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O’Sullivan J, Kothari C, Caron MC, Gagné JP, Jin Z, Nonfoux L, Beneyton A, Coulombe Y, Thomas M, Atalay N, Meng X, Milano L, Jean D, Boisvert FM, Kaufmann S, Hendzel M, Masson JY, Poirier G. ZNF432 stimulates PARylation and inhibits DNA resection to balance PARPi sensitivity and resistance. Nucleic Acids Res 2023; 51:11056-11079. [PMID: 37823600 PMCID: PMC10639050 DOI: 10.1093/nar/gkad791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 09/05/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Zinc finger (ZNF) motifs are some of the most frequently occurring domains in the human genome. It was only recently that ZNF proteins emerged as key regulators of genome integrity in mammalian cells. In this study, we report a new role for the Krüppel-type ZNF-containing protein ZNF432 as a novel poly(ADP-ribose) (PAR) reader that regulates the DNA damage response. We show that ZNF432 is recruited to DNA lesions via DNA- and PAR-dependent mechanisms. Remarkably, ZNF432 stimulates PARP-1 activity in vitro and in cellulo. Knockdown of ZNF432 inhibits phospho-DNA-PKcs and increases RAD51 foci formation following irradiation. Moreover, purified ZNF432 preferentially binds single-stranded DNA and impairs EXO1-mediated DNA resection. Consequently, the loss of ZNF432 in a cellular system leads to resistance to PARP inhibitors while its overexpression results in sensitivity. Taken together, our results support the emerging concept that ZNF-containing proteins can modulate PARylation, which can be embodied by the pivotal role of ZNF432 to finely balance the outcome of PARPi response by regulating homologous recombination.
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Affiliation(s)
- Julia O’Sullivan
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Charu Kothari
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Marie-Christine Caron
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Jean-Philippe Gagné
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Zhigang Jin
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Louis Nonfoux
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Adèle Beneyton
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Yan Coulombe
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Mélissa Thomas
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Nurgul Atalay
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - X Wei Meng
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Larissa Milano
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Dominique Jean
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Guy G Poirier
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
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Cesaro E, Lupo A, Rapuano R, Pastore A, Grosso M, Costanzo P. ZNF224 Protein: Multifaceted Functions Based on Its Molecular Partners. Molecules 2021; 26:molecules26206296. [PMID: 34684876 PMCID: PMC8537547 DOI: 10.3390/molecules26206296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 01/05/2023] Open
Abstract
The transcription factor ZNF224 is a Kruppel-like zinc finger protein that consists of 707 amino acids and contains 19 tandemly repeated C2H2 zinc finger domains that mediate DNA binding and protein-protein interactions. ZNF224 was originally identified as a transcriptional repressor of genes involved in energy metabolism, and it was demonstrated that ZNF224-mediated transcriptional repression needs the interaction of its KRAB repressor domain with the co-repressor KAP1 and its zinc finger domains 1-3 with the arginine methyltransferase PRMT5. Furthermore, the protein ZNF255 was identified as an alternative isoform of ZNF224 that possesses different domain compositions mediating distinctive functional interactions. Subsequent studies showed that ZNF224 is a multifunctional protein able to exert different transcriptional activities depending on the cell context and the variety of its molecular partners. Indeed, it has been shown that ZNF224 can act as a repressor, an activator and a cofactor for other DNA-binding transcription factors in different human cancers. Here, we provide a brief overview of the current knowledge on the multifaceted interactions of ZNF224 and the resulting different roles of this protein in various cellular contexts.
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Affiliation(s)
- Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
- Correspondence: (E.C.); (P.C.)
| | - Angelo Lupo
- Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Italy; (A.L.); (R.R.)
| | - Roberta Rapuano
- Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Italy; (A.L.); (R.R.)
| | - Arianna Pastore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
| | - Paola Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
- Correspondence: (E.C.); (P.C.)
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Developing ZNF Gene Signatures Predicting Radiosensitivity of Patients with Breast Cancer. JOURNAL OF ONCOLOGY 2021; 2021:9255494. [PMID: 34504527 PMCID: PMC8423582 DOI: 10.1155/2021/9255494] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/22/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
Adjuvant radiotherapy is one of the main treatment methods for breast cancer, but its clinical benefit depends largely on the characteristics of the patient. This study aimed to explore the relationship between the expression of zinc finger (ZNF) gene family proteins and the radiosensitivity of breast cancer patients. Clinical and gene expression data on a total of 976 breast cancer samples were obtained from The Cancer Genome Atlas (TCGA) database. ZNF gene expression was dichotomized into groups with a higher or lower level than the median level of expression. Univariate and multivariate Cox regression analyses were used to evaluate the relationship between ZNF gene expression levels and radiosensitivity. The Molecular Taxonomy Data of the International Federation of Breast Cancer (METABRIC) database was used for validation. The results revealed that 4 ZNF genes were possible radiosensitivity markers. High expression of ZNF644 and low expression levels of the other 3 genes (ZNF341, ZNF541, and ZNF653) were related to the radiosensitivity of breast cancer. Hierarchical cluster, Cox, and CoxBoost analysis based on these 4 ZNF genes indicated that patients with a favorable 4-gene signature had better overall survival on radiotherapy. Thus, this 4-gene signature may have value for selecting those patients most likely to benefit from radiotherapy. ZNF gene clusters could act as radiosensitivity signatures for breast cancer patients and may be involved in determining the radiosensitivity of cancer.
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Liu Y, Yin W, Wang J, Lei Y, Sun G, Li W, Huang Z, Guo M. KRAB-Zinc Finger Protein ZNF268a Deficiency Attenuates the Virus-Induced Pro-Inflammatory Response by Preventing IKK Complex Assembly. Cells 2019; 8:cells8121604. [PMID: 31835635 PMCID: PMC6953056 DOI: 10.3390/cells8121604] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/28/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023] Open
Abstract
Despite progress in understanding how virus-induced, NF-κB-dependent pro-inflammatory cytokines are regulated, there are still factors and mechanisms that remain to be explored. We aimed to uncover the relationship between KRAB-zinc finger protein ZNF268a and NF-κB-mediated cytokine production in response to viral infection. To this end, we established a ZNF268a-knockout cell line using a pair of sgRNAs that simultaneously target exon 3 in the coding sequence of the ZNF268 gene in HEK293T. HEK293T cells lacking ZNF268a showed less cytokine expression at the transcription and protein levels in response to Sendai virus/vesicular stomatitis virus (SeV/VSV) infection than wild-type cells. Consistent with HEK293T, knock-down of ZNF268a by siRNAs in THP-1 cells significantly dampened the inflammatory response. Mechanistically, ZNF268a facilitated NF-κB activation by targeting IKKα, helping to maintain the IKK signaling complex and thus enabling proper p65 phosphorylation and nuclear translocation. Taken together, our data suggest that ZNF268a plays a positive role in the regulation of virus-induced pro-inflammatory cytokine production. By interacting with IKKα, ZNF268a promotes NF-κB signal transduction upon viral infection by helping to maintain the association between IKK complex subunits.
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Affiliation(s)
- Yi Liu
- Hubei Key Laboratory of Cell Homeostasis & State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wei Yin
- Hubei Key Laboratory of Cell Homeostasis & State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jingwen Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yucong Lei
- Hubei Key Laboratory of Cell Homeostasis & State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Guihong Sun
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan 430071, China
| | - Wenxin Li
- Hubei Key Laboratory of Cell Homeostasis & State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zan Huang
- Hubei Key Laboratory of Cell Homeostasis & State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence: (Z.H.); (M.G.)
| | - Mingxiong Guo
- Hubei Key Laboratory of Cell Homeostasis & State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence: (Z.H.); (M.G.)
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Zhang X, Zhou H, Zhang Y, Cai L, Jiang G, Li A, Miao Y, Li Q, Qiu X, Wang E. ZNF452 facilitates tumor proliferation and invasion via activating AKT-GSK3β signaling pathway and predicts poor prognosis of non-small cell lung cancer patients. Oncotarget 2018; 8:38863-38875. [PMID: 28418919 PMCID: PMC5503578 DOI: 10.18632/oncotarget.16408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/24/2017] [Indexed: 01/05/2023] Open
Abstract
ZNF452 is a zinc-finger protein family member which contains an isolated SCAN (SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) zinc-finger domain. Despite the SCAN N-terminus domain is known to play a role in transcriptional regulation of genes involved in cell survival and differentiation, there are no precise cellular functions that have been assigned to ZNF452. In the present study, we found that either endogenous or exogenous ZNF452 was overexpressed in the cytoplasm of NSCLC cells and positive ratio of ZNF452 in NSCLC samples (50.8%, 93/183) was significantly higher than that in normal lung tissues (22.4%, 13/58, P<0.001). ZNF452 overexpression was correlated with advanced TNM stage (P=0.033), positive lymph node metastasis (P=0.002) and predicted poor overall survival of NSCLC patients (P<0.001). ZNF452 facilitated tumor growth, colony formation, G1-S phase arrest, migration and invasion through upregulating the levels of CyclinD1, CyclinE1, p-Rb, or Snail, and downregulating the expression of Zo-1. In nude mice xenografts, overexpressing ZNF452 also promoted tumor proliferation and metastasis. Subsequently, we found that the effect of ZNF452 on facilitating tumor proliferation and invasion was through activating its downstream AKT-GSK3β signaling pathway. Treatment of AKT inhibitor markedly prevented the phosphorylation of AKT and GSK3β which subsequently counteracted increasing expression of CyclinD1, CyclinE1 or Snail and restored the decreasing expression of Zo-1, as well as the upregulation of tumor proliferation and invasion, caused by ZNF452 overexpression. Taken together, the present study indicated that ZNF452 may be an upstream regulator of AKT-GSK3β signaling pathway and facilitates proliferation and invasion of NSCLC.
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Affiliation(s)
- Xiupeng Zhang
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Haijing Zhou
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yong Zhang
- Department of Pathology, Cancer Hospital of China Medical University, Shenyang, China
| | - Lin Cai
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Guiyang Jiang
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ailin Li
- Department of Radiotherapy, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yuan Miao
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Qingchang Li
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xueshan Qiu
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Enhua Wang
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
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Altemose N, Noor N, Bitoun E, Tumian A, Imbeault M, Chapman JR, Aricescu AR, Myers SR. A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis. eLife 2017; 6:e28383. [PMID: 29072575 PMCID: PMC5705219 DOI: 10.7554/elife.28383] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/24/2017] [Indexed: 12/31/2022] Open
Abstract
PRDM9 binding localizes almost all meiotic recombination sites in humans and mice. However, most PRDM9-bound loci do not become recombination hotspots. To explore factors that affect binding and subsequent recombination outcomes, we mapped human PRDM9 binding sites in a transfected human cell line and measured PRDM9-induced histone modifications. These data reveal varied DNA-binding modalities of PRDM9. We also find that human PRDM9 frequently binds promoters, despite their low recombination rates, and it can activate expression of a small number of genes including CTCFL and VCX. Furthermore, we identify specific sequence motifs that predict consistent, localized meiotic recombination suppression around a subset of PRDM9 binding sites. These motifs strongly associate with KRAB-ZNF protein binding, TRIM28 recruitment, and specific histone modifications. Finally, we demonstrate that, in addition to binding DNA, PRDM9's zinc fingers also mediate its multimerization, and we show that a pair of highly diverged alleles preferentially form homo-multimers.
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Affiliation(s)
- Nicolas Altemose
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Nudrat Noor
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Emmanuelle Bitoun
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Afidalina Tumian
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Michael Imbeault
- Global Health InstituteÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - J Ross Chapman
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - A Radu Aricescu
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Simon R Myers
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
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Co-expression analysis and identification of fecundity-related long non-coding RNAs in sheep ovaries. Sci Rep 2016; 6:39398. [PMID: 27982099 PMCID: PMC5159859 DOI: 10.1038/srep39398] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 11/23/2016] [Indexed: 11/08/2022] Open
Abstract
Small Tail Han sheep, including the FecBBFecBB (Han BB) and FecB+ FecB+ (Han++) genotypes, and Dorset sheep exhibit different fecundities. To identify novel long non-coding RNAs (lncRNAs) associated with sheep fecundity to better understand their molecular mechanisms, a genome-wide analysis of mRNAs and lncRNAs from Han BB, Han++ and Dorset sheep was performed. After the identification of differentially expressed mRNAs and lncRNAs, 16 significant modules were explored by using weighted gene coexpression network analysis (WGCNA) followed by functional enrichment analysis of the genes and lncRNAs in significant modules. Among these selected modules, the yellow and brown modules were significantly related to sheep fecundity. lncRNAs (e.g., NR0B1, XLOC_041882, and MYH15) in the yellow module were mainly involved in the TGF-β signalling pathway, and NYAP1 and BCORL1 were significantly associated with the oxytocin signalling pathway, which regulates several genes in the coexpression network of the brown module. Overall, we identified several gene modules associated with sheep fecundity, as well as networks consisting of hub genes and lncRNAs that may contribute to sheep prolificacy by regulating the target mRNAs related to the TGF-β and oxytocin signalling pathways. This study provides an alternative strategy for the identification of potential candidate regulatory lncRNAs.
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Ichida Y, Utsunomiya Y, Yasuda T, Nakabayashi K, Sato T, Onodera M. Functional Domains of ZFP809 Essential for Nuclear Localization and Gene Silencing. PLoS One 2015; 10:e0139274. [PMID: 26417948 PMCID: PMC4587795 DOI: 10.1371/journal.pone.0139274] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/09/2015] [Indexed: 12/02/2022] Open
Abstract
Zinc finger protein 809 (ZFP809) is a member of the Kruppel-associated box-containing zinc finger protein (KRAB-ZFP) family, and is highly expressed in mouse immature cells. ZFP809 is known to inhibit the expression of transduced genes driven by Moloney murine leukemia virus (MoMLV)-typed retroviral vectors by binding to the primer binding site (PBS) located downstream of the MLV-long terminal repeat (LTR) of the vectors and recruiting protein complexes that introduce epigenetic silencing marks such as histone modifications and DNA methylation at the MLV-LTR. However, it remains undetermined what domains of ZFP809 among the KRAB domain at N-terminus and the seven zinc fingers are critical for gene silencing. In this study, we assessed subcellular localization, gene silencing ability, and binding ability to the PBS of a series of truncated and mutated ZFP809 proteins. We revealed the essential role of the KRAB A box for all functions assessed, together with the accessory roles of a subset of zinc fingers. Our data also suggest that interaction between KAP1 and the KRAB A box of ZFP809 is critical in KAP1-dependent control of gene silencing for ZFP809 targets.
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Affiliation(s)
- Yu Ichida
- Department of Human Genetics, National Center for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Yuko Utsunomiya
- Department of Human Genetics, National Center for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Toru Yasuda
- Department of Human Genetics, National Center for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, 223-8522, Japan
| | - Masafumi Onodera
- Department of Human Genetics, National Center for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
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