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Fukushima HS, Ikeda T, Ikeda S, Takeda H. Cell cycle length governs heterochromatin reprogramming during early development in non-mammalian vertebrates. EMBO Rep 2024:10.1038/s44319-024-00188-5. [PMID: 38943003 DOI: 10.1038/s44319-024-00188-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/30/2024] Open
Abstract
Heterochromatin marks such as H3K9me3 undergo global erasure and re-establishment after fertilization, and the proper reprogramming of H3K9me3 is essential for early development. Despite the widely conserved dynamics of heterochromatin reprogramming in invertebrates and non-mammalian vertebrates, previous studies have shown that the underlying mechanisms may differ between species. Here, we investigate the molecular mechanism of H3K9me3 dynamics in medaka (Japanese killifish, Oryzias latipes) as a non-mammalian vertebrate model, and show that rapid cell cycle during cleavage stages causes DNA replication-dependent passive erasure of H3K9me3. We also find that cell cycle slowing, toward the mid-blastula transition, permits increasing nuclear accumulation of H3K9me3 histone methyltransferase Setdb1, leading to the onset of H3K9me3 re-accumulation. We further demonstrate that cell cycle length in early development also governs H3K9me3 reprogramming in zebrafish and Xenopus laevis. Together with the previous studies in invertebrates, we propose that a cell cycle length-dependent mechanism for both global erasure and re-accumulation of H3K9me3 is conserved among rapid-cleavage species of non-mammalian vertebrates and invertebrates such as Drosophila, C. elegans, Xenopus and teleost fish.
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Affiliation(s)
- Hiroto S Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
- Center for Integrative Medical Sciences, RIKEN, Yokohama, 230-0045, Japan.
| | - Takafumi Ikeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, 603-8555, Japan
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Shinra Ikeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan.
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2
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Kang YK, Eom J, Min B, Park JS. SETDB1 deletion causes DNA demethylation and upregulation of multiple zinc-finger genes. Mol Biol Rep 2024; 51:778. [PMID: 38904842 PMCID: PMC11192681 DOI: 10.1007/s11033-024-09703-2] [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: 03/18/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND SETDB1 (SET domain bifurcated-1) is a histone H3-lysine 9 (H3K9)-specific methyltransferase that mediates heterochromatin formation and repression of target genes. Despite the assumed functional link between DNA methylation and SETDB1-mediated H3K9 trimethylations, several studies have shown that SETDB1 operates autonomously of DNA methylation in a region- and cell-specific manner. This study analyzes SETDB1-null HAP1 cells through a linked methylome and transcriptome analysis, intending to explore genes controlled by SETDB1-involved DNA methylation. METHODS AND RESULTS We investigated SETDB1-mediated regulation of DNA methylation and gene transcription in human HAP1 cells using reduced-representation bisulfite sequencing (RRBS) and RNA sequencing. While two-thirds of differentially methylated CpGs (DMCs) in genic regions were hypomethylated in SETDB1-null cells, we detected a plethora of C2H2-type zinc-finger protein genes (C2H2-ZFP, 223 of 749) among the DMC-associated genes. Most C2H2-ZFPs with DMCs in their promoters were found hypomethylated in SETDB1-KO cells, while other non-ZFP genes with promoter DMCs were not. These C2H2-ZFPs with DMCs in their promoters were significantly upregulated in SETDB1-KO cells. Similarly, C2H2-ZFP genes were upregulated in SETDB1-null 293T cells, suggesting that SETDB1's function in ZFP gene repression is widespread. There are several C2H2-ZFP gene clusters on chromosome 19, which were selectively hypomethylated in SETDB1-KO cells. CONCLUSIONS SETDB1 collectively and specifically represses a substantial fraction of the C2H2-ZFP gene family. Through the en-bloc silencing of a set of ZFP genes, SETDB1 may help establish a panel of ZFP proteins that are expressed cell-type specifically and thereby can serve as signature proteins for cellular identity.
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Affiliation(s)
- Yong-Kook Kang
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea.
- Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea.
| | - Jaemin Eom
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
- Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea
| | - Byungkuk Min
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
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3
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Atinbayeva N, Valent I, Zenk F, Loeser E, Rauer M, Herur S, Quarato P, Pyrowolakis G, Gomez-Auli A, Mittler G, Cecere G, Erhardt S, Tiana G, Zhan Y, Iovino N. Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos. EMBO J 2024:10.1038/s44318-024-00127-z. [PMID: 38831123 DOI: 10.1038/s44318-024-00127-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024] Open
Abstract
Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 (H3K9me3) and recruitment of its epigenetic reader, heterochromatin protein 1a (HP1a), are hallmarks of constitutive heterochromatin. Here, we show that H3K9me3 is transmitted from the maternal germline to the next generation. Maternally inherited H3K9me3, and the histone methyltransferases (HMT) depositing it, are required for the organization of constitutive heterochromatin: early embryos lacking H3K9 methylation display de-condensation of pericentromeric regions, centromere-centromere de-clustering, mitotic defects, and nuclear shape irregularities, resulting in embryo lethality. Unexpectedly, quantitative CUT&Tag and 4D microscopy measurements of HP1a coupled with biophysical modeling revealed that H3K9me2/3 is largely dispensable for HP1a recruitment. Instead, the main function of H3K9me2/3 at this developmental stage is to drive HP1a clustering and subsequent heterochromatin compaction. Our results show that HP1a binding to constitutive heterochromatin in the absence of H3K9me2/3 is not sufficient to promote proper embryo development and heterochromatin formation. The loss of H3K9 HMTs and H3K9 methylation alters genome organization and hinders embryonic development.
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Affiliation(s)
- Nazerke Atinbayeva
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79085, Freiburg im Breisgau, Germany
| | - Iris Valent
- Karlsruhe Institute of Technology (KIT), Zoological Institute, 76131, Karlsruhe, Germany
| | - Fides Zenk
- Brain Mind Institute, School of Life Sciences EPFL, SV3809, 1015, Lausanne, Switzerland
| | - Eva Loeser
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Michael Rauer
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Shwetha Herur
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Piergiuseppe Quarato
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Giorgos Pyrowolakis
- Centre for Biological signaling studies, University of Freiburg, 79104, Freiburg im Breisgau, Germany
| | - Alejandro Gomez-Auli
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Germano Cecere
- Institute Pasteur, Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, UMR3738, CNRS, 75724, Cedex 15, Paris, France
| | - Sylvia Erhardt
- Karlsruhe Institute of Technology (KIT), Zoological Institute, 76131, Karlsruhe, Germany
| | - Guido Tiana
- Università degli Studi di Milano and INFN, Milan, Italy
| | - Yinxiu Zhan
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milan, Italy.
| | - Nicola Iovino
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany.
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4
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Hassanie H, Penteado AB, de Almeida LC, Calil RL, da Silva Emery F, Costa-Lotufo LV, Trossini GHG. SETDB1 as a cancer target: challenges and perspectives in drug design. RSC Med Chem 2024; 15:1424-1451. [PMID: 38799223 PMCID: PMC11113007 DOI: 10.1039/d3md00366c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 03/16/2024] [Indexed: 05/29/2024] Open
Abstract
Genome stability is governed by chromatin structural dynamics, which modify DNA accessibility under the influence of intra- and inter-nucleosomal contacts, histone post-translational modifications (PTMs) and variations, besides the activity of ATP-dependent chromatin remodelers. These are the main ways by which chromatin dynamics are regulated and connected to nuclear processes, which when dysregulated can frequently be associated with most malignancies. Recently, functional crosstalk between histone modifications and chromatin remodeling has emerged as a critical regulatory method of transcriptional regulation during cell destiny choice. Therefore, improving therapeutic outcomes for patients by focusing on epigenetic targets dysregulated in malignancies should help prevent cancer cells from developing resistance to anticancer treatments. For this reason, SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) has gained a lot of attention recently as a cancer target. SETDB1 is a histone lysine methyltransferase that plays an important role in marking euchromatic and heterochromatic regions. Hence, it promotes the silencing of tumor suppressor genes and contributes to carcinogenesis. Some studies revealed that SETDB1 was overexpressed in various human cancer types, which enhanced tumor growth and metastasis. Thus, SETDB1 appears to be an attractive epigenetic target for new cancer treatments. In this review, we have discussed the effects of its overexpression on the progression of tumors and the development of inhibitor drugs that specifically target this enzyme.
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Affiliation(s)
- Haifa Hassanie
- School of Pharmaceutical Sciences, University of São Paulo Brazil
| | | | | | | | - Flávio da Silva Emery
- School of Pharmaceutical Sciences of the Ribeirão Preto, University of São Paulo Brazil
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5
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Yang W, Wei Y, Wang T, Xu Y, Jin X, Qian H, Yang S, He S. Cytoplasmic localization of SETDB1‑induced Warburg effect via c‑MYC‑LDHA axis enhances migration and invasion in breast carcinoma. Int J Mol Med 2024; 53:40. [PMID: 38426579 PMCID: PMC10914311 DOI: 10.3892/ijmm.2024.5364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
SET domain bifurcated 1 (SETDB1), a pivotal histone lysine methyltransferase, is transported to the cytoplasm via a chromosome region maintenance 1 (CMR1)‑dependent pathway, contributing to non‑histone methylation. However, the function and underlying mechanism of cytoplasmic SETDB1 in breast cancer remain elusive. In the present study, immunohistochemistry revealed that elevated cytoplasmic SETDB1 was correlated with lymph node metastasis and more aggressive breast cancer subtypes. Functionally, wound healing and Transwell assays showed that cytoplasmic SETDB1 is key for cell migration and invasion, as well as induction of epithelial‑mesenchymal transition (EMT), which was reversed by leptomycin B (LMB, a CMR1 inhibitor) treatment. Furthermore, RNA‑seq and metabolite detection revealed that cytoplasmic SETDB1 was associated with metabolism pathway and elevated levels of metabolites involved in the Warburg effect, including glucose, pyruvate, lactate and ATP. Immunoblotting and reverse transcription‑quantitative PCR verified that elevation of cytoplasmic SETDB1 contributed to elevation of c‑MYC expression and subsequent upregulation of lactate dehydrogenase A (LDHA) expression. Notably, gain‑ and loss‑of‑function approaches revealed that LDHA overexpression in T47D cells enhanced migration and invasion by inducing EMT, while its depletion in SETDB1‑overexpressing MCF7 cells reversed SETDB1‑induced migration and invasion, as well as the Warburg effect and EMT. In conclusion, subcellular localization of cytoplasmic SETDB1 may be a pivotal factor in breast cancer progression. The present study offers valuable insight into the novel functions and mechanisms of cytoplasmic SETDB1.
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Affiliation(s)
- Wenlin Yang
- Department of Pathology, Nantong Tumor Hospital Affiliated to Nantong University, Nantong, Jiangsu 226006, P.R. China
| | - Yingze Wei
- Department of Pathology, Nantong Tumor Hospital Affiliated to Nantong University, Nantong, Jiangsu 226006, P.R. China
| | - Ting Wang
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Ying Xu
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Xiaoxia Jin
- Department of Pathology, Nantong Tumor Hospital Affiliated to Nantong University, Nantong, Jiangsu 226006, P.R. China
| | - Hongyan Qian
- Department of Pathology, Nantong Tumor Hospital Affiliated to Nantong University, Nantong, Jiangsu 226006, P.R. China
| | - Shuyun Yang
- Department of Pathology, Nantong Tumor Hospital Affiliated to Nantong University, Nantong, Jiangsu 226006, P.R. China
| | - Song He
- Department of Pathology, Nantong Tumor Hospital Affiliated to Nantong University, Nantong, Jiangsu 226006, P.R. China
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6
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Alavattam KG, Esparza JM, Hu M, Shimada R, Kohrs AR, Abe H, Munakata Y, Otsuka K, Yoshimura S, Kitamura Y, Yeh YH, Hu YC, Kim J, Andreassen PR, Ishiguro KI, Namekawa SH. ATF7IP2/MCAF2 directs H3K9 methylation and meiotic gene regulation in the male germline. Genes Dev 2024; 38:115-130. [PMID: 38383062 PMCID: PMC10982687 DOI: 10.1101/gad.351569.124] [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: 09/30/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024]
Abstract
H3K9 trimethylation (H3K9me3) plays emerging roles in gene regulation, beyond its accumulation on pericentric constitutive heterochromatin. It remains a mystery why and how H3K9me3 undergoes dynamic regulation in male meiosis. Here, we identify a novel, critical regulator of H3K9 methylation and spermatogenic heterochromatin organization: the germline-specific protein ATF7IP2 (MCAF2). We show that in male meiosis, ATF7IP2 amasses on autosomal and X-pericentric heterochromatin, spreads through the entirety of the sex chromosomes, and accumulates on thousands of autosomal promoters and retrotransposon loci. On the sex chromosomes, which undergo meiotic sex chromosome inactivation (MSCI), the DNA damage response pathway recruits ATF7IP2 to X-pericentric heterochromatin, where it facilitates the recruitment of SETDB1, a histone methyltransferase that catalyzes H3K9me3. In the absence of ATF7IP2, male germ cells are arrested in meiotic prophase I. Analyses of ATF7IP2-deficient meiosis reveal the protein's essential roles in the maintenance of MSCI, suppression of retrotransposons, and global up-regulation of autosomal genes. We propose that ATF7IP2 is a downstream effector of the DDR pathway in meiosis that coordinates the organization of heterochromatin and gene regulation through the spatial regulation of SETDB1-mediated H3K9me3 deposition.
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Affiliation(s)
- Kris G Alavattam
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Jasmine M Esparza
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Mengwen Hu
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Ryuki Shimada
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto 860-0811, Japan
| | - Anna R Kohrs
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Hironori Abe
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto 860-0811, Japan
| | - Yasuhisa Munakata
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Kai Otsuka
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Saori Yoshimura
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto 860-0811, Japan
| | - Yuka Kitamura
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Yu-Han Yeh
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Yueh-Chiang Hu
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
| | - Jihye Kim
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
| | - Paul R Andreassen
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Kei-Ichiro Ishiguro
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto 860-0811, Japan;
| | - Satoshi H Namekawa
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA;
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
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7
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Mahana Y, Ariyoshi M, Nozawa RS, Shibata S, Nagao K, Obuse C, Shirakawa M. Structural evidence for protein-protein interaction between the non-canonical methyl-CpG-binding domain of SETDB proteins and C11orf46. Structure 2024; 32:304-315.e5. [PMID: 38159574 DOI: 10.1016/j.str.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/26/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
SETDB1 and SETDB2 mediate trimethylation of histone H3 lysine 9 (H3K9), an epigenetic hallmark of repressive chromatin. They contain a non-canonical methyl-CpG-binding domain (MBD) and bifurcated SET domain, implying interplay between H3K9 trimethylation and DNA methylation in SETDB functions. Here, we report the crystal structure of human SETDB2 MBD bound to the cysteine-rich domain of a zinc-binding protein, C11orf46. SETDB2 MBD comprises the conserved MBD core and a unique N-terminal extension. Although the MBD core has the conserved basic concave surface for DNA binding, it utilizes it for recognition of the cysteine-rich domain of C11orf46. This interaction involves the conserved arginine finger motif and the unique N-terminal extension of SETDB2 MBD, with a contribution from intermolecular β-sheet formation. Thus, the non-canonical MBD of SETDB1/2 seems to have lost methylated DNA-binding ability but gained a protein-protein interaction surface. Our findings provide insight into the molecular assembly of SETDB-associated repression complexes.
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Affiliation(s)
- Yutaka Mahana
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Mariko Ariyoshi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Ryu-Suke Nozawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Sachiko Shibata
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan.
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8
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Kim SH, Park JH, Shin S, Shin S, Chun D, Kim YG, Yoo J, You WK, Lee JS, Lee GM. Genome-Wide CRISPR/Cas9 Screening Unveils a Novel Target ATF7IP-SETDB1 Complex for Enhancing Difficult-to-Express Protein Production. ACS Synth Biol 2024; 13:634-647. [PMID: 38240694 DOI: 10.1021/acssynbio.3c00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
With the emerging novel biotherapeutics that are typically difficult-to-express (DTE), improvement is required for high-yield production. To identify novel targets that can enhance DTE protein production, we performed genome-wide fluorescence-activated cell sorting (FACS)-based clustered regularly interspaced short palindromic repeats (CRISPR) knockout screening in bispecific antibody (bsAb)-producing Chinese hamster ovary (CHO) cells. The screen identified the two highest-scoring genes, Atf7ip and Setdb1, which are the binding partners for H3K9me3-mediated transcriptional repression. The ATF7IP-SETDB1 complex knockout in bsAb-producing CHO cells suppressed cell growth but enhanced productivity by up to 2.7-fold. Decreased H3K9me3 levels and an increased transcriptional expression level of the transgene were also observed. Furthermore, perturbation of the ATF7IP-SETDB1 complex in monoclonal antibody (mAb)-producing CHO cells led to substantial improvements in mAb production, increasing the productivity by up to 3.9-fold without affecting the product quality. Taken together, the genome-wide FACS-based CRISPR screen identified promising targets associated with histone methylation, whose perturbation enhanced the productivity by unlocking the transgene expression.
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Affiliation(s)
- Su Hyun Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Jong-Ho Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
- Biotherapeutics Translational Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Sungwook Shin
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Seunghyeon Shin
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Dahyun Chun
- Department of R&D, ABL Bio Inc, Seongnam 13488, Republic of Korea
| | - Yeon-Gu Kim
- Biotherapeutics Translational Research Center, KRIBB, Daejeon 34141, Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, UST, , Daejeon 34113, Republic of Korea
| | - Jiseon Yoo
- Department of R&D, ABL Bio Inc, Seongnam 13488, Republic of Korea
| | - Weon-Kyoo You
- Department of R&D, ABL Bio Inc, Seongnam 13488, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
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9
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Koryakov DE. Diversity and functional specialization of H3K9-specific histone methyltransferases. Bioessays 2024; 46:e2300163. [PMID: 38058121 DOI: 10.1002/bies.202300163] [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: 08/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Histone modifications play a critical role in the control over activities of the eukaryotic genome; among these chemical alterations, the methylation of lysine K9 in histone H3 (H3K9) is one of the most extensively studied. The number of enzymes capable of methylating H3K9 varies greatly across different organisms: in fission yeast, only one such methyltransferase is present, whereas in mammals, 10 are known. If there are several such enzymes, each of them must have some specific function, and they can interact with one another. Thus arises a complex system of interchangeability, "division of labor," and contacts with each other and with diverse proteins. Histone methyltransferases specialize in the number of methyl groups that they attach and have different intracellular localizations as well as different distributions on chromosomes. Each also shows distinct binding to different types of sequences and has a specific set of nonhistone substrates.
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Affiliation(s)
- Dmitry E Koryakov
- Lab of Molecular Cytogenetics, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
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10
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Lu X. Regulation of endogenous retroviruses in murine embryonic stem cells and early embryos. J Mol Cell Biol 2024; 15:mjad052. [PMID: 37604781 PMCID: PMC10794949 DOI: 10.1093/jmcb/mjad052] [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: 06/08/2022] [Revised: 11/24/2022] [Accepted: 08/19/2023] [Indexed: 08/23/2023] Open
Abstract
Endogenous retroviruses (ERVs) are important components of transposable elements that constitute ∼40% of the mouse genome. ERVs exhibit dynamic expression patterns during early embryonic development and are engaged in numerous biological processes. Therefore, ERV expression must be closely monitored in cells. Most studies have focused on the regulation of ERV expression in mouse embryonic stem cells (ESCs) and during early embryonic development. This review touches on the classification, expression, and functions of ERVs in mouse ESCs and early embryos and mainly discusses ERV modulation strategies from the perspectives of transcription, epigenetic modification, nucleosome/chromatin assembly, and post-transcriptional control.
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Affiliation(s)
- Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China
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11
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Müller I, Helin K. Keep quiet: the HUSH complex in transcriptional silencing and disease. Nat Struct Mol Biol 2024; 31:11-22. [PMID: 38216658 DOI: 10.1038/s41594-023-01173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/23/2023] [Indexed: 01/14/2024]
Abstract
The human silencing hub (HUSH) complex is an epigenetic repressor complex whose role has emerged as an important guardian of genome integrity. It protects the genome from exogenous DNA invasion and regulates endogenous retroelements by recruiting histone methyltransferases catalyzing histone 3 lysine 9 trimethylation (H3K9me3) and additional proteins involved in chromatin compaction. In particular, its regulation of transcriptionally active LINE1 retroelements, by binding to and neutralizing LINE1 transcripts, has been well characterized. HUSH is required for mouse embryogenesis and is associated with disease, in particular cancer. Here we provide insights into the structural and biochemical features of the HUSH complex. Furthermore, we discuss the molecular mechanisms by which the HUSH complex is recruited to specific genomic regions and how it silences transcription. Finally, we discuss the role of HUSH complex members in mammalian development, antiretroviral immunity, and diseases such as cancer.
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Affiliation(s)
- Iris Müller
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristian Helin
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- The Institute of Cancer Research, London, UK.
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12
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Luo H, Wu X, Zhu XH, Yi X, Du D, Jiang DS. The functions of SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) in biological process and disease. Epigenetics Chromatin 2023; 16:47. [PMID: 38057834 DOI: 10.1186/s13072-023-00519-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 12/08/2023] Open
Abstract
Histone methyltransferase SETDB1 (SET domain bifurcated histone lysine methyltransferase 1, also known as ESET or KMT1E) is known to be involved in the deposition of the di- and tri-methyl marks on H3K9 (H3K9me2 and H3K9me3), which are associated with transcription repression. SETDB1 exerts an essential role in the silencing of endogenous retroviruses (ERVs) in embryonic stem cells (mESCs) by tri-methylating H3K9 (H3K9me3) and interacting with DNA methyltransferases (DNMTs). Additionally, SETDB1 is engaged in regulating multiple biological processes and diseases, such as ageing, tumors, and inflammatory bowel disease (IBD), by methylating both histones and non-histone proteins. In this review, we provide an overview of the complex biology of SETDB1, review the upstream regulatory mechanisms of SETDB1 and its partners, discuss the functions and molecular mechanisms of SETDB1 in cell fate determination and stem cell, as well as in tumors and other diseases. Finally, we discuss the current challenges and prospects of targeting SETDB1 for the treatment of different diseases, and we also suggest some future research directions in the field of SETDB1 research.
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Affiliation(s)
- Hanshen Luo
- Division of Cardiovascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, 430030, China
| | - Xingliang Wu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xue-Hai Zhu
- Division of Cardiovascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, China
| | - Xin Yi
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Dunfeng Du
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, China.
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Ding-Sheng Jiang
- Division of Cardiovascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, 430030, China.
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, China.
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13
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Sarkar K, Kotb NM, Lemus A, Martin ET, McCarthy A, Camacho J, Iqbal A, Valm AM, Sammons MA, Rangan P. A feedback loop between heterochromatin and the nucleopore complex controls germ-cell-to-oocyte transition during Drosophila oogenesis. Dev Cell 2023; 58:2580-2596.e6. [PMID: 37673064 DOI: 10.1016/j.devcel.2023.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/12/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023]
Abstract
Germ cells differentiate into oocytes that launch the next generation upon fertilization. How the highly specialized oocyte acquires this distinct cell fate is poorly understood. During Drosophila oogenesis, H3K9me3 histone methyltransferase SETDB1 translocates from the cytoplasm to the nucleus of germ cells concurrently with oocyte specification. Here, we discovered that nuclear SETDB1 is required for silencing a cohort of differentiation-promoting genes by mediating their heterochromatinization. Intriguingly, SETDB1 is also required for upregulating 18 of the ∼30 nucleoporins (Nups) that compose the nucleopore complex (NPC), promoting NPC formation. NPCs anchor SETDB1-dependent heterochromatin at the nuclear periphery to maintain H3K9me3 and gene silencing in the egg chambers. Aberrant gene expression due to the loss of SETDB1 or Nups results in the loss of oocyte identity, cell death, and sterility. Thus, a feedback loop between heterochromatin and NPCs promotes transcriptional reprogramming at the onset of oocyte specification, which is critical for establishing oocyte identity.
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Affiliation(s)
- Kahini Sarkar
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Noor M Kotb
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA; Department of Biomedical Sciences, School of Public Health, University at Albany SUNY, Albany, NY 12222, USA
| | - Alex Lemus
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Elliot T Martin
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Alicia McCarthy
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Justin Camacho
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Ayman Iqbal
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Alex M Valm
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Morgan A Sammons
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Prashanth Rangan
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA.
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14
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Cui X, Shang X, Xie J, Xie C, Tang Z, Luo Q, Wu C, Wang G, Wang N, He K, Wang L, Huang L, Wan B, Roeder RG, Han ZG. Cooperation between IRTKS and deubiquitinase OTUD4 enhances the SETDB1-mediated H3K9 trimethylation that promotes tumor metastasis via suppressing E-cadherin expression. Cancer Lett 2023; 575:216404. [PMID: 37739210 DOI: 10.1016/j.canlet.2023.216404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Elevated expression and genetic aberration of IRTKS, also named as BAIAP2L1, have been observed in many tumors, especially in tumor progression. however, the molecular and cellular mechanisms involved in the IRTKS-enhanced tumor progression are obscure. Here we show that higher IRTKS level specifically increases histone H3 lysine 9 trimethylation (H3K9me3) by promoting accumulation of the histone methyltransferase SETDB1. Furthermore, we reveal that IRTKS recruits the deubiquitinase OTUD4 to remove Lys48-linked polyubiquitination at K182/K1050 sites of SETDB1, thus blocking SETDB1 degradation via the ubiquitin-proteasome pathway. Interestingly, the enhanced IRTKS-OTUD4-SETDB1-H3K9me3 axis leads to a general decrease in chromatin accessibility, which inhibits transcription of CDH1 encoding E-cadherin, a key molecule essential for maintaining epithelial cell phenotype, and therefore results in epithelial-mesenchymal transition (EMT) and malignant cell metastasis. Clinically, the elevated IRTKS levels in tumor specimens correlate with SETDB1 levels, but negatively associate with survival time. Our data reveal a novel mechanism for the IRTKS-enhanced tumor progression, where IRTKS cooperates with OTUD4 to enhance SETDB1-mediated H3K9 trimethylation that promotes tumor metastasis via suppressing E-cadherin expression. This study also provides a potential approach to reduce the activity and stability of the known therapeutic target SETDB1 possibly through regulating IRTKS or deubiquitinase OTUD4.
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Affiliation(s)
- Xiaofang Cui
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueying Shang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jia Xie
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chenyi Xie
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Qing Luo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chongchao Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guangxing Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Na Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kunyan He
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liyu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bingbing Wan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
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15
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Alavattam KG, Esparza JM, Hu M, Shimada R, Kohrs AR, Abe H, Munakata Y, Otsuka K, Yoshimura S, Kitamura Y, Yeh YH, Hu YC, Kim J, Andreassen PR, Ishiguro KI, Namekawa SH. ATF7IP2/MCAF2 directs H3K9 methylation and meiotic gene regulation in the male germline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560314. [PMID: 37873266 PMCID: PMC10592865 DOI: 10.1101/2023.09.30.560314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
H3K9 tri-methylation (H3K9me3) plays emerging roles in gene regulation, beyond its accumulation on pericentric constitutive heterochromatin. It remains a mystery why and how H3K9me3 undergoes dynamic regulation in male meiosis. Here, we identify a novel, critical regulator of H3K9 methylation and spermatogenic heterochromatin organization: the germline-specific protein ATF7IP2 (MCAF2). We show that, in male meiosis, ATF7IP2 amasses on autosomal and X pericentric heterochromatin, spreads through the entirety of the sex chromosomes, and accumulates on thousands of autosomal promoters and retrotransposon loci. On the sex chromosomes, which undergo meiotic sex chromosome inactivation (MSCI), the DNA damage response pathway recruits ATF7IP2 to X pericentric heterochromatin, where it facilitates the recruitment of SETDB1, a histone methyltransferase that catalyzes H3K9me3. In the absence of ATF7IP2, male germ cells are arrested in meiotic prophase I. Analyses of ATF7IP2-deficient meiosis reveal the protein's essential roles in the maintenance of MSCI, suppression of retrotransposons, and global upregulation of autosomal genes. We propose that ATF7IP2 is a downstream effector of the DDR pathway in meiosis that coordinates the organization of heterochromatin and gene regulation through the spatial regulation of SETDB1-mediated H3K9me3 deposition.
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Affiliation(s)
- Kris G. Alavattam
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- These authors contributed equally to this work
| | - Jasmine M. Esparza
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616, USA
- These authors contributed equally to this work
| | - Mengwen Hu
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616, USA
- These authors contributed equally to this work
| | - Ryuki Shimada
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, 860-0811, Japan
- These authors contributed equally to this work
| | - Anna R. Kohrs
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Hironori Abe
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616, USA
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yasuhisa Munakata
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616, USA
| | - Kai Otsuka
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616, USA
| | - Saori Yoshimura
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yuka Kitamura
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616, USA
| | - Yu-Han Yeh
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616, USA
| | - Yueh-Chiang Hu
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
| | - Jihye Kim
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1, Yayoi, Tokyo, 113-0032, Japan
| | - Paul R. Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
| | - Kei-ichiro Ishiguro
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, 860-0811, Japan
| | - Satoshi H. Namekawa
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
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16
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Shao Q, Zhang Y, Liu Y, Shang Y, Li S, Liu L, Wang G, Zhou X, Wang P, Gao J, Zhou J, Zhang L, Wang S. ATF7IP2, a meiosis-specific partner of SETDB1, is required for proper chromosome remodeling and crossover formation during spermatogenesis. Cell Rep 2023; 42:112953. [PMID: 37542719 DOI: 10.1016/j.celrep.2023.112953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/25/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023] Open
Abstract
Meiotic crossovers are required for the faithful segregation of homologous chromosomes and to promote genetic diversity. However, it is unclear how crossover formation is regulated, especially on the XY chromosomes, which show a homolog only at the tiny pseudoautosomal region. Here, we show that ATF7IP2 is a meiosis-specific ortholog of ATF7IP and a partner of SETDB1. In the absence of ATF7IP2, autosomes show increased axis length and more crossovers; however, many XY chromosomes lose the obligatory crossover, although the overall XY axis length is also increased. Additionally, meiotic DNA double-strand break formation/repair may also be affected by altered histone modifications. Ultimately, spermatogenesis is blocked, and male mice are infertile. These findings suggest that ATF7IP2 constraints autosomal axis length and crossovers on autosomes; meanwhile, it also modulates XY chromosomes to establish meiotic sex chromosome inactivation for cell-cycle progression and to ensure XY crossover formation during spermatogenesis.
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Affiliation(s)
- Qiqi Shao
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China
| | - Yanan Zhang
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China
| | - Yanlei Liu
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China
| | - Yongliang Shang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Si Li
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Lin Liu
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China
| | - Guoqiang Wang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Xu Zhou
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Ping Wang
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China
| | - Jinmin Gao
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan 250014, Shandong, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan 250014, Shandong, China
| | - Liangran Zhang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China; Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan 250014, Shandong, China.
| | - Shunxin Wang
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.
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17
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Graham-Paquin AL, Saini D, Sirois J, Hossain I, Katz MS, Zhuang QKW, Kwon SY, Yamanaka Y, Bourque G, Bouchard M, Pastor WA. ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development. Nucleic Acids Res 2023; 51:7314-7329. [PMID: 37395395 PMCID: PMC10415128 DOI: 10.1093/nar/gkad540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/24/2023] [Accepted: 06/09/2023] [Indexed: 07/04/2023] Open
Abstract
ZMYM2 is a transcriptional repressor whose role in development is largely unexplored. We found that Zmym2-/- mice show embryonic lethality by E10.5. Molecular characterization of Zmym2-/- embryos revealed two distinct defects. First, they fail to undergo DNA methylation and silencing of germline gene promoters, resulting in widespread upregulation of germline genes. Second, they fail to methylate and silence the evolutionarily youngest and most active LINE element subclasses in mice. Zmym2-/- embryos show ubiquitous overexpression of LINE-1 protein as well as aberrant expression of transposon-gene fusion transcripts. ZMYM2 homes to sites of PRC1.6 and TRIM28 complex binding, mediating repression of germline genes and transposons respectively. In the absence of ZMYM2, hypermethylation of histone 3 lysine 4 occurs at target sites, creating a chromatin landscape unfavourable for establishment of DNA methylation. ZMYM2-/- human embryonic stem cells also show aberrant upregulation and demethylation of young LINE elements, indicating a conserved role in repression of active transposons. ZMYM2 is thus an important new factor in DNA methylation patterning in early embryonic development.
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Affiliation(s)
- Adda-Lee Graham-Paquin
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Deepak Saini
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jacinthe Sirois
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Ishtiaque Hossain
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Megan S Katz
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Qinwei Kim-Wee Zhuang
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan
| | - Sin Young Kwon
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Yojiro Yamanaka
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan
- Canadian Center for Computational Genomics,McGill University, Montreal, Quebec, Canada
| | - Maxime Bouchard
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - William A Pastor
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
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18
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Liu Y, Hu L, Wu Z, Yuan K, Hong G, Lian Z, Feng J, Li N, Li D, Wong J, Chen J, Liu M, He J, Pang X. Loss of PHF8 induces a viral mimicry response by activating endogenous retrotransposons. Nat Commun 2023; 14:4225. [PMID: 37454216 PMCID: PMC10349869 DOI: 10.1038/s41467-023-39943-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: 12/10/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
Immunotherapy has become established as major treatment modality for multiple types of solid tumors, including colorectal cancer. Identifying novel immunotherapeutic targets to enhance anti-tumor immunity and sensitize current immune checkpoint blockade (ICB) in colorectal cancer is needed. Here we report the histone demethylase PHD finger protein 8 (PHF8, KDM7B), a Jumonji C domain-containing protein that erases repressive histone methyl marks, as an essential mediator of immune escape. Ablation the function of PHF8 abrogates tumor growth, activates anti-tumor immune memory, and augments sensitivity to ICB therapy in mouse models of colorectal cancer. Strikingly, tumor PHF8 deletion stimulates a viral mimicry response in colorectal cancer cells, where the depletion of key components of endogenous nucleic acid sensing diminishes PHF8 loss-meditated antiviral immune responses and anti-tumor effects in vivo. Mechanistically, PHF8 inhibition elicits H3K9me3-dependent retrotransposon activation by promoting proteasomal degradation of the H3K9 methyltransferase SETDB1 in a demethylase-independent manner. Moreover, PHF8 expression is anti-correlated with canonical immune signatures and antiviral immune responses in human colorectal adenocarcinoma. Overall, our study establishes PHF8 as an epigenetic checkpoint, and targeting PHF8 is a promising viral mimicry-inducing approach to enhance intrinsic anti-tumor immunity or to conquer immune resistance.
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Affiliation(s)
- Yanan Liu
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Longmiao Hu
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhengzhen Wu
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Kun Yuan
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | | | - Zhengke Lian
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Juanjuan Feng
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Na Li
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiekai Chen
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | | | - Xiufeng Pang
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China.
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19
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Seczynska M, Lehner PJ. The sound of silence: mechanisms and implications of HUSH complex function. Trends Genet 2023; 39:251-267. [PMID: 36754727 DOI: 10.1016/j.tig.2022.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/14/2022] [Accepted: 12/30/2022] [Indexed: 02/08/2023]
Abstract
The vertebrate genome is under constant threat of invasion by genetic parasites. Whether the host can immediately recognize and respond to invading elements has been unclear. The discovery of the human silencing hub (HUSH) complex, and the finding that it provides immediate protection from genome invasion by silencing products of reverse transcription, have important implications for mammalian genome evolution. In this review, we summarize recent insights into HUSH function and describe how cellular introns provide a novel means of self-nonself discrimination, allowing HUSH to recognize and transcriptionally repress a broad range of intronless genetic elements. We discuss how HUSH contributes to genome evolution, and highlight studies reporting the critical role of HUSH in development and implicating HUSH in the control of immune signaling and cancer progression.
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Affiliation(s)
- Marta Seczynska
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Paul J Lehner
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
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20
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Atf7ip Inhibits Osteoblast Differentiation via Negative Regulation of the Sp7 Transcription Factor. Int J Mol Sci 2023; 24:ijms24054305. [PMID: 36901736 PMCID: PMC10002255 DOI: 10.3390/ijms24054305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/03/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
Epigenetic modifications are critical for cell differentiation and growth. As a regulator of H3K9 methylation, Setdb1 is implicated in osteoblast proliferation and differentiation. The activity and nucleus localization of Setdb1 are regulated by its binding partner, Atf7ip. However, whether Atf7ip is involved in the regulation of osteoblast differentiation remains largely unclear. In the present study, we found that Atf7ip expression was upregulated during the osteogenesis of primary bone marrow stromal cells and MC3T3-E1 cells, and was induced in PTH-treated cells. The overexpression of Atf7ip impaired osteoblast differentiation in MC3T3-E1 cells regardless of PTH treatment, as measured by the expression of osteoblast differentiation markers, Alp-positive cells, Alp activity, and calcium deposition. Conversely, the depletion of Atf7ip in MC3T3-E1 cells promoted osteoblast differentiation. Compared with the control mice, animals with Atf7ip deletion in the osteoblasts (Oc-Cre;Atf7ipf/f) showed more bone formation and a significant increase in the bone trabeculae microarchitecture, as reflected by μ-CT and bone histomorphometry. Mechanistically, Atf7ip contributed to the nucleus localization of Setdb1 in MC3T3-E1, but did not affect Setdb1 expression. Atf7ip negatively regulated Sp7 expression, and through specific siRNA, Sp7 knockdown attenuated the enhancing role of Atf7ip deletion in osteoblast differentiation. Through these data, we identified Atf7ip as a novel negative regulator of osteogenesis, possibly via its epigenetic regulation of Sp7 expression, and demonstrated that Atf7ip inhibition is a potential therapeutic measure for enhancing bone formation.
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21
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van Puffelen JH, Novakovic B, van Emst L, Kooper D, Zuiverloon TCM, Oldenhof UTH, Witjes JA, Galesloot TE, Vrieling A, Aben KKH, Kiemeney LALM, Oosterwijk E, Netea MG, Boormans JL, van der Heijden AG, Joosten LAB, Vermeulen SH. Intravesical BCG in patients with non-muscle invasive bladder cancer induces trained immunity and decreases respiratory infections. J Immunother Cancer 2023; 11:jitc-2022-005518. [PMID: 36693678 PMCID: PMC9884868 DOI: 10.1136/jitc-2022-005518] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND BCG is recommended as intravesical immunotherapy to reduce the risk of tumor recurrence in patients with non-muscle invasive bladder cancer (NMIBC). Currently, it is unknown whether intravesical BCG application induces trained immunity. METHODS The aim of this research was to determine whether BCG immunotherapy induces trained immunity in NMIBC patients. We conducted a prospective observational cohort study in 17 NMIBC patients scheduled for BCG therapy and measured trained immunity parameters at 9 time points before and during a 1-year BCG maintenance regimen. Ex vivo cytokine production by peripheral blood mononuclear cells, epigenetic modifications, and changes in the monocyte transcriptome were measured. The frequency of respiratory infections was investigated in two larger cohorts of BCG-treated and non-BCG treated NMIBC patients as a surrogate measurement of trained immunity. Gene-based association analysis of genetic variants in candidate trained immunity genes and their association with recurrence-free survival and progression-free survival after BCG therapy was performed to investigate the hypothesized link between trained immunity and clinical response. RESULTS We found that intravesical BCG does induce trained immunity based on an increased production of TNF and IL-1β after heterologous ex vivo stimulation of circulating monocytes 6-12 weeks after intravesical BCG treatment; and a 37% decreased risk (OR 0.63 (95% CI 0.40 to 1.01)) for respiratory infections in BCG-treated versus non-BCG-treated NMIBC patients. An epigenomics approach combining chromatin immuno precipitation-sequencing and RNA-sequencing with in vitro trained immunity experiments identified enhanced inflammasome activity in BCG-treated individuals. Finally, germline variation in genes that affect trained immunity was associated with recurrence and progression after BCG therapy in NMIBC. CONCLUSION We conclude that BCG immunotherapy induces trained immunity in NMIBC patients and this may account for the protective effects against respiratory infections. The data of our gene-based association analysis suggest that a link between trained immunity and oncological outcome may exist. Future studies should further investigate how trained immunity affects the antitumor immune responses in BCG-treated NMIBC patients.
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Affiliation(s)
- Jelmer H van Puffelen
- Department of Internal Medicine, Radboudumc, Nijmegen, The Netherlands,Department for Health Evidence, Radboudumc, Nijmegen, The Netherlands
| | - Boris Novakovic
- Department of Paediatrics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Liesbeth van Emst
- Department of Internal Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Denise Kooper
- Department of Urology, Erasmus MC Cancer Centre, Rotterdam, The Netherlands
| | | | | | - J Alfred Witjes
- Department of Urology, Radboudumc, Nijmegen, The Netherlands
| | | | - Alina Vrieling
- Department for Health Evidence, Radboudumc, Nijmegen, The Netherlands
| | - Katja K H Aben
- Department for Health Evidence, Radboudumc, Nijmegen, The Netherlands,IKNL, Utrecht, The Netherlands
| | | | | | - Mihai G Netea
- Department of Internal Medicine, Radboudumc, Nijmegen, The Netherlands,Department of Immunology and Metabolism, University of Bonn, Life & Medical Sciences Institute, Bonn, Germany
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Centre, Rotterdam, The Netherlands
| | | | - Leo A B Joosten
- Department of Internal Medicine, Radboudumc, Nijmegen, The Netherlands,Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Sita H Vermeulen
- Department for Health Evidence, Radboudumc, Nijmegen, The Netherlands
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22
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Wu J, Li J, Chen K, Liu G, Zhou Y, Chen W, Zhu X, Ni TT, Zhang B, Jin D, Li D, Kang L, Wu Y, Zhu P, Xie P, Zhong TP. Atf7ip and Setdb1 interaction orchestrates the hematopoietic stem and progenitor cell state with diverse lineage differentiation. Proc Natl Acad Sci U S A 2023; 120:e2209062120. [PMID: 36577070 PMCID: PMC9910619 DOI: 10.1073/pnas.2209062120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/21/2022] [Indexed: 12/29/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are a heterogeneous group of cells with expansion, differentiation, and repopulation capacities. How HSPCs orchestrate the stemness state with diverse lineage differentiation at steady condition or acute stress remains largely unknown. Here, we show that zebrafish mutants that are deficient in an epigenetic regulator Atf7ip or Setdb1 methyltransferase undergo excessive myeloid differentiation with impaired HSPC expansion, manifesting a decline in T cells and erythroid lineage. We find that Atf7ip regulates hematopoiesis through Setdb1-mediated H3K9me3 modification and chromatin remodeling. During hematopoiesis, the interaction of Atf7ip and Setdb1 triggers H3K9me3 depositions in hematopoietic regulatory genes including cebpβ and cdkn1a, preventing HSPCs from loss of expansion and premature differentiation into myeloid lineage. Concomitantly, loss of Atf7ip or Setdb1 derepresses retrotransposons that instigate the viral sensor Mda5/Rig-I like receptor (RLR) signaling, leading to stress-driven myelopoiesis and inflammation. We find that ATF7IP or SETDB1 depletion represses human leukemic cell growth and induces myeloid differentiation with retrotransposon-triggered inflammation. These findings establish that Atf7ip/Setdb1-mediated H3K9me3 deposition constitutes a genome-wide checkpoint that impedes the myeloid potential and maintains HSPC stemness for diverse blood cell production, providing unique insights into potential intervention in hematological malignancy.
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Affiliation(s)
- Jiaxin Wu
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Juan Li
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Kang Chen
- School of Life Sciences and Technology, Tongji University, Shanghai200092, China
| | - Guolong Liu
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Yating Zhou
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Wenqi Chen
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Xiangzhan Zhu
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Terri T. Ni
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Bianhong Zhang
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Daqing Jin
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Lan Kang
- School of Life Sciences and Technology, Tongji University, Shanghai200092, China
| | - Yuxuan Wu
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong510100, China
| | - Peng Xie
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu210096, China
| | - Tao P. Zhong
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
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23
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Eom J, Jeon K, Park JS, Kang YK. Functional dissection of N-terminal nuclear trafficking signals of SETDB1. Front Cell Dev Biol 2022; 10:1069765. [PMID: 36605719 PMCID: PMC9807615 DOI: 10.3389/fcell.2022.1069765] [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: 10/14/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
SETDB1 is a histone H3-lysine 9-specific methyltransferase that fulfills epigenetic functions inside the nucleus; however, when overexpressed, SETDB1 majorily localizes in the cytoplasm. SETDB1 has a single nuclear-localization-signal (NLS) motif and two successive nuclear-export-signal (NES1 and NES2) motifs in the N-terminus, suggesting that SETDB1 localization is the consequence of a balance between the two antithetic motifs. Here, we performed a series of motif deletions to characterize their effects on the cellular movement of SETDB1. Given the cytoplasmic localization of GFP-SETDB1 in the whole form, without the NES motifs, GFP-SETDB1 was not nuclear, and 3xNLS addition plus NES removal held the majority of GFP-SETDB1 within the nucleus. The results indicated that the cytoplasmic localization of GFP-SETDB1 is the combined result of weak NLS and robust NESs. In ATF7IP-overexpressing cells, GFP-SETDB1 entered the nucleus only in the presence of the NES1 motif; neither the NES2 nor NLS motif was necessary. Since subcellular fractionation results showed that ATF7IP was nuclear-only, an intermediary protein may interact specifically with the NES1 motif after stimulation by ATF7IP. When GFP-SETDB1 had either NES1 or NES2, it was precipitated (in immunoprecipitation) and colocalized (in immunofluorescence) with ATF7IP, indicating that GFP-SETDB1 interacts with ATF7IP through the NES motifs in the nucleus. The regulated nuclear entry of SETDB1 is assumed to set a tight restriction on its abundance within the nucleus, thereby ensuring balanced nuclear SETDB1 levels.
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Affiliation(s)
- Jaemin Eom
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Daejeon, Korea,Department of Functional Genomics, Korea University of Science and Technology (UST), Daejeon, South Korea
| | - Kyuheum Jeon
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Daejeon, Korea,Department of Functional Genomics, Korea University of Science and Technology (UST), Daejeon, South Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Daejeon, Korea
| | - Yong-Kook Kang
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Daejeon, Korea,Department of Functional Genomics, Korea University of Science and Technology (UST), Daejeon, South Korea,*Correspondence: Yong-Kook Kang,
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24
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Levinsky AJ, McEdwards G, Sethna N, Currie MA. Targets of histone H3 lysine 9 methyltransferases. Front Cell Dev Biol 2022; 10:1026406. [PMID: 36568972 PMCID: PMC9768651 DOI: 10.3389/fcell.2022.1026406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022] Open
Abstract
Histone H3 lysine 9 di- and trimethylation are well-established marks of constitutively silenced heterochromatin domains found at repetitive DNA elements including pericentromeres, telomeres, and transposons. Loss of heterochromatin at these sites causes genomic instability in the form of aberrant DNA repair, chromosome segregation defects, replication stress, and transposition. H3K9 di- and trimethylation also regulate cell type-specific gene expression during development and form a barrier to cellular reprogramming. However, the role of H3K9 methyltransferases extends beyond histone methylation. There is a growing list of non-histone targets of H3K9 methyltransferases including transcription factors, steroid hormone receptors, histone modifying enzymes, and other chromatin regulatory proteins. Additionally, two classes of H3K9 methyltransferases modulate their own function through automethylation. Here we summarize the structure and function of mammalian H3K9 methyltransferases, their roles in genome regulation and constitutive heterochromatin, as well as the current repertoire of non-histone methylation targets including cases of automethylation.
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Affiliation(s)
- Aidan J. Levinsky
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Gregor McEdwards
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Nasha Sethna
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Mark A. Currie
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada,*Correspondence: Mark A. Currie,
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25
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Hernandez‐Vicens R, Singh J, Pernicone N, Listovsky T, Gerlitz G. SETDB1 regulates microtubule dynamics. Cell Prolif 2022; 55:e13348. [DOI: 10.1111/cpr.13348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
| | - Jagreeti Singh
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
| | - Nomi Pernicone
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
| | - Tamar Listovsky
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
- Ariel Center for Applied Cancer Research Ariel University Ariel Israel
- Adelson School of Medicine Ariel University Ariel Israel
| | - Gabi Gerlitz
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
- Ariel Center for Applied Cancer Research Ariel University Ariel Israel
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26
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Fernandes LP, Enriquez-Gasca R, Gould PA, Holt JH, Conde L, Ecco G, Herrero J, Gifford R, Trono D, Kassiotis G, Rowe HM. A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819. SCIENCE ADVANCES 2022; 8:eabp8085. [PMID: 36306355 PMCID: PMC9616502 DOI: 10.1126/sciadv.abp8085] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 09/08/2022] [Indexed: 06/11/2023]
Abstract
Mammalian genomes are a battleground for genetic conflict between repetitive elements and KRAB-zinc finger proteins (KZFPs). We asked whether KZFPs can regulate cell fate by using ZFP819, which targets a satellite DNA array, ZP3AR. ZP3AR coats megabase regions of chromosome 7 encompassing genes encoding ZSCAN4, a master transcription factor of totipotency. Depleting ZFP819 in mouse embryonic stem cells (mESCs) causes them to transition to a 2-cell (2C)-like state, whereby the ZP3AR array switches from a poised to an active enhancer state. This is accompanied by a global erosion of heterochromatin roadblocks, which we link to decreased SETDB1 stability. These events result in transcription of active LINE-1 elements and impaired differentiation. In summary, ZFP819 and TRIM28 partner up to close chromatin across Zscan4, to promote exit from totipotency. We propose that satellite DNAs may control developmental fate transitions by barcoding and switching off master transcription factor genes.
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Affiliation(s)
- Liane P. Fernandes
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Rocio Enriquez-Gasca
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Poppy A. Gould
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - James H. Holt
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK
| | - Gabriela Ecco
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK
| | - Robert Gifford
- MRC–University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Helen M. Rowe
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
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27
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Basha NJ, Basavarajaiah SM. An insight into therapeutic efficacy of heterocycles as histone modifying enzyme inhibitors that targets cancer epigenetic pathways. Chem Biol Drug Des 2022; 100:682-698. [PMID: 36059065 DOI: 10.1111/cbdd.14135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 01/10/2023]
Abstract
Histone modifying enzymes are the key regulators involved in the post-translational modification of histone and non-histone. These enzymes are responsible for the epigenetic control of cellular functions. However, deregulation of the activity of these enzymes results in uncontrolled disorders such as cancer and inflammatory and neurological diseases. The study includes histone acetyltransferases, deacetylases, methyl transferases, demethylases, DNA methyl transferases, and their potent inhibitors which are in a clinical trial and used as medicinal drugs. The present review covers the heterocycles as target-specific inhibitors of histone-modifying enzyme, more specifically histone acetyltransferases. This review also confers more recent reports on heterocycles as potential HAT inhibitors covered from 2016-2022 and future perspectives of these heterocycles in epigenetic therapy.
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Affiliation(s)
- N Jeelan Basha
- Department of Chemistry, Indian Academy Degree College-Autonomous, Bengaluru, Karnataka, India
| | - S M Basavarajaiah
- P.G. Department of Chemistry, Vijaya College, Bengaluru, Karnataka, India
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28
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Zhang Q, Pan J, Cong Y, Mao J. Transcriptional Regulation of Endogenous Retroviruses and Their Misregulation in Human Diseases. Int J Mol Sci 2022; 23:ijms231710112. [PMID: 36077510 PMCID: PMC9456331 DOI: 10.3390/ijms231710112] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Endogenous retroviruses (ERVs), deriving from exogenous retroviral infections of germ line cells occurred millions of years ago, represent ~8% of human genome. Most ERVs are highly inactivated because of the accumulation of mutations, insertions, deletions, and/or truncations. However, it is becoming increasingly apparent that ERVs influence host biology through genetic and epigenetic mechanisms under particular physiological and pathological conditions, which provide both beneficial and deleterious effects for the host. For instance, certain ERVs expression is essential for human embryonic development. Whereas abnormal activation of ERVs was found to be involved in numbers of human diseases, such as cancer and neurodegenerative diseases. Therefore, understanding the mechanisms of regulation of ERVs would provide insights into the role of ERVs in health and diseases. Here, we provide an overview of mechanisms of transcriptional regulation of ERVs and their dysregulation in human diseases.
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29
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Methyltransferase Setdb1 Promotes Osteoblast Proliferation by Epigenetically Silencing Macrod2 with the Assistance of Atf7ip. Cells 2022; 11:cells11162580. [PMID: 36010655 PMCID: PMC9406310 DOI: 10.3390/cells11162580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/31/2022] [Accepted: 08/09/2022] [Indexed: 12/03/2022] Open
Abstract
Bone loss caused by mechanical unloading is a threat to prolonged space flight and human health. Epigenetic modifications play a crucial role in varied biological processes, but the mechanism of histone modification on unloading-induced bone loss has rarely been studied. Here, we discovered for the first time that the methyltransferase Setdb1 was downregulated under the mechanical unloading both in vitro and in vivo so as to attenuate osteoblast proliferation. Furthermore, we found these interesting processes depended on the repression of Macrod2 expression triggered by Setdb1 catalyzing the formation of H3K9me3 in the promoter region. Mechanically, we revealed that Macrod2 was upregulated under mechanical unloading and suppressed osteoblast proliferation through the GSK-3β/β-catenin signaling pathway. Moreover, Atf7ip cooperatively contributed to osteoblast proliferation by changing the localization of Setdb1 under mechanical loading. In summary, this research elucidated the role of the Atf7ip/Setdb1/Macrod2 axis in osteoblast proliferation under mechanical unloading for the first time, which can be a potential protective strategy against unloading-induced bone loss.
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30
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Balinth S, Fisher ML, Hwangbo Y, Wu C, Ballon C, Sun X, Mills AA. EZH2 regulates a SETDB1/ΔNp63α axis via RUNX3 to drive a cancer stem cell phenotype in squamous cell carcinoma. Oncogene 2022; 41:4130-4144. [PMID: 35864175 PMCID: PMC10132824 DOI: 10.1038/s41388-022-02417-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 01/01/2023]
Abstract
Enhancer of zeste homolog 2 (EZH2) and SET domain bifurcated 1 (SETDB1, also known as ESET) are oncogenic methyltransferases implicated in a number of human cancers. These enzymes typically function as epigenetic repressors of target genes by methylating histone H3 K27 and H3-K9 residues, respectively. Here, we show that EZH2 and SETDB1 are essential to proliferation in 3 SCC cell lines, HSC-5, FaDu, and Cal33. Additionally, we find both of these proteins highly expressed in an aggressive stem-like SCC sub-population. Depletion of either EZH2 or SETDB1 disrupts these stem-like cells and their associated phenotypes of spheroid formation, invasion, and tumor growth. We show that SETDB1 regulates this SCC stem cell phenotype through cooperation with ΔNp63α, an oncogenic isoform of the p53-related transcription factor p63. Furthermore, EZH2 is upstream of both SETDB1 and ΔNp63α, activating these targets via repression of the tumor suppressor RUNX3. We show that targeting this pathway with inhibitors of EZH2 results in activation of RUNX3 and repression of both SETDB1 and ΔNp63α, antagonizing the SCC cancer stem cell phenotype. This work highlights a novel pathway that drives an aggressive cancer stem cell phenotype and demonstrates a means of pharmacological intervention.
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Affiliation(s)
- Seamus Balinth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY, USA
| | | | - Yon Hwangbo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Caizhi Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Carlos Ballon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xueqin Sun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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31
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Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat Rev Mol Cell Biol 2022; 23:623-640. [PMID: 35562425 PMCID: PMC9099300 DOI: 10.1038/s41580-022-00483-w] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 12/14/2022]
Abstract
Heterochromatin is characterized by dimethylated or trimethylated histone H3 Lys9 (H3K9me2 or H3K9me3, respectively) and is found at transposable elements, satellite repeats and genes, where it ensures their transcriptional silencing. The histone methyltransferases (HMTs) that methylate H3K9 — in mammals Suppressor of variegation 3–9 homologue 1 (SUV39H1), SUV39H2, SET domain bifurcated 1 (SETDB1), SETDB2, G9A and G9A-like protein (GLP) — and the ‘readers’ of H3K9me2 or H3K9me3 are highly conserved and show considerable redundancy. Despite their redundancy, genetic ablation or mistargeting of an individual H3K9 methyltransferase can correlate with impaired cell differentiation, loss of tissue identity, premature aging and/or cancer. In this Review, we discuss recent advances in understanding the roles of the known H3K9-specific HMTs in ensuring transcriptional homeostasis during tissue differentiation in mammals. We examine the effects of H3K9-methylation-dependent gene repression in haematopoiesis, muscle differentiation and neurogenesis in mammals, and compare them with mechanistic insights obtained from the study of model organisms, notably Caenorhabditis elegans and Drosophila melanogaster. In all these organisms, H3K9-specific HMTs have both unique and redundant roles that ensure the maintenance of tissue integrity by restricting the binding of transcription factors to lineage-specific promoters and enhancer elements. Histone H3 Lys9 (H3K9)-methylated heterochromatin ensures transcriptional silencing of repetitive elements and genes, and its deregulation leads to impaired cell and tissue identity, premature aging and cancer. Recent studies in mammals clarified the roles H3K9-specific histone methyltransferases in ensuring transcriptional homeostasis during tissue differentiation.
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SETDB1-like MET-2 promotes transcriptional silencing and development independently of its H3K9me-associated catalytic activity. Nat Struct Mol Biol 2022; 29:85-96. [PMID: 35102319 PMCID: PMC8850192 DOI: 10.1038/s41594-021-00712-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022]
Abstract
Transcriptionally silenced heterochromatin bearing methylation of histone H3 on lysine 9 (H3K9me) is critical for maintaining organismal viability and tissue integrity. Here we show that in addition to ensuring H3K9me, MET-2, the Caenorhabditis elegans homolog of the SETDB1 histone methyltransferase, has a noncatalytic function that contributes to gene repression. Subnuclear foci of MET-2 coincide with H3K9me deposition, yet these foci also form when MET-2 is catalytically deficient and H3K9me is compromised. Whereas met-2 deletion triggers a loss of silencing and increased histone acetylation, foci of catalytically deficient MET-2 maintain silencing of a subset of genes, blocking acetylation on H3K9 and H3K27. In normal development, this noncatalytic MET-2 activity helps to maintain fertility. Under heat stress MET-2 foci disperse, coinciding with increased acetylation and transcriptional derepression. Our study suggests that the noncatalytic, focus-forming function of this SETDB1-like protein and its intrinsically disordered cofactor LIN-65 is physiologically relevant. Genetic and genome-wide analysis of a catalytically deficient SETDB1-like enzyme, MET-2, in Caenorhabditiselegans reveals that MET-2 promotes transcriptional silencing and fertility through both H3K9 methylation and focus formation, which blocks histone acetylation.
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33
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Barnes CE, English DM, Broderick M, Collins MO, Cowley SM. Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation. Mol Omics 2022; 18:31-44. [PMID: 34709266 PMCID: PMC8763317 DOI: 10.1039/d1mo00236h] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Lysine specific demethylase 1 (LSD1) regulates gene expression as part of the CoREST complex, along with co-repressor of REST (CoREST) and histone deacetylase 1 (HDAC1). CoREST is recruited to specific genomic loci by core components and numerous transient interactions with chromatin-associated factors and transcription factors. We hypothesise that many of these weaker and transient associations may be difficult to identify using traditional co-immunoprecipitation methods. We have therefore employed proximity-dependent biotin-identification (BioID) with four different members of the CoREST complex, in three different cell types, to identify a comprehensive network of LSD1/CoREST associated proteins. In HEK293T cells, we identified 302 CoREST-associated proteins. Among this group were 16 of 18 known CoREST components and numerous novel associations, including readers (CHD3, 4, 6, 7 and 8), writers (KMT2B and KMT2D) and erasers (KDM2B) of histone methylation. However, components of other HDAC1 containing complexes (e.g. Sin3) were largely absent. To examine the dynamic nature of the CoREST interactome in a primary cell type, we replaced endogenous LSD1 with BirA*-LSD1 in embryonic stem (ES) cells and performed BioID in pluripotent, early- and late-differentiating environments. We identified 156 LSD1-associated proteins of which 67 were constitutively associated across all three time-points (43%), including novel associations with the MMB and ChAHP complexes, implying that the majority of interactors are both dynamic and cell type dependent. In total, we have performed 16 independent BioID experiments for LSD1 in three different cell types, producing a definitive network of LSD1-assoicated proteins that should provide a major resource for the field.
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Affiliation(s)
- Claire E Barnes
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
| | - David M English
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
| | - Megan Broderick
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
| | - Mark O Collins
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
- Faculty of Science Mass Spectrometry Centre, University of Sheffield, Brook Hill Road, Sheffield, S3 7HF, UK
| | - Shaun M Cowley
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
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34
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Butz S, Schmolka N, Karemaker ID, Villaseñor R, Schwarz I, Domcke S, Uijttewaal ECH, Jude J, Lienert F, Krebs AR, de Wagenaar NP, Bao X, Zuber J, Elling U, Schübeler D, Baubec T. DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions. Nat Genet 2022; 54:1702-1710. [PMID: 36333500 PMCID: PMC9649441 DOI: 10.1038/s41588-022-01210-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
Abstract
Genomic imprinting is regulated by parental-specific DNA methylation of imprinting control regions (ICRs). Despite an identical DNA sequence, ICRs can exist in two distinct epigenetic states that are memorized throughout unlimited cell divisions and reset during germline formation. Here, we systematically study the genetic and epigenetic determinants of this epigenetic bistability. By iterative integration of ICRs and related DNA sequences to an ectopic location in the mouse genome, we first identify the DNA sequence features required for maintenance of epigenetic states in embryonic stem cells. The autonomous regulatory properties of ICRs further enabled us to create DNA-methylation-sensitive reporters and to screen for key components involved in regulating their epigenetic memory. Besides DNMT1, UHRF1 and ZFP57, we identify factors that prevent switching from methylated to unmethylated states and show that two of these candidates, ATF7IP and ZMYM2, are important for the stability of DNA and H3K9 methylation at ICRs in embryonic stem cells.
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Affiliation(s)
- Stefan Butz
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Nina Schmolka
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Present Address: Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ino D. Karemaker
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Rodrigo Villaseñor
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.5252.00000 0004 1936 973XPresent Address: Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Isabel Schwarz
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Silvia Domcke
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland ,grid.34477.330000000122986657Present Address: Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Esther C. H. Uijttewaal
- grid.473822.80000 0005 0375 3232Institute of Molecular Biotechnology Austria (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julian Jude
- grid.14826.390000 0000 9799 657XResearch Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Florian Lienert
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland
| | - Arnaud R. Krebs
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.4709.a0000 0004 0495 846XPresent Address: European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Nathalie P. de Wagenaar
- grid.5477.10000000120346234Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Xue Bao
- grid.5477.10000000120346234Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Johannes Zuber
- grid.14826.390000 0000 9799 657XResearch Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Ulrich Elling
- grid.473822.80000 0005 0375 3232Institute of Molecular Biotechnology Austria (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dirk Schübeler
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland. .,Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands.
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35
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Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells. Nat Commun 2021; 12:6718. [PMID: 34795250 PMCID: PMC8602306 DOI: 10.1038/s41467-021-26949-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
In mammals, imprinted genes are regulated by differentially methylated regions (DMRs) that are inherited from germ cells, leading to monoallelic expression in accordance with parent-of-origin. Yet, it is largely unknown how imprinted DMRs are maintained in human embryos despite global DNA demethylation following fertilization. Here, we explored the mechanisms involved in imprinting regulation by employing human parthenogenetic embryonic stem cells (hpESCs), which lack paternal alleles. We show that although global loss of DNA methylation in hpESCs affects most imprinted DMRs, many paternally-expressed genes (PEGs) remain repressed. To search for factors regulating PEGs, we performed a genome-wide CRISPR/Cas9 screen in haploid hpESCs. This revealed ATF7IP as an essential repressor of a set of PEGs, which we further show is also required for silencing sperm-specific genes. Our study reinforces an important role for histone modifications in regulating imprinted genes and suggests a link between parental imprinting and germ cell identity. Genetic imprinting ensures monoallelic gene expression critical for normal embryonic development. Here the authors take advantage of human haploid parthenogenic embryonic stem cells lacking paternal alleles to identify, by genome-wide screening, factors involved in the regulation of imprinted genes.
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36
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Markouli M, Strepkos D, Piperi C. Structure, Activity and Function of the SETDB1 Protein Methyltransferase. Life (Basel) 2021; 11:life11080817. [PMID: 34440561 PMCID: PMC8397983 DOI: 10.3390/life11080817] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
The SET Domain Bifurcated Histone Lysine Methyltransferase 1 (SETDB1) is a prominent member of the Suppressor of Variegation 3–9 (SUV39)-related protein lysine methyltransferases (PKMTs), comprising three isoforms that differ in length and domain composition. SETDB1 is widely expressed in human tissues, methylating Histone 3 lysine 9 (H3K9) residues, promoting chromatin compaction and exerting negative regulation on gene expression. SETDB1 has a central role in normal physiology and nervous system development, having been implicated in the regulation of cell cycle progression, inactivation of the X chromosome, immune cells function, expression of retroelements and formation of promyelocytic leukemia (PML) nuclear bodies (NB). SETDB1 has been frequently deregulated in carcinogenesis, being implicated in the pathogenesis of gliomas, melanomas, as well as in lung, breast, gastrointestinal and ovarian tumors, where it mainly exerts an oncogenic role. Aberrant activity of SETDB1 has also been implicated in several neuropsychiatric, cardiovascular and gastrointestinal diseases, including schizophrenia, Huntington’s disease, congenital heart defects and inflammatory bowel disease. Herein, we provide an update on the unique structural and biochemical features of SETDB1 that contribute to its regulation, as well as its molecular and cellular impact in normal physiology and disease with potential therapeutic options.
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37
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Funyu T, Kanemaru Y, Onoda H, Arita K. Preparation of the ubiquitination-triggered active form of SETDB1 in E. coli for biochemical and structural analyses. J Biochem 2021; 170:655-662. [PMID: 34324684 DOI: 10.1093/jb/mvab087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
Trimethylation of histone H3 at K9 by the lysine methyltransferase, SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) plays a pivotal role in silencing tissue-specific genes and retrotransposable elements. In mammalian cells, SETDB1 undergoes monoubiquitination in the insertion region of the SET domain in an E3 ubiquitin ligase-independent manner. This ubiquitination has been shown to enhance the histone H3-K9 methyltransferase activity of SETDB1; however, the molecular mechanism underlying SETDB1 activation by ubiquitination is unknown. In this study, we developed an E. coli ubiquitination plasmid for the preparation of ubiquitinated SETDB1. Western blotting and mutational analyses showed that coexpression of the SET domain of SETDB1 with the proteins encoded by the ubiquitination plasmid led to site-specific monoubiquitination of the SET domain at K867. An in vitro histone H3 methylation assay demonstrated that the ubiquitinated SET domain of SETDB1 acquired enzymatic activity. Taken together, these findings demonstrate successful preparation of the active form of SETDB1 with the E. coli ubiquitination system, which will aid biochemical and structural studies of ubiquitinated SETDB1.
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Affiliation(s)
- Tomoko Funyu
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yuka Kanemaru
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroki Onoda
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kyohei Arita
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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38
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Yuan L, Sun B, Xu L, Chen L, Ou W. The Updating of Biological Functions of Methyltransferase SETDB1 and Its Relevance in Lung Cancer and Mesothelioma. Int J Mol Sci 2021; 22:ijms22147416. [PMID: 34299035 PMCID: PMC8306223 DOI: 10.3390/ijms22147416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/11/2022] Open
Abstract
SET domain bifurcated 1 (SETDB1) is a histone H3 lysine 9 (H3K9) methyltransferase that exerts important effects on epigenetic gene regulation. SETDB1 complexes (SETDB1-KRAB-KAP1, SETDB1-DNMT3A, SETDB1-PML, SETDB1-ATF7IP-MBD1) play crucial roles in the processes of histone methylation, transcriptional suppression and chromatin remodelling. Therefore, aberrant trimethylation at H3K9 due to amplification, mutation or deletion of SETDB1 may lead to transcriptional repression of various tumour-suppressing genes and other related genes in cancer cells. Lung cancer is the most common type of cancer worldwide in which SETDB1 amplification and H3K9 hypermethylation have been indicated as potential tumourigenesis markers. In contrast, frequent inactivation mutations of SETDB1 have been revealed in mesothelioma, an asbestos-associated, locally aggressive, highly lethal, and notoriously chemotherapy-resistant cancer. Above all, the different statuses of SETDB1 indicate that it may have different biological functions and be a potential diagnostic biomarker and therapeutic target in lung cancer and mesothelioma.
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Affiliation(s)
| | | | | | | | - Wenbin Ou
- Correspondence: ; Tel./Fax: +86-571-86843303
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39
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Zhang J, Matsumura Y, Kano Y, Yoshida A, Kawamura T, Hirakawa H, Inagaki T, Tanaka T, Kimura H, Yanagi S, Fukami K, Doi T, Osborne TF, Kodama T, Aburatani H, Sakai J. Ubiquitination-dependent and -independent repression of target genes by SETDB1 reveal a context-dependent role for its methyltransferase activity during adipogenesis. Genes Cells 2021; 26:513-529. [PMID: 33971063 DOI: 10.1111/gtc.12868] [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: 04/06/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022]
Abstract
The lysine methyltransferase SETDB1, an enzyme responsible for methylation of histone H3 at lysine 9, plays a key role in H3K9 tri-methylation-dependent silencing of endogenous retroviruses and developmental genes. Recent studies have shown that ubiquitination of human SETDB1 complements its catalytic activity and the silencing of endogenous retroviruses in human embryonic stem cells. However, it is not known whether SETDB1 ubiquitination is essential for its other major role in epigenetic silencing of developmental gene programs. We previously showed that SETDB1 contributes to the formation of H3K4/H3K9me3 bivalent chromatin domains that keep adipogenic Cebpa and Pparg genes in a poised state for activation and restricts the differentiation potential of pre-adipocytes. Here, we show that ubiquitin-resistant K885A mutant of SETDB1 represses adipogenic genes and inhibits pre-adipocyte differentiation similar to wild-type SETDB1. We show this was due to a compensation mechanism for H3K9me3 chromatin modifications on the Cebpa locus by other H3K9 methyltransferases Suv39H1 and Suv39H2. In contrast, the K885A mutant did not repress other SETDB1 target genes such as Tril and Gas6 suggesting SETDB1 represses its target genes by two mechanisms; one that requires its ubiquitination and another that still requires SETDB1 but not its enzyme activity.
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Affiliation(s)
- Ji Zhang
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshihiro Matsumura
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Yuka Kano
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Laboratory of Molecular Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Ayano Yoshida
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Laboratory of Genome and Biosignal, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Takeshi Kawamura
- Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Proteomics Laboratory, Isotope Science Center, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Hirakawa
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Department of Physiology and Cell Biology, Tokyo Medical and Dental University (TMDU), Graduate School, Tokyo, Japan
| | - Takeshi Inagaki
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Toshiya Tanaka
- Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Shigeru Yanagi
- Laboratory of Molecular Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kiyoko Fukami
- Laboratory of Genome and Biosignal, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Takefumi Doi
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Timothy F Osborne
- Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, and Medicine in the Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, St. Petersburg, FL, USA
| | - Tatsuhiko Kodama
- Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
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40
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Lazaro-Camp VJ, Salari K, Meng X, Yang S. SETDB1 in cancer: overexpression and its therapeutic implications. Am J Cancer Res 2021; 11:1803-1827. [PMID: 34094655 PMCID: PMC8167684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023] Open
Abstract
SET Domain Bifurcated Histone Lysine Methyltransferase 1 (SETDB1, ESET, KMT1E) is a H3K9 methyltransferase involved in gene silencing. In recent years, SETDB1 has been implicated as an oncogene in various cancers, highlighting a critical need to better understand the mechanisms underlying SETDB1 amplification, overexpression, and activation. In the following review, we first examine the history of SETDB1, starting from its discovery in 1999 and ending with recent findings. We follow with an outline of the structure and subcellular location of SETDB1, as well as potential mechanisms for regulation of its nuclear transport. Subsequently, we introduce SETDB1's various functions, including its roles in promyelocytic leukemia nuclear body (PML-NB) formation, the methylation and activation of Akt, the silencing of the androgen receptor (AR) gene, retroelement silencing, the inhibition of tumor suppressor p53, and its role in promoting intestinal differentiation and survival. The Cancer Cell Line Encyclopedia (CCLE) screened SETDB1 dependency in 796 cancer cell lines, identifying SETDB1 as a common essential gene in 531 of them, demonstrating that SETDB1 expression is critical for the survival of the majority of cancers. Therefore, we provide a detailed review of the oncogenic effects of SETDB1 overexpression in breast cancer, non-small cell lung cancer, prostate cancer, colorectal cancer, acute myeloid leukemia, glioma, melanoma, pancreatic ductal adenocarcinoma, liver cancer, nasopharyngeal carcinoma, gastric carcinoma, and endometrial cancer. Accordingly, we review several methods that have been used to target SETDB1, such as using Mithramycin A, Mithralog EC-8042, 3'-deazaneplanocin A (DZNep), and paclitaxel. Finally, we conclude by highlighting remaining gaps in knowledge and challenges surrounding SETDB1. Ultimately, our review captures the wide scope of findings on SETDB1's history, function, its implications in cancer, and provides suggestions for future research in the field.
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Affiliation(s)
- Vanessa J Lazaro-Camp
- Department of Pathology, Carver College of Medicine, University of IowaIowa, IA, USA
| | - Kiarash Salari
- Department of Pathology, Carver College of Medicine, University of IowaIowa, IA, USA
| | - Xiangbing Meng
- Department of Pathology, Carver College of Medicine, University of IowaIowa, IA, USA
- Holden Comprehensive Cancer Center, Carver College of Medicine, University of IowaIA, USA
| | - Shujie Yang
- Department of Pathology, Carver College of Medicine, University of IowaIowa, IA, USA
- Holden Comprehensive Cancer Center, Carver College of Medicine, University of IowaIA, USA
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41
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Wan C, Zhang F, Yao H, Li H, Tuan RS. Histone Modifications and Chondrocyte Fate: Regulation and Therapeutic Implications. Front Cell Dev Biol 2021; 9:626708. [PMID: 33937229 PMCID: PMC8085601 DOI: 10.3389/fcell.2021.626708] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
The involvement of histone modifications in cartilage development, pathology and regeneration is becoming increasingly evident. Understanding the molecular mechanisms and consequences of histone modification enzymes in cartilage development, homeostasis and pathology provides fundamental and precise perspectives to interpret the biological behavior of chondrocytes during skeletal development and the pathogenesis of various cartilage related diseases. Candidate molecules or drugs that target histone modifying proteins have shown promising therapeutic potential in the treatment of cartilage lesions associated with joint degeneration and other chondropathies. In this review, we summarized the advances in the understanding of histone modifications in the regulation of chondrocyte fate, cartilage development and pathology, particularly the molecular writers, erasers and readers involved. In addition, we have highlighted recent studies on the use of small molecules and drugs to manipulate histone signals to regulate chondrocyte functions or treat cartilage lesions, in particular osteoarthritis (OA), and discussed their potential therapeutic benefits and limitations in preventing articular cartilage degeneration or promoting its repair or regeneration.
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Affiliation(s)
- Chao Wan
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Fengjie Zhang
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Hanyu Yao
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Rocky S Tuan
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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Tsusaka T, Fukuda K, Shimura C, Kato M, Shinkai Y. The fibronectin type-III (FNIII) domain of ATF7IP contributes to efficient transcriptional silencing mediated by the SETDB1 complex. Epigenetics Chromatin 2020; 13:52. [PMID: 33256805 PMCID: PMC7706265 DOI: 10.1186/s13072-020-00374-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/13/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The histone methyltransferase SETDB1 (also known as ESET) represses genes and various types of transposable elements, such as endogenous retroviruses (ERVs) and integrated exogenous retroviruses, through a deposition of trimethylation on lysine 9 of histone H3 (H3K9me3) in mouse embryonic stem cells (mESCs). ATF7IP (also known as MCAF1 or AM), a binding partner of SETDB1, regulates the nuclear localization and enzymatic activities of SETDB1 and plays a crucial role in SETDB1-mediated transcriptional silencing. In this study, we further dissected the ATF7IP function with its truncated mutants in Atf7ip knockout (KO) mESCs. RESULTS We demonstrated that the SETDB1-interaction region within ATF7IP is essential for ATF7IP-dependent SETDB1 nuclear localization and silencing of both ERVs and integrated retroviral transgenes, whereas its C-terminal fibronectin type-III (FNIII) domain is dispensable for both these functions; rather, it has a role in efficient silencing mediated by the SETDB1 complex. Proteomic analysis identified a number of FNIII domain-interacting proteins, some of which have a consensus binding motif. We showed that one of the FNIII domain-binding proteins, ZMYM2, was involved in the efficient silencing of a transgene by ATF7IP. RNA-seq analysis of Atf7ip KO and WT or the FNIII domain mutant of ATF7IP-rescued Atf7ip KO mESCs showed that the FNIII domain mutant re-silenced most de-repressed SETDB1/ATF7IP-targeted ERVs compared to the WT. However, the silencing activity of the FNIII domain mutant was weaker than that of the ATF7IP WT, and some of the de-repressed germ cell-related genes in Atf7ip KO mESCs were not silenced by the FNIII domain mutant. Such germ cell-related genes are targeted and silenced by the MAX/MGA complex, and MGA was also identified as another potential binding molecule of the ATF7IP FNIII domain in the proteomic analysis. This suggests that the FNIII domain of ATF7IP acts as a binding hub of ATF7IP-interacting molecules possessing a specific interacting motif we named FAM and contributes to one layer of the SETDB1/ATF7IP complex-mediated silencing mechanisms. CONCLUSIONS Our findings contributed to further understanding the function of ATF7IP in the SETDB1 complex, revealed the role of the FNIII domain of ATF7IP in transcriptional silencing, and suggested a potential underlying molecular mechanism for it.
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Affiliation(s)
- Takeshi Tsusaka
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
| | - Chikako Shimura
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
| | - Masaki Kato
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan. .,Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan.
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan.
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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: 52] [Impact Index Per Article: 13.0] [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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SATO K, SIOMI MC. The piRNA pathway in Drosophila ovarian germ and somatic cells. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:32-42. [PMID: 31932527 PMCID: PMC6974405 DOI: 10.2183/pjab.96.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 10/28/2019] [Indexed: 05/30/2023]
Abstract
RNA silencing refers to gene silencing pathways mediated by small non-coding RNAs, including microRNAs. Piwi-interacting RNAs (piRNAs) constitute the largest class of small non-coding RNAs in animal gonads, which repress transposons to protect the germline genome from the selfish invasion of transposons. Deterioration of the system causes DNA damage, leading to severe defects in gametogenesis and infertility. Studies using Drosophila ovaries show that piRNAs originate from specific genomic loci, termed piRNA clusters, and that in piRNA biogenesis, cluster transcripts are processed into mature piRNAs via three distinct pathways: initiator or responder for ping-pong piRNAs and trailing for phased piRNAs. piRNAs then assemble with PIWI members of the Argonaute family of proteins to form piRNA-induced RNA silencing complexes (piRISCs), the core engine of the piRNA-mediated silencing pathway. Upon piRISC assembly, the PIWI member, Piwi, is translocated to the nucleus and represses transposons co-transcriptionally by inducing local heterochromatin formation at target transposon loci.
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Affiliation(s)
- Kaoru SATO
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mikiko C. SIOMI
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Abstract
Transposon silencing requires the histone methyltransferase SETDB1. In this issue of EMBO Reports, Tsusaka et al [1] and Osumi et al [2] illustrate how the cofactor ATF7IP and its fly homolog Windei (Wde) regulate the methyltransferase function of SETDB1 through its nuclear licensing. The new insight gained from these two articles will shift how we think about epigenetic regulation and its multiple layers of control.
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Affiliation(s)
- Poppy A Gould
- Division of Infection and Immunity, University College London, London, UK
| | - Helen M Rowe
- Division of Infection and Immunity, University College London, London, UK
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Tsusaka T, Shimura C, Shinkai Y. ATF7IP regulates SETDB1 nuclear localization and increases its ubiquitination. EMBO Rep 2019; 20:e48297. [PMID: 31576654 DOI: 10.15252/embr.201948297] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/02/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022] Open
Abstract
Understanding of the appropriate regulation of enzymatic activities of histone-modifying enzymes remains poor. The lysine methyltransferase, SETDB1, is one of the enzymes responsible for the methylation of histone H3 at lysine 9 (H3K9) and plays a key role in H3K9 trimethylation-mediated silencing of genes and retrotransposons. Here, we reported that how SETDB1's enzymatic activities can be regulated by the nuclear protein, ATF7IP, a known binding partner of SETDB1. Mechanistically, ATF7IP mediates SETDB1 retention inside the nucleus, presumably by inhibiting its nuclear export by binding to the N-terminal region of SETDB1, which harbors the nuclear export signal motifs, and also by promoting its nuclear import. The nuclear localization of SETDB1 increases its ubiquitinated, enzymatically more active form. Our results provided an insight as to how ATF7IP can regulate the histone methyltransferase activity of SETDB1 accompanied by its nuclear translocation.
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Affiliation(s)
- Takeshi Tsusaka
- Cellular Memory Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Japan
| | - Chikako Shimura
- Cellular Memory Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Japan
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Osumi K, Sato K, Murano K, Siomi H, Siomi MC. Essential roles of Windei and nuclear monoubiquitination of Eggless/SETDB1 in transposon silencing. EMBO Rep 2019; 20:e48296. [PMID: 31576653 DOI: 10.15252/embr.201948296] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/02/2019] [Accepted: 09/11/2019] [Indexed: 11/09/2022] Open
Abstract
Eggless/SETDB1 (Egg), the only essential histone methyltransferase (HMT) in Drosophila, plays a role in gene repression, including piRNA-mediated transposon silencing in the ovaries. Previous studies suggested that Egg is post-translationally modified and showed that Windei (Wde) regulates Egg nuclear localization through protein-protein interaction. Monoubiquitination of mammalian SETDB1 is necessary for the HMT activity. Here, using cultured ovarian somatic cells, we show that Egg is monoubiquitinated and phosphorylated but that only monoubiquitination is required for piRNA-mediated transposon repression. Egg monoubiquitination occurs in the nucleus. Egg has its own nuclear localization signal, and the nuclear import of Egg is Wde-independent. Wde recruits Egg to the chromatin at target gene silencing loci, but their interaction is monoubiquitin-independent. The abundance of nuclear Egg is governed by that of nuclear Wde. These results illuminate essential roles of nuclear monoubiquitination of Egg and the role of Wde in piRNA-mediated transposon repression.
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Affiliation(s)
- Ken Osumi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kaoru Sato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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