and adaptability of a cell. The environment and the needs of the cell dictate how chromatin is remodeled; particularly where and which histones are deposited, thus changing the canonical histone array to regulate chromatin structure and gene expression. Chromatin is highly dynamic, and histone variants and their chaperones play a crucial role in maintaining the epigenetic regulation at different genomic regions. Despite the large number of histone variants reported to date, studies on their roles in physiological processes and pathologies are emerging but continue to be scarce. Here, we present recent advances in the research on histone variants and their chaperones, with a focus on their importance in molecular mechanisms such as replication, transcription, and DNA damage repair. Additionally, we discuss the emerging role they have in transposable element regulation, aging, and chromatin remodeling syndromes. Finally, we describe currently used methods and their limitations in the study of these proteins and highlight the importance of improving the experimental approaches to further understand this epigenetic machinery.
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Affiliation(s)
- Karla Torres-Arciga
- Doctorado en Ciencias Biológicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Manuel Flores-León
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Samuel Ruiz-Pérez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Magalli Trujillo-Pineda
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Luis A. Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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4
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Zhang M, Zhao X, Feng X, Hu X, Zhao X, Lu W, Lu X. Histone chaperone HIRA complex regulates retrotransposons in embryonic stem cells. Stem Cell Res Ther 2022; 13:137. [PMID: 35365225 PMCID: PMC8973876 DOI: 10.1186/s13287-022-02814-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone cell cycle regulator (HIRA) complex is an important histone chaperone that mediates the deposition of the H3.3 histone variant onto chromatin independently from DNA synthesis. However, it is still unknown whether it participates in the expression control of retrotransposons and cell fate determination. METHODS We screened the role of HIRA complex members in repressing the expression of retrotransposons by shRNA depletion in embryonic stem cells (ESCs) followed by RT-qPCR. RNA-seq was used to study the expression profiles after depletion of individual HIRA member. RT-qPCR and western blot were used to determine overexpression of HIRA complex members. Chromatin immunoprecipitation (ChIP)-qPCR was used to find the binding of H3.3, HIRA members to chromatin. Co-immunoprecipitation was used to identify the interaction between Hira mutant and Ubn2. ChIP-qPCR was used to identify H3.3 deposition change and western blot of chromatin extract was used to validate the epigenetic change. Bioinformatics analysis was applied for the analysis of available ChIP-seq data. RESULTS We revealed that Hira, Ubn2, and Ubn1 were the main repressors of 2-cell marker retrotransposon MERVL among HIRA complex members. Surprisingly, Ubn2 and Hira targeted different groups of retrotransposons and retrotransposon-derived long noncoding RNAs (lncRNAs), despite that they partially shared target genes. Furthermore, Ubn2 prevented ESCs to gain a 2-cell like state or activate trophectodermal genes upon differentiation. Mechanistically, Ubn2 and Hira suppressed retrotransposons by regulating the deposition of histone H3.3. Decreased H3.3 deposition, that was associated with the loss of Ubn2 or Hira, caused the reduction of H3K9me2 and H3K9me3, which are known repressive marks of retrotransposons. CONCLUSIONS Overall, our findings shed light on the distinct roles of HIRA complex members in controlling retrotransposons and cell fate conversion in ESCs.
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Affiliation(s)
- Miao Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | - Xin Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | - Xiao Feng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | | | - Xuan Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | - Wange Lu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China.
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5
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Geis FK, Sabo Y, Chen X, Li Y, Lu C, Goff SP. CHAF1A/B mediate silencing of unintegrated HIV-1 DNAs early in infection. Proc Natl Acad Sci U S A 2022; 119:e2116735119. [PMID: 35074917 PMCID: PMC8795523 DOI: 10.1073/pnas.2116735119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/20/2021] [Indexed: 12/27/2022] Open
Abstract
Early events of the retroviral life cycle are the targets of many host restriction factors that have evolved to prevent establishment of infection. Incoming retroviral DNAs are transcriptionally silenced before integration in most cell types, and efficient viral gene expression occurs only after formation of the provirus. The molecular machinery for silencing unintegrated retroviral DNAs of HIV-1 remains poorly characterized. Here, we identified the histone chaperones CHAF1A and CHAF1B as essential factors for silencing of unintegrated HIV-1 DNAs. Using RNAi-mediated knockdown (KD) of multiple histone chaperones, we found that KD of CHAF1A or CHAF1B resulted in a pronounced increase in expression of incoming viral DNAs. The function of these two proteins in silencing was independent of their interaction partner RBBP4. Viral DNA levels accumulated to significantly higher levels in CHAF1A KD cells over controls, suggesting enhanced stabilization of actively transcribed DNAs. Chromatin immunoprecipitation assays revealed no major changes in histone loading onto viral DNAs in the absence of CHAF1A, but levels of the H3K9 trimethylation silencing mark were reduced. KD of the H3K9me3-binding protein HP1γ accelerated the expression of unintegrated HIV-1 DNAs. While CHAF1A was critical for silencing HIV-1 DNAs, it showed no role in silencing of unintegrated retroviral DNAs of mouse leukemia virus. Our study identifies CHAF1A and CHAF1B as factors involved specifically in silencing of HIV-1 DNAs early in infection. The results suggest that these factors act by noncanonical pathways, distinct from their histone loading activities, to mediate silencing of newly synthesized HIV-1 DNAs.
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Affiliation(s)
- Franziska K Geis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032
- HHMI, Columbia University Medical Center, New York, NY 10032
- Aaron Diamond AIDS Research Center, Columbia University Medical Center, New York, NY 10032
| | - Yosef Sabo
- Aaron Diamond AIDS Research Center, Columbia University Medical Center, New York, NY 10032
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032
| | - Yinglu Li
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032
| | - Chao Lu
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032
- HHMI, Columbia University Medical Center, New York, NY 10032
- Aaron Diamond AIDS Research Center, Columbia University Medical Center, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032
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6
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Goff SP. Silencing of Unintegrated Retroviral DNAs. Viruses 2021; 13:v13112248. [PMID: 34835055 PMCID: PMC8621569 DOI: 10.3390/v13112248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/23/2022] Open
Abstract
Retroviral infection delivers an RNA genome into the cytoplasm that serves as the template for the synthesis of a linear double-stranded DNA copy by the viral reverse transcriptase. Within the nucleus this linear DNA gives rise to extrachromosomal circular forms, and in a key step of the life cycle is inserted into the host genome to form the integrated provirus. The unintegrated DNA forms, like those of DNAs entering cells by other means, are rapidly loaded with nucleosomes and heavily silenced by epigenetic histone modifications. This review summarizes our present understanding of the silencing machinery for the DNAs of the mouse leukemia viruses and human immunodeficiency virus type 1. We consider the potential impact of the silencing on virus replication, on the sensing of the virus by the innate immune system, and on the formation of latent proviruses. We also speculate on the changeover to high expression from the integrated proviruses in permissive cell types, and briefly consider the silencing of proviruses even after integration in embryonic stem cells and other developmentally primitive cell types.
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Affiliation(s)
- Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
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7
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Morc3 silences endogenous retroviruses by enabling Daxx-mediated histone H3.3 incorporation. Nat Commun 2021; 12:5996. [PMID: 34650047 PMCID: PMC8516933 DOI: 10.1038/s41467-021-26288-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 09/22/2021] [Indexed: 11/08/2022] Open
Abstract
Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1-mediated H3K9me3 and DNA methylation. However, the protein network which regulates the deposition of these chromatin modifications is still incompletely understood. Here, we perform a genome-wide single guide RNA (sgRNA) screen for genes involved in ERV silencing and identify the GHKL ATPase protein Morc3 as a top-scoring hit. Morc3 knock-out (ko) cells display de-repression, reduced H3K9me3, and increased chromatin accessibility of distinct ERV families. We find that the Morc3 ATPase cycle and Morc3 SUMOylation are important for ERV chromatin regulation. Proteomic analyses reveal that Morc3 mutant proteins fail to interact with the histone H3.3 chaperone Daxx. This interaction depends on Morc3 SUMOylation and Daxx SUMO binding. Notably, in Morc3 ko cells, we observe strongly reduced histone H3.3 on Morc3 binding sites. Thus, our data demonstrate Morc3 as a critical regulator of Daxx-mediated histone H3.3 incorporation to ERV regions. Endogenous retroviruses (ERVs) compose a significant portion of mammalian genomes; however, how ERVs are regulated is not well known. Here the authors performed a genome-wide sgRNA screen to identify Morc3 as a mediator of ERV silencing. They show Morc3 associates with the H3.3 chaperone Daxx, and that loss of Morc3 leads to reduced H3.3 at ERVs.
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8
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Pastorino L, Grillo F, Albertelli M, Ghiorzo P, Bruno W. Insights into Mechanisms of Tumorigenesis in Neuroendocrine Neoplasms. Int J Mol Sci 2021; 22:ijms221910328. [PMID: 34638668 PMCID: PMC8508699 DOI: 10.3390/ijms221910328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Genomic studies have identified some of the most relevant genetic players in Neuroendocrine Neoplasm (NEN) tumorigenesis. However, we are still far from being able to draw a model that encompasses their heterogeneity, elucidates the different biological effects consequent to the identified molecular events, or incorporates extensive knowledge of molecular biomarkers and therapeutic targets. Here, we reviewed recent insights in NEN tumorigenesis from selected basic research studies on animal models, highlighting novel players in the intergenic cooperation and peculiar mechanisms including splicing dysregulation, chromatin stability, or cell dedifferentiation. Furthermore, models of tumorigenesis based on composite interactions other than a linear progression of events are proposed, exemplified by the involvement in NEN tumorigenesis of genes regulating complex functions, such as MEN1 or DAXX. Although limited by interspecies differences, animal models have proved helpful for the more in-depth study of every facet of tumorigenesis, showing that the identification of driver mutations is only one of the many necessary steps and that other mechanisms are worth investigating.
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Affiliation(s)
- Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (L.P.); (P.G.)
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy;
| | - Federica Grillo
- Anatomic Pathology Unit, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy;
- Anatomic Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 1632 Genoa, Italy
| | - Manuela Albertelli
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy;
- Endocrinology Unit, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (L.P.); (P.G.)
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy;
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (L.P.); (P.G.)
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy;
- Correspondence: ; Tel.: +39-(01)-0555-7254
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9
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Geis FK, Goff SP. Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview. Viruses 2020; 12:v12080884. [PMID: 32823517 PMCID: PMC7472088 DOI: 10.3390/v12080884] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Almost half of the human genome is made up of transposable elements (TEs), and about 8% consists of endogenous retroviruses (ERVs). ERVs are remnants of ancient exogenous retrovirus infections of the germ line. Most TEs are inactive and not detrimental to the host. They are tightly regulated to ensure genomic stability of the host and avoid deregulation of nearby gene loci. Histone-based posttranslational modifications such as H3K9 trimethylation are one of the main silencing mechanisms. Trim28 is one of the identified master regulators of silencing, which recruits most prominently the H3K9 methyltransferase Setdb1, among other factors. Sumoylation and ATP-dependent chromatin remodeling factors seem to contribute to proper localization of Trim28 to ERV sequences and promote Trim28 interaction with Setdb1. Additionally, DNA methylation as well as RNA-mediated targeting of TEs such as piRNA-based silencing play important roles in ERV regulation. Despite the involvement of ERV overexpression in several cancer types, autoimmune diseases, and viral pathologies, ERVs are now also appreciated for their potential positive role in evolution. ERVs can provide new regulatory gene elements or novel binding sites for transcription factors, and ERV gene products can even be repurposed for the benefit of the host.
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Affiliation(s)
- Franziska K. Geis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
| | - Stephen P. Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
- Correspondence: ; Tel.: +1-212-305-3794
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10
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Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans-Acting Modifiers. Viruses 2020; 12:v12080810. [PMID: 32727076 PMCID: PMC7472028 DOI: 10.3390/v12080810] [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: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation.
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11
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Fukuda K, Shinkai Y. SETDB1-Mediated Silencing of Retroelements. Viruses 2020; 12:E596. [PMID: 32486217 PMCID: PMC7354471 DOI: 10.3390/v12060596] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
SETDB1 (SET domain bifurcated histone lysine methyltransferase 1) is a protein lysine methyltransferase and methylates histone H3 at lysine 9 (H3K9). Among other H3K9 methyltransferases, SETDB1 and SETDB1-mediated H3K9 trimethylation (H3K9me3) play pivotal roles for silencing of endogenous and exogenous retroelements, thus contributing to genome stability against retroelement transposition. Furthermore, SETDB1 is highly upregulated in various tumor cells. In this article, we describe recent advances about how SETDB1 activity is regulated, how SETDB1 represses various types of retroelements such as L1 and class I, II, and III endogenous retroviruses (ERVs) in concert with other epigenetic factors such as KAP1 and the HUSH complex and how SETDB1-mediated H3K9 methylation can be maintained during replication.
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Affiliation(s)
- Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako 351-0198, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako 351-0198, Japan
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12
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Unintegrated HIV-1 DNAs are loaded with core and linker histones and transcriptionally silenced. Proc Natl Acad Sci U S A 2019; 116:23735-23742. [PMID: 31685613 DOI: 10.1073/pnas.1912638116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Upon delivery into the nucleus of the host cell, linear double-stranded retroviral DNAs are either integrated into the host genome to form the provirus or act as a target of the DNA damage response and become circularized. Little is known about the chromatinization status of the unintegrated retroviral DNAs of the human immunodeficiency virus type 1 (HIV-1). In this study, we used chromatin immunoprecipitation to investigate the nature of unintegrated HIV-1 DNAs and discovered that core histones, the histone variant H3.3, and H1 linker histones are all deposited onto extrachromosomal HIV-1 DNA. We performed a time-course analysis and determined that the loading of core and linker histones occurred early after virus application. H3.3 and H1 linker histones were also found to be loaded onto unintegrated DNAs of the Moloney murine leukemia virus. The unintegrated retroviral DNAs are potently silenced, and we provide evidence that the suppression of extrachromosomal HIV-1 DNA is histone-related. Unintegrated DNAs were marked by posttranslational histone modifications characteristic of transcriptionally inactive genes: high levels of H3K9 trimethylation and low levels of H3 acetylation. These findings reveal insights into the nature of unintegrated retroviral DNAs.
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Vermeulen N, Pleyers G, Mermillod M, Corneille O, Schaefer A. Desperately seeking friends: How expectation of punishment modulates attention to angry and happy faces. VISUAL COGNITION 2019. [DOI: 10.1080/13506285.2019.1676351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Nicolas Vermeulen
- Psychological Science Research Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- National Fund for Scientific Research, Belgium
| | - Gordy Pleyers
- Louvain School of Management, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Olivier Corneille
- Psychological Science Research Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Alexandre Schaefer
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Subang Jaya, Malaysia
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Ishak CA, Classon M, De Carvalho DD. Deregulation of Retroelements as an Emerging Therapeutic Opportunity in Cancer. Trends Cancer 2018; 4:583-597. [DOI: 10.1016/j.trecan.2018.05.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 12/26/2022]
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Robbez-Masson L, Tie CH, Conde L, Tunbak H, Husovsky C, Tchasovnikarova IA, Timms RT, Herrero J, Lehner PJ, Rowe HM. The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes. Genome Res 2018; 28:836-845. [PMID: 29728366 PMCID: PMC5991525 DOI: 10.1101/gr.228171.117] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/23/2018] [Indexed: 11/24/2022]
Abstract
Retrotransposons encompass half of the human genome and contribute to the formation of heterochromatin, which provides nuclear structure and regulates gene expression. Here, we asked if the human silencing hub (HUSH) complex is necessary to silence retrotransposons and whether it collaborates with TRIM28 and the chromatin remodeler ATRX at specific genomic loci. We show that the HUSH complex contributes to de novo repression and DNA methylation of an SVA retrotransposon reporter. By using naïve versus primed mouse pluripotent stem cells, we reveal a critical role for the HUSH complex in naïve cells, implicating it in programming epigenetic marks in development. Although the HUSH component FAM208A binds to endogenous retroviruses (ERVs) and long interspersed element-1s (LINE-1s or L1s), it is mainly required to repress evolutionarily young L1s (mouse-specific lineages <5 million years old). TRIM28, in contrast, is necessary to repress both ERVs and young L1s. Genes co-repressed by TRIM28 and FAM208A are evolutionarily young, or exhibit tissue-specific expression, are enriched in young L1s, and display evidence for regulation through LTR promoters. Finally, we demonstrate that the HUSH complex is also required to repress L1 elements in human cells. Overall, these data indicate that the HUSH complex and TRIM28 co-repress young retrotransposons and new genes rewired by retrotransposon noncoding DNA.
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Affiliation(s)
- Luisa Robbez-Masson
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Christopher H.C. Tie
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
| | - Hale Tunbak
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Connor Husovsky
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Iva A. Tchasovnikarova
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Richard T. Timms
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
| | - Paul J. Lehner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Helen M. Rowe
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
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Affiliation(s)
- Simon J Elsässer
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Kyung-Min Noh
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Nichole Diaz
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Laura A Banaszynski
- Cecil H. and Ida Green Center for Reproductive Biology Science and Children's Medical Center Research Institute, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
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