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Barakat S, Ezen E, Devecioğlu İ, Gezen M, Piepoli S, Erman B. Dimerization choice and alternative functions of ZBTB transcription factors. FEBS J 2024; 291:237-255. [PMID: 37450366 DOI: 10.1111/febs.16905] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 06/09/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Zinc Finger DNA-binding domain-containing proteins are the most populous family among eukaryotic transcription factors. Among these, members of the BTB domain-containing ZBTB sub-family are mostly known for their transcriptional repressive functions. In this Viewpoint article, we explore molecular mechanisms that potentially diversify the function of ZBTB proteins based on their homo and heterodimerization, alternative splicing and post-translational modifications. We describe how the BTB domain is as much a scaffold for the assembly of co-repressors, as a domain that regulates protein stability. We highlight another mechanism that regulates ZBTB protein stability: phosphorylation in the zinc finger domain. We explore the non-transcriptional, structural roles of ZBTB proteins and highlight novel findings that describe the ability of ZBTB proteins to associate with poly adenosine ribose in the nucleus during the DNA damage response. Herein, we discuss the contribution of BTB domain scaffolds to the formation of transcriptional repressive complexes, to chromosome compartmentalization and their non-transcriptional, purely structural functions in the nucleus.
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Affiliation(s)
- Sarah Barakat
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Ege Ezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - İzem Devecioğlu
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Melike Gezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Sofia Piepoli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
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2
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Lear TB, Boudreau ÁN, Lockwood KC, Chu E, Camarco DP, Cao Q, Nguyen M, Evankovich JW, Finkel T, Liu Y, Chen BB. E3 ubiquitin ligase ZBTB25 suppresses beta coronavirus infection through ubiquitination of the main viral protease MPro. J Biol Chem 2023; 299:105388. [PMID: 37890782 PMCID: PMC10679490 DOI: 10.1016/j.jbc.2023.105388] [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: 05/19/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The main protease of severe acute respiratory syndrome coronavirus 2, Mpro, is a key viral protein essential for viral infection and replication. Mpro has been the target of many pharmacological efforts; however, the host-specific regulation of Mpro protein remains unclear. Here, we report the ubiquitin-proteasome-dependent degradation of Mpro protein in human cells, facilitated by the human E3 ubiquitin ligase ZBTB25. We demonstrate that Mpro has a short half-life that is prolonged via proteasomal inhibition, with its Lys-100 residue serving as a potential ubiquitin acceptor. Using in vitro binding assays, we observed ZBTB25 and Mpro bind to each other in vitro, and using progressive deletional mapping, we further uncovered the required domains for this interaction. Finally, we used an orthologous beta-coronavirus infection model and observed that genetic ablation of ZBTB25 resulted in a more highly infective virus, an effect lost upon reconstitution of ZBTB25 to deleted cells. In conclusion, these data suggest a new mechanism of Mpro protein regulation as well as identify ZBTB25 as an anticoronaviral E3 ubiquitin ligase.
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Affiliation(s)
- Travis B Lear
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Áine N Boudreau
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Karina C Lockwood
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Elise Chu
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Daniel P Camarco
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Qing Cao
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Matthew Nguyen
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - John W Evankovich
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Toren Finkel
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuan Liu
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bill B Chen
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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3
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Ct Chow C, Kobayashi M, Kambe G, Harada H. ZBTB2 is recruited to a specific subset of HIF-1 target loci to facilitate full gene expression under hypoxia. J Mol Biol 2023:168162. [PMID: 37257772 DOI: 10.1016/j.jmb.2023.168162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
The cellular response to hypoxia is mainly governed by a transcription factor, hypoxia-inducible factor 1 (HIF-1). Although upregulation of HIF-1 target genes has been hypothesized to require interaction of HIF-1 with other coactivators, much remains to be elucidated regarding the underlying mechanisms. Here, we demonstrate that zinc finger and BTB domain-containing protein 2 (ZBTB2) enhances the expression of certain HIF-1 target genes under hypoxia. ChIP-Seq analysis showed that there is a subset of HIF-1 target genes with overlapping HIF-1 and ZBTB2 peaks. Examination of a representative gene, EGFR antisense RNA 1 (EGFR-AS1), showed that HIF-1 binding to the consensus hypoxia-responsive element (HRE) sequence resulted in the recruitment of ZBTB2 to the gene locus and increased p300-mediated histone acetylation, leading to enhanced gene expression under hypoxia. In contrast, expression of HIF-1 target genes lacking ZBTB2 peaks, such as carbonic anhydrase 9 (CA9), was not upregulated by ZBTB2. These findings demonstrate that ZBTB2 is a novel factor that can be recruited to the vicinity of HREs on a subset of HIF-1 target gene loci, and is required for their full expression under hypoxia.
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Affiliation(s)
- Christalle Ct Chow
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Minoru Kobayashi
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Genome Repair Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Gouki Kambe
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroshi Harada
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Genome Repair Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.
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4
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Bonchuk A, Balagurov K, Georgiev P. BTB domains: A structural view of evolution, multimerization, and protein-protein interactions. Bioessays 2023; 45:e2200179. [PMID: 36449605 DOI: 10.1002/bies.202200179] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 12/02/2022]
Abstract
Broad-complex, Tramtrack, and Bric-à-brac/poxvirus and zinc finger (BTB/POZ) is a conserved domain found in many eukaryotic proteins with diverse cellular functions. Recent studies revealed its importance in multiple developmental processes as well as in the onset and progression of oncological diseases. Most BTB domains can form multimers and selectively interact with non-BTB proteins. Structural studies of BTB domains delineated the presence of different interfaces involved in various interactions mediated by BTBs and provided a basis for the specific inhibition of distinct protein-interaction interfaces. BTB domains originated early in eukaryotic evolution and progressively adapted their structural elements to perform distinct functions. In this review, we summarize and discuss the structural principles of protein-protein interactions mediated by BTB domains based on the recently published structural data and advances in protein modeling. We propose an update to the structure-based classification of BTB domain families and discuss their evolutionary interconnections.
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Affiliation(s)
- Artem Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Balagurov
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
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Piepoli S, Barakat S, Nogay L, Şimşek B, Akkose U, Taskiran H, Tolay N, Gezen M, Yeşilada CY, Tuncay M, Adebali O, Atilgan C, Erman B. Sibling rivalry among the ZBTB transcription factor family: homodimers versus heterodimers. Life Sci Alliance 2022; 5:5/11/e202201474. [PMID: 36096675 PMCID: PMC9468604 DOI: 10.26508/lsa.202201474] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
BTB domains potentially can form homo- or heterodimers. The study examines the dimerization choice of several BTB domains and finds only one heterodimer, while all tested pairs can homodimerize. The BTB domain is an oligomerization domain found in over 300 proteins encoded in the human genome. In the family of BTB domain and zinc finger–containing (ZBTB) transcription factors, 49 members share the same protein architecture. The N-terminal BTB domain is structurally conserved among the family members and serves as the dimerization site, whereas the C-terminal zinc finger motifs mediate DNA binding. The available BTB domain structures from this family reveal a natural inclination for homodimerization. In this study, we investigated the potential for heterodimer formation in the cellular environment. We selected five BTB homodimers and four heterodimer structures. We performed cell-based binding assays with fluorescent protein–BTB domain fusions to assess dimer formation. We tested the binding of several BTB pairs, and we were able to confirm the heterodimeric physical interaction between the BTB domains of PATZ1 and PATZ2, previously reported only in an interactome mapping experiment. We also found this pair to be co-expressed in several immune system cell types. Finally, we used the available structures of BTB domain dimers and newly constructed models in extended molecular dynamics simulations (500 ns) to understand the energetic determinants of homo- and heterodimer formation. We conclude that heterodimer formation, although frequently described as less preferred than homodimers, is a possible mechanism to increase the combinatorial specificity of this transcription factor family.
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Affiliation(s)
- Sofia Piepoli
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Sarah Barakat
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Liyne Nogay
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Büşra Şimşek
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Umit Akkose
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Hakan Taskiran
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Nazife Tolay
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Melike Gezen
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Canberk Yarkın Yeşilada
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Mustafa Tuncay
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Ogün Adebali
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
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Jayathirtha M, Neagu AN, Whitham D, Alwine S, Darie CC. Investigation of the effects of downregulation of jumping translocation breakpoint (JTB) protein expression in MCF7 cells for potential use as a biomarker in breast cancer. Am J Cancer Res 2022; 12:4373-4398. [PMID: 36225631 PMCID: PMC9548009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/18/2022] [Indexed: 06/16/2023] Open
Abstract
MCF7 is a commonly used luminal type A non-invasive/poor-invasive human breast cancer cell line that does not usually migrate or invade compared with MDA-MB-231 highly metastatic cells, which emphasize an invasive and migratory behavior. Under special conditions, MCF7 cells might acquire invasive features. The aberration in expression and biological functions of the jumping translocation breackpoint (JTB) protein is associated with malignant transformation of cells, based on mitochondrial dysfunction, inhibition of tumor suppressive function of TGF-β, and involvement in cancer cell cycle. To investigate new putative functions of JTB by cellular proteomics, we analyzed the biological processes and pathways that are associated with the JTB protein downregulation. The results demonstrated that MCF7 cell line developed a more "aggressive" phenotype and behavior. Most of the proteins that were overexpressed in this experiment promoted the actin cytoskeleton reorganization that is involved in growth and metastatic dissemination of cancer cells. Some of these proteins are involved in the epithelial-mesenchymal transition (EMT) process (ACTBL2, TUBA4A, MYH14, CSPG5, PKM, UGDH, HSP90AA2, and MIF), in correlation with the energy metabolism reprogramming (PKM, UGDH), stress-response (HSP10, HSP70A1A, HSP90AA2), and immune and inflammatory response (MIF and ERp57-TAPBP). Almost all upregulated proteins in JTB downregulated condition promote viability, motility, proliferation, invasion, survival into a hostile microenvironment, metabolic reprogramming, and escaping of tumor cells from host immune control, leading to a more invasive phenotype for MCF7 cell line. Due to their downregulated condition, four proteins, such as CREBZF, KMT2B, SELENOS and CACNA1I are also involved in maintenance of the invasive phenotype of cancer cells, promoting cell proliferation, migration, invasion and tumorigenesis. Other downregulated proteins, such as MAZ, PLEKHG2, ENO1, TPI2, TOR2A, and CNNM1, may promote suppression of cancer cell growth, invasion, EMT, tumorigenic abilities, interacting with glucose and lipid metabolism, disrupting nuclear envelope stability, or suppressing apoptosis and developing anti-angiogenetic activities. Therefore, the main biological processes and pathways that may increase the tumorigenic potential of the MCF7 cells in JTB downregulated condition are related to the actin cytoskeleton organization, EMT, mitotic cell cycle, glycolysis and fatty acid metabolism, inflammatory response and macrophage activation, chemotaxis and migration, cellular response to stress condition (oxidative stress and hypoxia), transcription control, histone modification and ion transport.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of IasiCarol I bvd. No. 22, Iasi 700505, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Shelby Alwine
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
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Gao Y, Zamisch M, Vacchio M, Chopp L, Ciucci T, Paine EL, Lyons GC, Nie J, Xiao Q, Zvezdova E, Love PE, Vinson CR, Jenkins LM, Bosselut R. NuRD complex recruitment to Thpok mediates CD4 + T cell lineage differentiation. Sci Immunol 2022; 7:eabn5917. [PMID: 35687698 DOI: 10.1126/sciimmunol.abn5917] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although BTB-zinc finger (BTB-ZF) transcription factors control the differentiation of multiple hematopoietic and immune lineages, how they function is poorly understood. The BTB-ZF factor Thpok controls intrathymic CD4+ T cell development and the expression of most CD4+ and CD8+ lineage genes. Here, we identify the nucleosome remodeling and deacetylase (NuRD) complex as a critical Thpok cofactor. Using mass spectrometry and coimmunoprecipitation in primary T cells, we show that Thpok binds NuRD components independently of DNA association. We locate three amino acid residues within the Thpok BTB domain that are required for both NuRD binding and Thpok functions. Conversely, a chimeric protein merging the NuRD component Mta2 to a BTB-less version of Thpok supports CD4+ T cell development, indicating that NuRD recruitment recapitulates the functions of the Thpok BTB domain. We found that NuRD mediates Thpok repression of CD8+ lineage genes, including the transcription factor Runx3, but is dispensable for Cd4 expression. We show that these functions cannot be performed by the BTB domain of the Thpok-related factor Bcl6, which fails to bind NuRD. Thus, cofactor binding critically contributes to the functional specificity of BTB-ZF factors, which control the differentiation of most hematopoietic subsets.
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Affiliation(s)
- Yayi Gao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Monica Zamisch
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Melanie Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Laura Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.,Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA, USA
| | - Thomas Ciucci
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Elliott L Paine
- Collaborative Protein Technology Resource, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gaelyn C Lyons
- Collaborative Protein Technology Resource, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jia Nie
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Qi Xiao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ekaterina Zvezdova
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Paul E Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Charles R Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa M Jenkins
- Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA, USA
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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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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