1
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Bhaduri-McIntosh S, Rousseau BA. KAP1/TRIM28 - antiviral and proviral protagonist of herpesvirus biology. Trends Microbiol 2024:S0966-842X(24)00138-0. [PMID: 38871562 DOI: 10.1016/j.tim.2024.05.007] [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: 03/22/2024] [Revised: 05/19/2024] [Accepted: 05/21/2024] [Indexed: 06/15/2024]
Abstract
Dysregulation of the constitutive heterochromatin machinery (HCM) that silences pericentromeric regions and endogenous retroviral elements in the human genome has consequences for aging and cancer. By recruiting epigenetic regulators, Krüppel-associated box (KRAB)-associated protein 1 (KAP1/TRIM28/TIF1β) is integral to the function of the HCM. Epigenetically silencing DNA genomes of incoming herpesviruses to enforce latency, KAP1 and HCM also serve in an antiviral capacity. In addition to gene silencing, newer reports highlight KAP1's ability to directly activate cellular gene transcription. Here, we discuss the many facets of KAP1, including recent findings that unexpectedly connect KAP1 to the inflammasome, reveal KAP1 cleavage as a novel mode of regulation, and argue for a pro-herpesviral KAP1 function that ensures transition from transcription to replication of the herpesvirus genome.
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Affiliation(s)
- Sumita Bhaduri-McIntosh
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA.
| | - Beth A Rousseau
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL, USA
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2
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Li D, Cheng J, Zhang W, Zhang L, Maghsoudloo M, Fu J, Liu X, Xiao X, Wei C, Fu J. Tripartite motif-containing 28 (TRIM28) expression and cordycepin inhibition in progression, prognosis, and therapeutics of patients with breast invasive carcinoma. J Cancer 2024; 15:4374-4385. [PMID: 38947392 PMCID: PMC11212093 DOI: 10.7150/jca.95876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/12/2024] [Indexed: 07/02/2024] Open
Abstract
Breast cancer (BC) is the most common tumor in women worldwide. TRIM28 (RNF96) plays pleiotropic biological functions, such as silencing target genes, facilitating DNA repair, stimulating cellular proliferation and differentiation, and contributing to cancer progression. TRIM28 plays an increasingly crucial role in cancer, but its impact on BC, including breast invasive carcinoma, remains poorly understood. In the current study, analyses of online databases, quantitative real-time quantitative PCR, immunohistochemistry, and western blotting were performed on patients with breast invasive carcinoma (BRCA). Cordycepin (CD) was used to monitor BC progression and TRIM28 expression in vivo. As a result, we observed that TRIM28 is highly expressed in breast invasive carcinoma tissues compared with the corresponding normal tissues and is correlated with metastatic / invasive progression. High expression of TRIM28 might serve as a prognostic marker for long-term survival in triple-negative BC, advanced BC, or breast invasive carcinoma. Although TRIM28 methylation in tumor tissues of breast invasive carcinoma is not significantly changed compared to the matched normal tissues, the expressions and methylation of TRIM28 are significantly reversely correlated. TRIM28 expression was inhibited by CD in the mouse model, indicating its role in preventing BC progression. Thus, TRIM28 might be a potentially valuable molecular target for forecasting the progression / prognosis of patients with breast invasive carcinoma. CD, which represses BC growth/metastasis, may be involved partially through suppressing TRIM28 expression.
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Affiliation(s)
- Dabing Li
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Wenqian Zhang
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Lianmei Zhang
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
- Department of Pathology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an 223300, Jiangsu Province, China
| | - Mazaher Maghsoudloo
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Xiaoyan Liu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Xiuli Xiao
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
- Department of Pathology, the Affiliated Hospital, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Chunli Wei
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
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3
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Roy A, Ghosh A. Epigenetic Restriction Factors (eRFs) in Virus Infection. Viruses 2024; 16:183. [PMID: 38399958 PMCID: PMC10892949 DOI: 10.3390/v16020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The ongoing arms race between viruses and their hosts is constantly evolving. One of the ways in which cells defend themselves against invading viruses is by using restriction factors (RFs), which are cell-intrinsic antiviral mechanisms that block viral replication and transcription. Recent research has identified a specific group of RFs that belong to the cellular epigenetic machinery and are able to restrict the gene expression of certain viruses. These RFs can be referred to as epigenetic restriction factors or eRFs. In this review, eRFs have been classified into two categories. The first category includes eRFs that target viral chromatin. So far, the identified eRFs in this category include the PML-NBs, the KRAB/KAP1 complex, IFI16, and the HUSH complex. The second category includes eRFs that target viral RNA or, more specifically, the viral epitranscriptome. These epitranscriptomic eRFs have been further classified into two types: those that edit RNA bases-adenosine deaminase acting on RNA (ADAR) and pseudouridine synthases (PUS), and those that covalently modify viral RNA-the N6-methyladenosine (m6A) writers, readers, and erasers. We delve into the molecular machinery of eRFs, their role in limiting various viruses, and the mechanisms by which viruses have evolved to counteract them. We also examine the crosstalk between different eRFs, including the common effectors that connect them. Finally, we explore the potential for new discoveries in the realm of epigenetic networks that restrict viral gene expression, as well as the future research directions in this area.
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Affiliation(s)
- Arunava Roy
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
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4
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Rosspopoff O, Trono D. Take a walk on the KRAB side. Trends Genet 2023; 39:844-857. [PMID: 37716846 DOI: 10.1016/j.tig.2023.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Canonical Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) act as major repressors of transposable elements (TEs) via the KRAB-mediated recruitment of the heterochromatin scaffold KRAB-associated protein (KAP)1. KZFP genes emerged some 420 million years ago in the last common ancestor of coelacanth, lungfish, and tetrapods, and dramatically expanded to give rise to lineage-specific repertoires in contemporary species paralleling their TE load and turnover. However, the KRAB domain displays sequence and function variations that reveal repeated diversions from a linear TE-KZFP trajectory. This Review summarizes current knowledge on the evolution of KZFPs and discusses how ancestral noncanonical KZFPs endowed with variant KRAB, SCAN or DUF3669 domains have been utilized to achieve KAP1-independent functions.
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Affiliation(s)
- Olga Rosspopoff
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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5
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Shang Z, Wu X, Zheng S, Wei Y, Hong Z, Ye D. A systematic pan-cancer analysis identifies TRIM28 as an immunological and prognostic predictor and involved in immunotherapy resistance. J Cancer 2023; 14:2798-2810. [PMID: 37781084 PMCID: PMC10539564 DOI: 10.7150/jca.86742] [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: 06/02/2023] [Accepted: 08/20/2023] [Indexed: 10/03/2023] Open
Abstract
Tripartite motif-containing protein 28 (TRIM28), as a transcriptional cofactor, has pleiotropic biological effects, such as silencing genes, promoting cellular proliferation and differentiation, and facilitating DNA repair. It is reported that TRIM28 is also correlated with immune infiltration in liver cancer that highlights an unnoticed function of TRIM28 in immune system. However, the prognostic and immunotherapeutic role of TRIM28 in human cancer has not been elucidated. In this study, we conducted a systematic pan-cancer analysis and partial experimental validation of TRIM28 as an immunological and prognostic predictor and its involvement in immunotherapy resistance. We found that TRIM28 expression was higher in various tumor tissues than in normal tissues. Higher TRIM28 expression was associated with poorer prognosis in multiple cancers. The expression of TRIM28 was positively correlated with the presence of T cells, macrophages and neutrophils, and TRIM28 also promoted the infiltration of a series of immune cell. Moreover, TRIM28 affected a wide range of cancer-related scores, and the abnormal expression of TRIM28 was also involved in tumor mutational burden, drug sensitivity, and microsatellite instability in cancer. The results suggest that TRIM28 is a potentially valuable immune response indicator and a molecular biomarker for predicting the prognosis of cancer patients.
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Affiliation(s)
- Zhi Shang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Xinqiang Wu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Shengfeng Zheng
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Yaru Wei
- Institute for translational brain research, Fudan University, Shanghai, China
| | - Zhe Hong
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
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6
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Huang M, Yao F, Nie L, Wang C, Su D, Zhang H, Li S, Tang M, Feng X, Yu B, Chen Z, Wang S, Yin L, Mou L, Hart T, Chen J. FACS-based genome-wide CRISPR screens define key regulators of DNA damage signaling pathways. Mol Cell 2023; 83:2810-2828.e6. [PMID: 37541219 PMCID: PMC10421629 DOI: 10.1016/j.molcel.2023.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/17/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
DNA damage-activated signaling pathways are critical for coordinating multiple cellular processes, which must be tightly regulated to maintain genome stability. To provide a comprehensive and unbiased perspective of DNA damage response (DDR) signaling pathways, we performed 30 fluorescence-activated cell sorting (FACS)-based genome-wide CRISPR screens in human cell lines with antibodies recognizing distinct endogenous DNA damage signaling proteins to identify critical regulators involved in DDR. We discovered that proteasome-mediated processing is an early and prerequisite event for cells to trigger camptothecin- and etoposide-induced DDR signaling. Furthermore, we identified PRMT1 and PRMT5 as modulators that regulate ATM protein level. Moreover, we discovered that GNB1L is a key regulator of DDR signaling via its role as a co-chaperone specifically regulating PIKK proteins. Collectively, these screens offer a rich resource for further investigation of DDR, which may provide insight into strategies of targeting these DDR pathways to improve therapeutic outcomes.
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Affiliation(s)
- Min Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fuwen Yao
- Department of Hepatopancreatobiliary Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Yu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shimin Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ling Yin
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lisha Mou
- Department of Hepatopancreatobiliary Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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7
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Chen YY, Ran XH, Ni RZ, Mu D. TRIM28 negatively regulates the RLR signaling pathway by targeting MAVS for degradation via K48-linked polyubiquitination. J Biol Chem 2023; 299:104660. [PMID: 37119745 PMCID: PMC10165269 DOI: 10.1016/j.jbc.2023.104660] [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: 01/21/2023] [Revised: 03/14/2023] [Accepted: 03/18/2023] [Indexed: 05/01/2023] Open
Abstract
Mitochondrial antiviral signaling (MAVS) protein is a core signaling adapter in the retinoid acid-inducible gene-I-like receptor (RLR) signaling pathway that recruits downstream signaling factors, ultimately leading to the activation of type Ⅰ interferons. However, the mechanisms that modulate the RLR signaling pathway by manipulating MAVS are not fully understood. Previous studies suggested that tripartite motif 28 (TRIM28) participates in regulating innate immune signaling pathways by inhibiting the expression of immune-related genes at the transcriptional level. In this study, we characterized TRIM28 as a negative regulator of the RLR signaling pathway in a MAVS-dependent manner. Overexpression of TRIM28 inhibited the MAVS-induced production of type Ⅰ interferons and proinflammatory cytokines, while knocking down TRIM28 exerted the opposite effect. Mechanistically, TRIM28 targeted MAVS for proteasome-mediated degradation via K48-linked polyubiquitination. The RING domain of TRIM28, especially the cysteine residues at positions 65 and 68, was critical for the suppressive effect of TRIM28 on MAVS-mediated RLR signaling, while each of the C-terminal domains of TRIM28 contributed to its interaction with MAVS. Further investigation revealed that TRIM28 transferred ubiquitin chains to the K7, K10, K371, K420, and K500 residues of MAVS. Together, our results reveal a previously uncharacterized mechanism involving TRIM28 in fine-tuning innate immune responses and provide new insights into the mechanisms by which MAVS is regulated, which contribute to the understanding of the molecular mechanisms underlying immune homeostasis maintenance.
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Affiliation(s)
- Ya-Yun Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Xiang-Hong Ran
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Run-Ze Ni
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Dan Mu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.
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8
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Jung P, Schmalbrock L, Wirth M. CRISPR Activation/Interference Screen to Identify Genetic Networks in HDAC-Inhibitor-Resistant Cells. Methods Mol Biol 2023; 2589:429-454. [PMID: 36255641 DOI: 10.1007/978-1-0716-2788-4_28] [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: 06/16/2023]
Abstract
Epigenetic alterations have been identified in various tumor types. In part, these alterations are mediated via increased histone deacetylase activity. Although preclinical results of monotherapies with histone deacetylase inhibitors (HDACi) are promising, success in clinical trials is limited. Reasons for these limitations may be de novo or acquired resistance to HDAC inhibitors that could be overcome with rational combination therapies. This requires knowledge of resistance mechanism along with the involved genetic networks. One way to identify such genetic networks is the implementation of a CRISPR-based technology allowing transcriptional repression (CRISPRi) and activation (CRISPRa) at a genome-wide scale. We describe a simple approach to amplify and validate sgRNA libraries, generate a myeloid progenitor cell line expressing catalytically dead Cas9 (dCas9) fusion proteins with transcriptional effectors to repress or activate genetic regions of interest and demonstrate a complementary genome-wide HDACi resistance screening approach. Furthermore, we present bioinformatics tools for quality control and analysis of the sequencing data.
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Affiliation(s)
- Paul Jung
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Laura Schmalbrock
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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9
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Mills C, Riching A, Keller A, Stombaugh J, Haupt A, Maksimova E, Dickerson SM, Anderson E, Hemphill K, Ebmeier C, Schiel JA, Levenga J, Perkett M, Smith AVB, Strezoska Z. A Novel CRISPR Interference Effector Enabling Functional Gene Characterization with Synthetic Guide RNAs. CRISPR J 2022; 5:769-786. [PMID: 36257604 PMCID: PMC9805873 DOI: 10.1089/crispr.2022.0056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/15/2022] [Indexed: 01/31/2023] Open
Abstract
While CRISPR interference (CRISPRi) systems have been widely implemented in pooled lentiviral screening, there has been limited use with synthetic guide RNAs for the complex phenotypic readouts enabled by experiments in arrayed format. Here we describe a novel deactivated Cas9 fusion protein, dCas9-SALL1-SDS3, which produces greater target gene repression than first or second generation CRISPRi systems when used with chemically modified synthetic single guide RNAs (sgRNAs), while exhibiting high target specificity. We show that dCas9-SALL1-SDS3 interacts with key members of the histone deacetylase and Swi-independent three complexes, which are the endogenous functional effectors of SALL1 and SDS3. Synthetic sgRNAs can also be used with in vitro-transcribed dCas9-SALL1-SDS3 mRNA for short-term delivery into primary cells, including human induced pluripotent stem cells and primary T cells. Finally, we used dCas9-SALL1-SDS3 for functional gene characterization of DNA damage host factors, orthogonally to small interfering RNA, demonstrating the ability of the system to be used in arrayed-format screening.
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Affiliation(s)
- Clarence Mills
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Andrew Riching
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Ashleigh Keller
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Jesse Stombaugh
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Amanda Haupt
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Elena Maksimova
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Sarah M. Dickerson
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Emily Anderson
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Kevin Hemphill
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Chris Ebmeier
- Mass Spectrometry Core Facility, University of Colorado-Boulder, Boulder, Colorado, USA
| | - John A. Schiel
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Josien Levenga
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Matthew Perkett
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Anja van Brabant Smith
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Zaklina Strezoska
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
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10
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Stoll GA, Pandiloski N, Douse CH, Modis Y. Structure and functional mapping of the KRAB-KAP1 repressor complex. EMBO J 2022; 41:e111179. [PMID: 36341546 PMCID: PMC9753469 DOI: 10.15252/embj.2022111179] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is lost genome-wide in cells expressing a KAP1 variant with mutations that abolish KRAB binding. Our work identifies and functionally validates the KRAB-KAP1 molecular interface, which is critical for a central transcriptional control axis in vertebrates. In addition, the structure-based prediction of KAP1 recruitment efficiency will enable optimization of KRABs used in CRISPRi.
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Affiliation(s)
- Guido A Stoll
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUK,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)University of Cambridge School of Clinical MedicineCambridgeUK
| | - Ninoslav Pandiloski
- Department of Experimental Medical Science, Lund Stem Cell CenterLund UniversityLundSweden
| | - Christopher H Douse
- Department of Experimental Medical Science, Lund Stem Cell CenterLund UniversityLundSweden
| | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUK,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)University of Cambridge School of Clinical MedicineCambridgeUK
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11
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Rossitto M, Déjardin S, Rands CM, Le Gras S, Migale R, Rafiee MR, Neirijnck Y, Pruvost A, Nguyen AL, Bossis G, Cammas F, Le Gallic L, Wilhelm D, Lovell-Badge R, Boizet-Bonhoure B, Nef S, Poulat F. TRIM28-dependent SUMOylation protects the adult ovary from activation of the testicular pathway. Nat Commun 2022; 13:4412. [PMID: 35906245 PMCID: PMC9338040 DOI: 10.1038/s41467-022-32061-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/17/2022] [Indexed: 11/08/2022] Open
Abstract
Gonadal sexual fate in mammals is determined during embryonic development and must be actively maintained in adulthood. In the mouse ovary, oestrogen receptors and FOXL2 protect ovarian granulosa cells from transdifferentiation into Sertoli cells, their testicular counterpart. However, the mechanism underlying their protective effect is unknown. Here, we show that TRIM28 is required to prevent female-to-male sex reversal of the mouse ovary after birth. We found that upon loss of Trim28, ovarian granulosa cells transdifferentiate to Sertoli cells through an intermediate cell type, different from gonadal embryonic progenitors. TRIM28 is recruited on chromatin in the proximity of FOXL2 to maintain the ovarian pathway and to repress testicular-specific genes. The role of TRIM28 in ovarian maintenance depends on its E3-SUMO ligase activity that regulates the sex-specific SUMOylation profile of ovarian-specific genes. Our study identifies TRIM28 as a key factor in protecting the adult ovary from the testicular pathway.
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Affiliation(s)
- Moïra Rossitto
- Institute of Human Genetics, CNRS UMR9002 University of Montpellier, 34396, Montpellier, France
- Univ. Bordeaux, INRAE, Bordeaux INP, NutriNeuro, UMR 1286, F-33000, Bordeaux, France
| | - Stephanie Déjardin
- Institute of Human Genetics, CNRS UMR9002 University of Montpellier, 34396, Montpellier, France
| | - Chris M Rands
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva CMU, lab E09.2750.B 1, rue Michel-Servet CH 1211 Geneva 4, Geneva, Switzerland
| | - Stephanie Le Gras
- GenomEast platform, IGBMC, 1, rue Laurent Fries, 67404 ILLKIRCH Cedex, Illkirch-Graffenstaden, France
| | - Roberta Migale
- The Francis Crick Institute, 1 Midland Road, London, NW1 2 1AT, UK
| | | | - Yasmine Neirijnck
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva CMU, lab E09.2750.B 1, rue Michel-Servet CH 1211 Geneva 4, Geneva, Switzerland
| | - Alain Pruvost
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191, Gif-sur-Yvette, France
| | - Anvi Laetitia Nguyen
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191, Gif-sur-Yvette, France
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Florence Cammas
- Institut de Recherche en Cancérologie de Montpellier, IRCM, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, F-34298, France
| | - Lionel Le Gallic
- Institute of Human Genetics, CNRS UMR9002 University of Montpellier, 34396, Montpellier, France
| | - Dagmar Wilhelm
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | | | - Serge Nef
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva CMU, lab E09.2750.B 1, rue Michel-Servet CH 1211 Geneva 4, Geneva, Switzerland
| | - Francis Poulat
- Institute of Human Genetics, CNRS UMR9002 University of Montpellier, 34396, Montpellier, France.
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12
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Randolph K, Hyder U, D’Orso I. KAP1/TRIM28: Transcriptional Activator and/or Repressor of Viral and Cellular Programs? Front Cell Infect Microbiol 2022; 12:834636. [PMID: 35281453 PMCID: PMC8904932 DOI: 10.3389/fcimb.2022.834636] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 01/01/2023] Open
Abstract
Several transcriptional and epigenetic regulators have been functionally linked to the control of viral and cellular gene expression programs. One such regulator is Krüppel-associated box (KRAB)-associated protein 1 (KAP1: also named TRIM28 or TIF1β), which has been extensively studied in the past three decades. Here we offer an up-to date review of its various functions in a diversity of contexts. We first summarize the discovery of KAP1 repression of endogenous retroviruses during development. We then deliberate evidence in the literature suggesting KAP1 is both an activator and repressor of HIV-1 transcription and discuss experimental differences and limitations of previous studies. Finally, we discuss KAP1 regulation of DNA and RNA viruses, and then expand on KAP1 control of cellular responses and immune functions. While KAP1 positive and negative regulation of viral and cellular transcriptional programs is vastly documented, our mechanistic understanding remains narrow. We thus propose that precision genetic tools to reveal direct KAP1 functions in gene regulation will be required to not only illuminate new biology but also provide the foundation to translate the basic discoveries from the bench to the clinics.
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13
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Lorenz P, Steinbeck F, Krause L, Thiesen HJ. The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain. Int J Mol Sci 2022; 23:ijms23031072. [PMID: 35162997 PMCID: PMC8835667 DOI: 10.3390/ijms23031072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
Krüppel-associated box (KRAB) zinc finger proteins are a large class of tetrapod transcription factors that usually exert transcriptional repression through recruitment of TRIM28/KAP1. The evolutionary root of modern KRAB domains (mKRAB) can be traced back to an ancestral motif (aKRAB) that occurs even in invertebrates. Here, we first stratified three subgroups of aKRAB sequences from the animal kingdom (PRDM9, SSX and coelacanth KZNF families) and defined ancestral subdomains for KRAB-A and KRAB-B. Using human ZNF10 mKRAB-AB as blueprints for function, we then identified the necessary amino acid changes that transform the inactive aKRAB-A of human PRDM9 into an mKRAB domain capable of mediating silencing and complexing TRIM28/KAP1 in human cells when employed as a hybrid with ZNF10-B. Full gain of function required replacement of residues KR by the conserved motif MLE (positionsA32-A34), which inserted an additional residue, and exchange of A9/S for F, A20/M for L, and A27/R for V. AlphaFold2 modelling documented an evolutionary conserved L-shaped body of two α-helices in all KRAB domains. It is transformed into a characteristic spatial arrangement typical for mKRAB-AB upon the amino acid replacements and in conjunction with a third helix supplied by mKRAB-B. Side-chains pointing outward from the core KRAB 3D structure may reveal a protein-protein interaction code enabling graded binding of TRIM28 to different KRAB domains. Our data provide basic insights into structure-function relationships and emulate transitions of KRAB during evolution.
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Affiliation(s)
- Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Correspondence: ; Tel.: +49-(0)381-494-5879; Fax: +49-(0)381-494-5882
| | - Felix Steinbeck
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Ludwig Krause
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Hans-Jürgen Thiesen
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Gesellschaft für Individualisierte Medizin (IndyMed) mbH, 17, 18055 Rostock, Germany
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14
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Iouranova A, Grun D, Rossy T, Duc J, Coudray A, Imbeault M, de Tribolet-Hardy J, Turelli P, Persat A, Trono D. KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences. Mob DNA 2022; 13:4. [PMID: 35042549 PMCID: PMC8767690 DOI: 10.1186/s13100-021-00260-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to gene regulation in early human development and germ cells. RESULTS Here, after studying genes driven by the long terminal repeat (LTR) of endogenous retroviruses, we identify the ape-restricted ZNF676 as the sequence-specific repressor of a subset of contemporary LTR12 integrants responsible for a large fraction of transpochimeric gene transcripts (TcGTs) generated during human early embryogenesis. We go on to reveal that the binding of this KZFP correlates with the epigenetic marking of these TEeRS in the germline, and is crucial to the control of genes involved in ciliogenesis/flagellogenesis, a biological process that dates back to the last common ancestor of eukaryotes. CONCLUSION These results illustrate how KZFPs and their TE targets contribute to the evolutionary turnover of transcription networks and participate in the transgenerational inheritance of epigenetic traits.
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Affiliation(s)
| | - Delphine Grun
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Tamara Rossy
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | | | - Michael Imbeault
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | | | - Didier Trono
- School of Life Sciences, EPFL, Lausanne, Switzerland.
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15
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HIF-1 Interacts with TRIM28 and DNA-PK to release paused RNA polymerase II and activate target gene transcription in response to hypoxia. Nat Commun 2022; 13:316. [PMID: 35031618 PMCID: PMC8760265 DOI: 10.1038/s41467-021-27944-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022] Open
Abstract
Hypoxia-inducible factor-1 (HIF-1) is a transcription factor that acts as a regulator of oxygen (O2) homeostasis in metazoan species by binding to hypoxia response elements (HREs) and activating the transcription of hundreds of genes in response to reduced O2 availability. RNA polymerase II (Pol II) initiates transcription of many HIF target genes under non-hypoxic conditions but pauses after approximately 30–60 nucleotides and requires HIF-1 binding for release. Here we report that in hypoxic breast cancer cells, HIF-1 recruits TRIM28 and DNA-dependent protein kinase (DNA-PK) to HREs to release paused Pol II. We show that HIF-1α and TRIM28 assemble the catalytically-active DNA-PK heterotrimer, which phosphorylates TRIM28 at serine-824, enabling recruitment of CDK9, which phosphorylates serine-2 of the Pol II large subunit C-terminal domain as well as the negative elongation factor to release paused Pol II, thereby stimulating productive transcriptional elongation. Our studies reveal a molecular mechanism by which HIF-1 stimulates gene transcription and reveal that the anticancer effects of drugs targeting DNA-PK in breast cancer may be due in part to their inhibition of HIF-dependent transcription. Hypoxia-inducible factor-1 (HIF-1) is a transcription factor that modulates target gene expression in response to changes in oxygen availability. Here the authors show that HIF-1 forms a complex with TRIM28 and DNA-dependent protein kinase (DNA-PK) that phosphorylates TRIM28. This leads to CDK9 recruitment, which stimulates RNA polymerase II (RNAPII) pause release and transcriptional elongation.
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16
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Hernández-Quiles M, Baak R, Borgman A, den Haan S, Sobrevals Alcaraz P, van Es R, Kiss-Toth E, Vos H, Kalkhoven E. Comprehensive Profiling of Mammalian Tribbles Interactomes Implicates TRIB3 in Gene Repression. Cancers (Basel) 2021; 13:6318. [PMID: 34944947 PMCID: PMC8699236 DOI: 10.3390/cancers13246318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/30/2022] Open
Abstract
The three human Tribbles (TRIB) pseudokinases have been implicated in a plethora of signaling and metabolic processes linked to cancer initiation and progression and can potentially be used as biomarkers of disease and prognosis. While their modes of action reported so far center around protein-protein interactions, the comprehensive profiling of TRIB interactomes has not been reported yet. Here, we have developed a robust mass spectrometry (MS)-based proteomics approach to characterize Tribbles' interactomes and report a comprehensive assessment and comparison of the TRIB1, -2 and -3 interactomes, as well as domain-specific interactions for TRIB3. Interestingly, TRIB3, which is predominantly localized in the nucleus, interacts with multiple transcriptional regulators, including proteins involved in gene repression. Indeed, we found that TRIB3 repressed gene transcription when tethered to DNA in breast cancer cells. Taken together, our comprehensive proteomic assessment reveals previously unknown interacting partners and functions of Tribbles proteins that expand our understanding of this family of proteins. In addition, our findings show that MS-based proteomics provides a powerful tool to unravel novel pseudokinase biology.
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Affiliation(s)
- Miguel Hernández-Quiles
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Rosalie Baak
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Anouska Borgman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Suzanne den Haan
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Paula Sobrevals Alcaraz
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Robert van Es
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Endre Kiss-Toth
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2TN, UK;
| | - Harmjan Vos
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Eric Kalkhoven
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
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17
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Yuan P, Yan J, Wang S, Guo Y, Xi X, Han S, Yin J, Peng B, He X, Bodem J, Liu W. Trim28 acts as restriction factor of prototype foamy virus replication by modulating H3K9me3 marks and destabilizing the viral transactivator Tas. Retrovirology 2021; 18:38. [PMID: 34903241 PMCID: PMC8670036 DOI: 10.1186/s12977-021-00584-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/26/2021] [Indexed: 12/17/2022] Open
Abstract
Background Prototype foamy virus (PFV) is nonpathogenic complex retroviruses that express a transcriptional transactivator Tas, which is essential for the activity of viral long terminal repeat (LTR) promoter and internal promoter (IP). Tripartite motif-containing protein 28 (Trim28) is well known as a scaffold protein normally enriched in gene promoter region to repress transcription. We sought to determine if whether Trim28 could be enriched in PFV promoter region to participate the establishment of PFV latency infection. Results In this study, we show that Trim28 restricts Tas-dependent transactivation activity of PFV promoter and negatively regulates PFV replication. Trim28 was found to be enriched in LTR instead of IP promoter regions of PFV genome and contribute to the maintenance of histone H3K9me3 marks on the LTR promoter. Furthermore, Trim28 interacts with Tas and colocalizes with Tas in the nucleus. Besides, we found that Trim28, an E3 ubiquitin ligase, binds directly to and promotes Tas for ubiquitination and degradation. And the RBCC domain of Trim28 is required for the ubiquitination and degradation of Tas. Conclusions Collectively, our findings not only identify a host factor Trim28 negatively inhibits PFV replication by acting as transcriptional restriction factor enriched in viral LTR promoter through modulating H3K9me3 mark here, but also reveal that Trim28 mediated ubiquitin proteasome degradation of Tas as a mechanism underlying Trim28 restricts Tas-dependent transcription activity of PFV promoter and PFV replication. These findings provide new insights into the process of PFV latency establishment. Graphical Abstract ![]()
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Affiliation(s)
- Peipei Yuan
- Department of Immunology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China.,Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang District, Wuhan, 430071, China.,Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Jun Yan
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang District, Wuhan, 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Shuang Wang
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang District, Wuhan, 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yang Guo
- Department of Immunology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China.,Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xueyan Xi
- Department of Immunology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China.,Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Song Han
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang District, Wuhan, 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jun Yin
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang District, Wuhan, 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Biwen Peng
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang District, Wuhan, 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xiaohua He
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang District, Wuhan, 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jochen Bodem
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078, Würzburg, Germany
| | - Wanhong Liu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang District, Wuhan, 430071, China. .,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
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18
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Wang C, Songyang Z, Huang Y. TRIM28 inhibits alternative lengthening of telomere phenotypes by protecting SETDB1 from degradation. Cell Biosci 2021; 11:149. [PMID: 34330324 PMCID: PMC8325274 DOI: 10.1186/s13578-021-00660-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023] Open
Abstract
Background About 10–15% of tumor cells extend telomeres through the alternative lengthening of telomeres (ALT) mechanism, which is a recombination-dependent replication pathway. It is generally believed that ALT cells are related to the chromatin modification of telomeres. However, the mechanism of ALT needs to be further explored. Results Here we found that TRIM28/KAP1 is preferentially located on the telomeres of ALT cells and interacts with telomeric shelterin/telosome complex. Knocking down TRIM28 in ALT cells delayed cell growth, decreased the level of C-circle which is one kind of extrachromosomal circular telomeric DNA, increased the frequency of ALT-associated promyelocytic leukemia bodies (APBs), led to telomere prolongation and increased the telomere sister chromatid exchange in ALT cells. Mechanistically, TRIM28 protects telomere histone methyltransferase SETDB1 from degradation, thus maintaining the H3K9me3 heterochromatin state of telomere DNA. Conclusions Our work provides a model that TRIM28 inhibits alternative lengthening of telomere phenotypes by protecting SETDB1 from degradation. In general, our results reveal the mechanism of telomere heterochromatin maintenance and its effect on ALT, and TRIM28 may serve as a target for the treatment of ALT tumor cells. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00660-y.
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Affiliation(s)
- Chuanle Wang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Yan Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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19
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Boyson SP, Gao C, Quinn K, Boyd J, Paculova H, Frietze S, Glass KC. Functional Roles of Bromodomain Proteins in Cancer. Cancers (Basel) 2021; 13:3606. [PMID: 34298819 PMCID: PMC8303718 DOI: 10.3390/cancers13143606] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.
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Affiliation(s)
- Samuel P. Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Kathleen Quinn
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Joseph Boyd
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
- University of Vermont Cancer Center, Burlington, VT 05405, USA
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- University of Vermont Cancer Center, Burlington, VT 05405, USA
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20
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Ait-Ammar A, Bellefroid M, Daouad F, Martinelli V, Van Assche J, Wallet C, Rodari A, De Rovere M, Fahrenkrog B, Schwartz C, Van Lint C, Gautier V, Rohr O. Inhibition of HIV-1 gene transcription by KAP1 in myeloid lineage. Sci Rep 2021; 11:2692. [PMID: 33514850 PMCID: PMC7846785 DOI: 10.1038/s41598-021-82164-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 01/13/2021] [Indexed: 02/08/2023] Open
Abstract
HIV-1 latency generates reservoirs that prevent viral eradication by the current therapies. To find strategies toward an HIV cure, detailed understandings of the molecular mechanisms underlying establishment and persistence of the reservoirs are needed. The cellular transcription factor KAP1 is known as a potent repressor of gene transcription. Here we report that KAP1 represses HIV-1 gene expression in myeloid cells including microglial cells, the major reservoir of the central nervous system. Mechanistically, KAP1 interacts and colocalizes with the viral transactivator Tat to promote its degradation via the proteasome pathway and repress HIV-1 gene expression. In myeloid models of latent HIV-1 infection, the depletion of KAP1 increased viral gene elongation and reactivated HIV-1 expression. Bound to the latent HIV-1 promoter, KAP1 associates and cooperates with CTIP2, a key epigenetic silencer of HIV-1 expression in microglial cells. In addition, Tat and CTIP2 compete for KAP1 binding suggesting a dynamic modulation of the KAP1 cellular partners upon HIV-1 infection. Altogether, our results suggest that KAP1 contributes to the establishment and the persistence of HIV-1 latency in myeloid cells.
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Affiliation(s)
- Amina Ait-Ammar
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France ,grid.7886.10000 0001 0768 2743Center for Research in Infectious Diseases (CRID), School of Medicine and Medical Science (SMMS), University College Dublin (UCD), Dublin, Ireland ,grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Maxime Bellefroid
- grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Fadoua Daouad
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
| | - Valérie Martinelli
- grid.4989.c0000 0001 2348 0746Laboratory Biology of the Nucleus, Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium
| | - Jeanne Van Assche
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
| | - Clémentine Wallet
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
| | - Anthony Rodari
- grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Marco De Rovere
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
| | - Birthe Fahrenkrog
- grid.4989.c0000 0001 2348 0746Laboratory Biology of the Nucleus, Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium
| | - Christian Schwartz
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
| | - Carine Van Lint
- grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Virginie Gautier
- grid.7886.10000 0001 0768 2743Center for Research in Infectious Diseases (CRID), School of Medicine and Medical Science (SMMS), University College Dublin (UCD), Dublin, Ireland
| | - Olivier Rohr
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
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21
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Moore C, Monforte H, Teer JK, Zhang Y, Yoder S, Brohl AS, Reed DR. TRIM28 congenital predisposition to Wilms' tumor: novel mutations and presentation in a sibling pair. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004796. [PMID: 32699065 PMCID: PMC7476416 DOI: 10.1101/mcs.a004796] [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: 09/17/2019] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
Wilms’ tumor is the most common renal malignancy in children. In addition to staging, molecular risk stratification, such as loss of heterozygosity (LOH) in Chromosomes 1 and 16, is being increasingly used. Although genetic predisposition syndromes have been well-characterized in some Wilms’ tumors, recent sequencing and biology efforts are expanding the classification of this malignancy. Here we present a case of siblings with remarkably similar presentations of bilateral Wilms’ tumor at ∼12 mo of age. Thorough exam after the younger sibling was diagnosed did not reveal any signs to suggest one of the known Wilms’ predisposition syndromes. Both were treated with standard therapies with good response and long-term sustained complete remission of 53 and 97 mo, respectively. Whole-exome sequencing was performed on a tumor sample from each patient and matched blood from one, revealing a shared truncation mutation of TRIM28 in all three samples with heterozygosity in the germline sample. TRIM28 loss has been recently implicated in early-stage Wilms’ tumors with epithelioid morphology. These siblings expand the phenotype for presentation with multifocal disease with retained excellent response to standard therapy.
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Affiliation(s)
- Colin Moore
- Adolescent and Young Adult Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.,Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.,Center for Cancer and Blood Disorders, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
| | - Hector Monforte
- Department of Anatomic Pathology, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Yonghong Zhang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Andrew S Brohl
- Sarcoma Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Damon R Reed
- Adolescent and Young Adult Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.,Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.,Sarcoma Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
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22
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Raffeiner P, Hart JR, García-Caballero D, Bar-Peled L, Weinberg MS, Vogt PK. An MXD1-derived repressor peptide identifies noncoding mediators of MYC-driven cell proliferation. Proc Natl Acad Sci U S A 2020; 117:6571-6579. [PMID: 32156728 PMCID: PMC7104257 DOI: 10.1073/pnas.1921786117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MYC controls the transcription of large numbers of long noncoding RNAs (lncRNAs). Since MYC is a ubiquitous oncoprotein, some of these lncRNAs probably play a significant role in cancer. We applied CRISPR interference (CRISPRi) to the identification of MYC-regulated lncRNAs that are required for MYC-driven cell proliferation in the P493-6 and RAMOS human lymphoid cell lines. We identified 320 noncoding loci that play positive roles in cell growth. Transcriptional repression of any one of these lncRNAs reduces the proliferative capacity of the cells. Selected hits were validated by RT-qPCR and in CRISPRi competition assays with individual GFP-expressing sgRNA constructs. We also showed binding of MYC to the promoter of two candidate genes by chromatin immunoprecipitation. In the course of our studies, we discovered that the repressor domain SID (SIN3-interacting domain) derived from the MXD1 protein is highly effective in P493-6 and RAMOS cells in terms of the number of guides depleted in library screening and the extent of the induced transcriptional repression. In the cell lines used, SID is superior to the KRAB repressor domain, which serves routinely as a transcriptional repressor domain in CRISPRi. The SID transcriptional repressor domain is effective as a fusion to the MS2 aptamer binding protein MCP, allowing the construction of a doxycycline-regulatable CRISPRi system that allows controlled repression of targeted genes and will facilitate the functional analysis of growth-promoting lncRNAs.
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Affiliation(s)
- Philipp Raffeiner
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Jonathan R Hart
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | | | - Liron Bar-Peled
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Marc S Weinberg
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Peter K Vogt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037;
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23
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Singh PB, Newman AG. On the relations of phase separation and Hi-C maps to epigenetics. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191976. [PMID: 32257349 PMCID: PMC7062049 DOI: 10.1098/rsos.191976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/03/2020] [Indexed: 05/10/2023]
Abstract
The relationship between compartmentalization of the genome and epigenetics is long and hoary. In 1928, Heitz defined heterochromatin as the largest differentiated chromatin compartment in eukaryotic nuclei. Müller's discovery of position-effect variegation in 1930 went on to show that heterochromatin is a cytologically visible state of heritable (epigenetic) gene repression. Current insights into compartmentalization have come from a high-throughput top-down approach where contact frequency (Hi-C) maps revealed the presence of compartmental domains that segregate the genome into heterochromatin and euchromatin. It has been argued that the compartmentalization seen in Hi-C maps is owing to the physiochemical process of phase separation. Oddly, the insights provided by these experimental and conceptual advances have remained largely silent on how Hi-C maps and phase separation relate to epigenetics. Addressing this issue directly in mammals, we have made use of a bottom-up approach starting with the hallmarks of constitutive heterochromatin, heterochromatin protein 1 (HP1) and its binding partner the H3K9me2/3 determinant of the histone code. They are key epigenetic regulators in eukaryotes. Both hallmarks are also found outside mammalian constitutive heterochromatin as constituents of larger (0.1-5 Mb) heterochromatin-like domains and smaller (less than 100 kb) complexes. The well-documented ability of HP1 proteins to function as bridges between H3K9me2/3-marked nucleosomes contributes to polymer-polymer phase separation that packages epigenetically heritable chromatin states during interphase. Contacts mediated by HP1 'bridging' are likely to have been detected in Hi-C maps, as evidenced by the B4 heterochromatic subcompartment that emerges from contacts between large KRAB-ZNF heterochromatin-like domains. Further, mutational analyses have revealed a finer, innate, compartmentalization in Hi-C experiments that probably reflect contacts involving smaller domains/complexes. Proteins that bridge (modified) DNA and histones in nucleosomal fibres-where the HP1-H3K9me2/3 interaction represents the most evolutionarily conserved paradigm-could drive and generate the fundamental compartmentalization of the interphase nucleus. This has implications for the mechanism(s) that maintains cellular identity, be it a terminally differentiated fibroblast or a pluripotent embryonic stem cell.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, Nur-Sultan Z05K4F4, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Street 2, Novosibirsk 630090, Russian Federation
| | - Andrew G. Newman
- Institute of Cell and Neurobiology, Charité—Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
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24
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Al Chiblak M, Steinbeck F, Thiesen HJ, Lorenz P. DUF3669, a "domain of unknown function" within ZNF746 and ZNF777, oligomerizes and contributes to transcriptional repression. BMC Mol Cell Biol 2019; 20:60. [PMID: 31856708 PMCID: PMC6923878 DOI: 10.1186/s12860-019-0243-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/12/2019] [Indexed: 11/10/2022] Open
Abstract
Background ZNF746 and ZNF777 belong to a subset of the large Krüppel-associated box (KRAB) zinc finger (ZNF) transcription factor family. They contain, like four other members in human, an additional conserved domain, the “domain of unknown function 3669” (DUF3669). Previous work on members of this subfamily suggested involvement in transcriptional regulation and aberrant ZNF746 overexpression leads to neuronal cell death in Parkinson’s disease. Results Here we demonstrate that N-terminal protein segments of the ZNF746a major isoform and ZNF777 act in concert to exert moderate transcriptional repression activities. Full potency depended on the intact configuration consisting of DUF3669, a variant KRAB domain and adjacent sequences. While DUF3669 contributes an intrinsic weak inhibitory activity, the isolated KRAB-AB domains did not repress. Importantly, DUF3669 provides a novel protein-protein interaction interface and mediates direct physical interaction between the members of the subfamily in oligomers. The ZNF746 protein segment encoded by exons 5 and 6 boosted repressor potency, potentially due to the presence of an acceptor lysine for sumoylation at K189. Repressor activity of the potent canonical ZNF10 KRAB domain was not augmented by heterologous transfer of DUF3669, pointing to the importance of context for DUF3669’s impact on transcription. Neither ZNF746a nor ZNF777 protein segments stably associated with TRIM28 within cells. Isoform ZNF746b that contains, unlike the major isoform, a full-length KRAB-A subdomain, displayed substantially increased repressor potency. This increase is due to canonical mechanisms known for KRAB domains since it did not take place in HAP1 knockout models of TRIM28 and SETDB1. A glycine to glutamic acid replacement that complies with a bona fide conserved “MLE” sequence within KRAB-A led to a further strong gain in repressor potency to levels comparable to those of the canonical ZNF10 KRAB domain. Each gain of repressive activity was accompanied by an enhanced interaction with TRIM28 protein. Conclusion DUF3669 adds a protein-protein interaction surface to a subgroup of KRAB-ZNF proteins within an N-terminal configuration with variant KRAB and adjacent sequences likely regulated by sumoylation. DUF3669 contributes to transcriptional repression strength and its homo- and hetero-oligomerization characteristics probably extended the regulatory repertoire of KRAB-ZNF transcription factors during amniote evolution.
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Affiliation(s)
- Mohannad Al Chiblak
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Felix Steinbeck
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Hans-Jürgen Thiesen
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Peter Lorenz
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany.
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25
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Bruno M, Mahgoub M, Macfarlan TS. The Arms Race Between KRAB–Zinc Finger Proteins and Endogenous Retroelements and Its Impact on Mammals. Annu Rev Genet 2019; 53:393-416. [DOI: 10.1146/annurev-genet-112618-043717] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nearly half of the human genome consists of endogenous retroelements (EREs) and their genetic remnants, a small fraction of which carry the potential to propagate in the host genome, posing a threat to genome integrity and cell/organismal survival. The largest family of transcription factors in tetrapods, the Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs), binds to specific EREs and represses their transcription. Since their first appearance over 400 million years ago, KRAB-ZFPs have undergone dramatic expansion and diversification in mammals, correlating with the invasions of new EREs. In this article we review our current understanding of the structure, function, and evolution of KRAB-ZFPs and discuss growing evidence that the arms race between KRAB-ZFPs and the EREs they target is a major driving force for the evolution of new traits in mammals, often accompanied by domestication of EREs themselves.
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Affiliation(s)
- Melania Bruno
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mohamed Mahgoub
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Todd S. Macfarlan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
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26
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Zhang J, Luo J, Jiang H, Xie T, Zheng J, Tian Y, Li R, Wang B, Lin J, Xu A, Huang X, Yuan Y. The Tumor Suppressor Role of Zinc Finger Protein 671 ( ZNF671) in Multiple Tumors Based on Cancer Single-Cell Sequencing. Front Oncol 2019; 9:1214. [PMID: 31781507 PMCID: PMC6857622 DOI: 10.3389/fonc.2019.01214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/23/2019] [Indexed: 01/06/2023] Open
Abstract
In humans, zinc finger protein 671 (ZNF671) is a type of transcription factor. However, the contribution of tumor heterogeneity to the functional role of ZNF671 remains unknown. The present study aimed to determine the functional states of ZNF671 in cancer single cells based on single-cell sequencing datasets (scRNA-seq). We collected cancer-related ZNF671 scRNA-seq datasets and analyzed ZNF671 in the datasets. We evaluated 14 functional states of ZNF671 in cancers and performed ZNF671 expression and function state correlation analysis. We further applied t-distributed stochastic neighbor embedding to describe the distribution of cancer cells and to explore the functional state of ZNF671 in cancer subgroups. We found that ZNF671 was downregulated in eight cancer-related ZNF671 scRNA-seq datasets. Functional analysis identified that ZNF671 might play a tumor suppressor role in cancer. The heterogeneous functional states of cell subgroups and correlation analysis showed that ZNF671 played tumor suppressor roles in heterogeneous cancer cell populations. Western blot and transwell assays identified that ZNF671 inhibited EMT, migration, and invasion of CNS cancers, lung cancer, melanoma, and breast carcinoma in vitro. These results from cancer single-cell sequencing indicated that ZNF671 played a tumor suppressor role in multiple tumors and may provide us with new insights into the role of ZNF671 for cancer treatment.
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Affiliation(s)
- Jian Zhang
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Jianli Luo
- Department of General Disease, Health Center of Shuichun Town, Shanwei, China
| | - Huali Jiang
- Department of Cardiovascularology, Tungwah Hospital of Sun Yat-sen University, Dongguan, China
| | - Tao Xie
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Jieling Zheng
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yunhong Tian
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Rong Li
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Baiyao Wang
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Jie Lin
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Anan Xu
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Xiaoting Huang
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Yawei Yuan
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
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27
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Jiang Y, Wang X, Dong C. Molecular mechanisms of T helper 17 cell differentiation: Emerging roles for transcription cofactors. Adv Immunol 2019; 144:121-153. [PMID: 31699215 DOI: 10.1016/bs.ai.2019.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
T helper 17 (Th17) cells, characterized by secretion of IL-17 and IL-17F, are a specialized CD4+ effector T cell lineage that not only facilitates host defense against pathogen infection and maintenance of mucosal barrier, but also potently induces tissue inflammation and autoimmune diseases. Since its discovery in 2005, the developmental program of Th17 cells has been characterized, which involves a number of key cytokines, transcription factors and multiple layers of epigenetic modifications. However, how these mechanisms integrate into the complex regulatory network in Th17 cells has not been well defined. Emerging evidences have revealed essential roles of cofactors in controlling chromosome accessibilities and activities of Th17-specific transcription factors. Moreover, cofactors also act as critical signaling integrators to coordinate multiple signaling pathways and transcriptional programs. Deficiency or dysregulation of these cofactors results in defects in Th17 responses and induction of associated autoimmune diseases. Our lab has recently reported several important cofactors in Th17 cells. Here we summarize our findings regarding this new scenario of developmental regulation of Th17 cells. These findings may benefit the development of innovative strategies to treat autoimmune diseases.
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Affiliation(s)
- Yu Jiang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Xiaohu Wang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Chen Dong
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China; Beijing Key Lab for Immunological Research on Chronic Diseases, Beijing, China.
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28
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Expression of ZNF695 Transcript Variants in Childhood B-Cell Acute Lymphoblastic Leukemia. Genes (Basel) 2019; 10:genes10090716. [PMID: 31527520 PMCID: PMC6771147 DOI: 10.3390/genes10090716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/17/2019] [Accepted: 09/10/2019] [Indexed: 11/17/2022] Open
Abstract
B-cell acute lymphoblastic leukemia is the most commonly diagnosed childhood malignancy worldwide; more than 50% of these cases are diagnosed in Mexico. Although the five-year survival rate is >80%, 30% of patients experience relapse with poor prognosis. Cancer-associated gene expression profiles have been identified in several malignancies, and some transcripts have been used to predict disease prognosis. The human transcriptome is incompletely elucidated; moreover, more than 80% of transcripts can be processed via alternative splicing (AS), which increases transcript and protein diversity. The human transcriptome is divided; coding RNA accounts for 2%, and the remaining 98% is noncoding RNA. Noncoding RNA can undergo AS, promoting the diversity of noncoding transcripts. We designed specific primers to amplify previously reported alternative transcript variants of ZNF695 and showed that six ZNF695 transcript variants are co-expressed in cancer cell lines. The amplicons were sequenced and identified. Additionally, we analyzed the expression of these six transcript variants in bone marrow from B-cell acute lymphoblastic leukemia patients and observed that ZNF695 transcript variants one and three were the predominant variants expressed in leukemia. Moreover, our results showed the co-expression of coding and long noncoding RNA. Finally, we observed that long noncoding RNA ZNF695 expression predicted survival rates.
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29
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Fonti G, Marcaida MJ, Bryan LC, Träger S, Kalantzi AS, Helleboid PYJ, Demurtas D, Tully MD, Grudinin S, Trono D, Fierz B, Dal Peraro M. KAP1 is an antiparallel dimer with a functional asymmetry. Life Sci Alliance 2019; 2:2/4/e201900349. [PMID: 31427381 PMCID: PMC6701479 DOI: 10.26508/lsa.201900349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 01/10/2023] Open
Abstract
This study reveals the architecture of human KAP1 by integrating molecular modeling with small-angle X-ray scattering and single-molecule experiments. KAP1 dimers feature a structural asymmetry at the C-terminal domains that has functional implications for recruitment of HP1. KAP1 (KRAB domain–associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular interactions and as an E3 small ubiquitin modifier ligase. This work sheds light on the overall organization of the full-length protein combining solution scattering data, integrative modeling, and single-molecule experiments. We show that KAP1 is an elongated antiparallel dimer with an asymmetry at the C-terminal domains. This conformation is consistent with the finding that the Really Interesting New Gene (RING) domain contributes to KAP1 auto-SUMOylation. Importantly, this intrinsic asymmetry has key functional implications for the KAP1 network of interactions, as the heterochromatin protein 1 (HP1) occupies only one of the two putative HP1 binding sites on the KAP1 dimer, resulting in an unexpected stoichiometry, even in the context of chromatin fibers.
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Affiliation(s)
- Giulia Fonti
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Louise C Bryan
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sylvain Träger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra S Kalantzi
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pierre-Yves Jl Helleboid
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Davide Demurtas
- Interdisciplinary Centre for Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mark D Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Sergei Grudinin
- University Grenoble Alpes, Centre National de la Recherche Scientifique, Inria, Grenoble Institut Polytechnique de Grenoble, Laboratoire Jean Kuntzmann, Grenoble, France
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Beat Fierz
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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30
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Cui J, Hu J, Ye Z, Fan Y, Li Y, Wang G, Wang L, Wang Z. TRIM28 protects CARM1 from proteasome-mediated degradation to prevent colorectal cancer metastasis. Sci Bull (Beijing) 2019; 64:986-997. [PMID: 36659810 DOI: 10.1016/j.scib.2019.05.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/03/2019] [Accepted: 05/05/2019] [Indexed: 01/21/2023]
Abstract
TRIM28 (Tripartite motif-containing protein 28), a member of TRIM family, is aberrantly expressed and reportedly has different functions in many types of human cancer. However, the biological roles of TRIM28 and related mechanism in colorectal cancer (CRC) remain unclear. Here, we showed that TRIM28 was downregulated in colorectal cancer compared with normal mucosa, especially at advanced stages, and acted as an independent prognostic factor of favorable outcome. Functional studies demonstrated that TRIM28 restrained CRC migration and invasion in vitro and in vivo. Mechanistically, we reported that CARM1 (co-activator-associated arginine methyltransferase1) was a critical player downstream of TRIM28. TRIM28 interacted with CARM1, and protected CARM1 from proteasome-mediated degradation through physical protein-protein interaction to suppress CRC metastasis. Further, TRIM28 suppressed the migration and invasion of CRC cells through inhibiting WNT/β-catenin signaling in a CARM1-dependent manner, but independent of CARM1's methyltransferase activity. The protein expression of CARM1 was positively correlated with TRIM28 in CRC tissues. Patients with high levels of TRIM28 and CARM1 had improved prognosis, whereas patients with low TRIM28 and CARM1 expression had the poor outcomes. Thus, our study reveals an inhibitory role of TRIM28 in CRC metastasis, which was achieved through a TRIM28-CARM1-WNT/β-catenin axis. This work provides potential prognostic and therapeutic targets for CRC treatment.
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Affiliation(s)
- Jinyuan Cui
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jia Hu
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhilan Ye
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yongli Fan
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yuqin Li
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Guobin Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Lin Wang
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Zheng Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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A Dissection of Oligomerization by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family. J Mol Biol 2019; 431:2511-2527. [PMID: 31078555 DOI: 10.1016/j.jmb.2019.05.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 01/15/2023]
Abstract
TRIM28 (also known as KAP1 or TIF1β) is the universal co-repressor of the Krüppel-associated box-containing zinc finger proteins (Krab-ZFPs), the largest family of transcription factors in mammals. During early embryogenesis, TRIM28 mediates the transcriptional silencing of many endogenous retroviral elements and genomic imprinted sites. Silencing is initiated by the recruitment of TRIM28 to a target locus by members of the Krab-ZFP. Subsequently, TRIM28 functions as a scaffold protein to recruit chromatin modifying effectors featuring SETDB1, HP1 and the NuRD complex. Although many protein partners involved in silencing have been identified, the molecular basis of the protein interactions that mediate silencing remains largely unclear. In the present study, we identified the first Bbox domain (T28_B1 135-203) as a molecular interface responsible for the formation of higher-order oligomers of TRIM28. The structure of this domain reveals a new interface on the surface of the Bbox domain. Mutants disrupting the interface disrupt the formation of oligomers but have no observed effect on transcriptional silencing defining a single TRIM28 dimer as the functional unit for silencing. Using assembly-deficient mutants, we employed small-angle X-ray scattering and biophysical techniques to characterize binding to member of the Krab-ZFP family. This allows us to narrow and define the binding interface to the center of the coiled-coil region (residues 294-321) of TRIM28 and define mutants that abolish binding to the Krab-ZFP proteins.
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Zhang J, Zheng Z, Zheng J, Xie T, Tian Y, Li R, Wang B, Lin J, Xu A, Huang X, Yuan Y. Epigenetic-Mediated Downregulation of Zinc Finger Protein 671 ( ZNF671) Predicts Poor Prognosis in Multiple Solid Tumors. Front Oncol 2019; 9:342. [PMID: 31134149 PMCID: PMC6514233 DOI: 10.3389/fonc.2019.00342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/15/2019] [Indexed: 01/21/2023] Open
Abstract
Zinc finger protein 671 (ZNF671) is a member of the largest transcription factor family in the human genome. However, the methylation status, expression, and prognostic role of ZNF671 in solid tumors remain unclear. The aim of this study was to explore the relationship between ZNF671 and the prognosis of patients with solid tumors. We performed a pan-cancer analysis of the methylation status and mRNA and protein expression of ZNF671 using The Cancer Genome Atlas (TCGA) database and the Human Protein Atlas. We further evaluated the prognostic value of ZNF671 expression among numerous cancer types using the "Kaplan-Meier plotter" (KM plotter) database. We found that downregulation of ZNF671 is associated with hypermethylation of its promoter. Survival analysis established that the downregulation of ZNF671 predicts poor prognosis in breast invasive carcinoma (BRCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), head and neck squamous cell carcinoma (HNSC), kidney renal papillary cell carcinoma (KIRP), lung adenocarcinoma (LUAD), pancreatic adenocarcinoma (PAAD), and uterine corpus endometrial carcinoma (UCEC) solid tumors. CCK-8 and Transwell functional assays showed that ZNF671 could inhibit tumor cell proliferation, migration, and invasion. These results indicate that ZNF671 is an excellent predictive factor for BRCA, CESC, HNSC, KIRP, LUAD, PAAD, SARC, and UCEC solid tumors and may play crucial roles in the development and progression of these tumors.
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Affiliation(s)
- Jian Zhang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Ziqi Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jieling Zheng
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tao Xie
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Yunhong Tian
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Rong Li
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Baiyao Wang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jie Lin
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Anan Xu
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xiaoting Huang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Yawei Yuan
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
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Cukrov D, Newman TAC, Leask M, Leeke B, Sarogni P, Patimo A, Kline AD, Krantz ID, Horsfield JA, Musio A. Antioxidant treatment ameliorates phenotypic features of SMC1A-mutated Cornelia de Lange syndrome in vitro and in vivo. Hum Mol Genet 2019; 27:3002-3011. [PMID: 29860495 DOI: 10.1093/hmg/ddy203] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/17/2018] [Indexed: 12/30/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a rare disease characterized by cognitive impairment, multisystemic alterations and premature aging. Furthermore, CdLS cells display gene expression dysregulation and genomic instability. Here, we demonstrated that treatment with antioxidant drugs, such as ascorbic acid and riboceine, reduced the level of genomic instability and extended the in vitro lifespan of CdLS cell lines. We also found that antioxidant treatment partially rescued the phenotype of a zebrafish model of CdLS. Gene expression profiling showed that antioxidant drugs caused dysregulation of gene transcription; notably, a number of genes coding for the zinc finger (ZNF)-containing Krueppel-associated box (KRAB) protein domain (KRAB-ZNF) were found to be downregulated. Taken together, these data suggest that antioxidant drugs have the potential to ameliorate the developmental phenotype of CdLS.
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Affiliation(s)
- Dubravka Cukrov
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
| | - Trent A C Newman
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Megan Leask
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Bryony Leeke
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Patrizia Sarogni
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
| | - Alessandra Patimo
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
| | - Antonie D Kline
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, MD, USA
| | - Ian D Krantz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- The Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag, Auckland, New Zealand
| | - Antonio Musio
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
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34
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Fernandez-Marrero Y, Bachmann D, Lauber E, Kaufmann T. Negative Regulation of BOK Expression by Recruitment of TRIM28 to Regulatory Elements in Its 3' Untranslated Region. iScience 2018; 9:461-474. [PMID: 30471638 PMCID: PMC6260365 DOI: 10.1016/j.isci.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/23/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023] Open
Abstract
BCL-2-related ovarian killer (BOK) is a pro-apoptotic BAX-like member of the BCL-2 family with suggested tumor suppressor activity. The molecular mechanisms regulating BOK expression are poorly understood and fail to explain a frequent lack of concordance between protein and transcript levels. Here, we describe a potent post-transcriptional mechanism that negatively regulates BOK expression mediated by conserved (AU/U)-rich elements within its 3’ UTR. Using proteomics approaches we identified TRIM28 as a key component associating with U-rich elements in the human BOK 3’ UTR, resulting in a dramatic reduction of BOK expression. TRIM28 is overexpressed in several cancers, correlating with poor patient outcome, whereas the BOK locus is frequently deleted or its expression downregulated in human cancers. Data mining indicated that, for certain cancers, high TRIM28 and low BOK expression are significantly correlated in the stratum of patients with the worst survival, suggesting that this mechanism might be of potential therapeutic value. BOK mRNA is destabilized by AU-(mouse) or U-rich (human) elements within its 3’ UTR Mutation of these ARE/URE sequences results in increased BOK RNA and protein levels TRIM28 represses BOK expression by associating with the UREs of human BOK mRNA Inverse correlation of TRIM28 and BOK levels predicts survival in selected cancers
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Affiliation(s)
- Yuniel Fernandez-Marrero
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland
| | - Daniel Bachmann
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland
| | - Emanuel Lauber
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland
| | - Thomas Kaufmann
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland.
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35
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Song X, Guo C, Zheng Y, Wang Y, Jin Z, Yin Y. Post-transcriptional regulation of cancer/testis antigen MAGEC2 expression by TRIM28 in tumor cells. BMC Cancer 2018; 18:971. [PMID: 30309319 PMCID: PMC6182782 DOI: 10.1186/s12885-018-4844-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 09/21/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cancer/testis antigen MAGEC2 (also known as HCA587) is highly expressed in a wide variety of tumors and plays an active role in promoting growth and metastasis of tumor cells. However, little is known for the regulation of MAGEC2 expression in cancer cells. METHODS Western blotting and quantitative RT-PCR were performed to analyze MAGEC2 expression. Co-immunoprecipitation assay was applied for detecting the endogenous interaction of MAGEC2 and TRIM28 in tumor cells. Overexpression and knockdown assays were used to examine the effects of TRIM28 on the expression of MAGEC2 protein. Immunohistochemistry (IHC) staining was performed in hepatocellular carcinoma patients to evaluate the association between the expression of MAGEC2 and TRIM28. Proteasome inhibitors MG132 or PS-341 and lysosome inhibitor Chloroquine (CQ) were used to inhibit proteasomal or lysosomal-mediated protein degradation respectively. RESULTS We demonstrate that MAGEC2 interacts with TRIM28 in melanoma cells and MAGEC2 expression in tumor cells depends on the expression of TRIM28. The expression level of MAGEC2 protein was significantly reduced when TRIM28 was depleted in tumor cells, and no changes were observed in MAGEC2 mRNA level. Furthermore, expression levels of MAGEC2 and TRIM28 are positively correlated in MAGEC2-positive human hepatocellular carcinoma tissues (p = 0.0011). Mechanistic studies indicate that the regulatory role of TRIM28 on MAGEC2 protein expression in tumor cells depends on proteasome-mediated pathway. CONCLUSIONS Our findings show that TRIM28 is necessary for MAGEC2 expression in cancer cells, and TRIM28 may serve as a new potential target for immunotherapy of cancer.
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Affiliation(s)
- Xiao Song
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Health, Peking University, Beijing, 100191, China
| | - Chengli Guo
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Health, Peking University, Beijing, 100191, China
| | - Yutian Zheng
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Health, Peking University, Beijing, 100191, China
| | - Ying Wang
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Health, Peking University, Beijing, 100191, China
| | - Zhongtian Jin
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, 100044, China.
| | - Yanhui Yin
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Health, Peking University, Beijing, 100191, China.
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36
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Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D, Kuo CC, Guo X, Sharma S, Tung A, Cecchi RJ, Tuttle M, Pradhan S, Lim ET, Davidsohn N, Ebrahimkhani MR, Collins JJ, Lewis NE, Kiani S, Church GM. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods 2018; 15:611-616. [PMID: 30013045 PMCID: PMC6129399 DOI: 10.1038/s41592-018-0048-5] [Citation(s) in RCA: 279] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/03/2018] [Indexed: 01/12/2023]
Abstract
The RNA-guided endonuclease Cas9 can be converted into a programmable transcriptional repressor, but inefficiencies in target-gene silencing have limited its utility. Here we describe an improved Cas9 repressor based on the C-terminal fusion of a rationally designed bipartite repressor domain, KRAB-MeCP2, to nuclease-dead Cas9. We demonstrate the system's superiority in silencing coding and noncoding genes, simultaneously repressing a series of target genes, improving the results of single and dual guide RNA library screens, and enabling new architectures of synthetic genetic circuits.
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Affiliation(s)
- Nan Cher Yeo
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
| | - Alissa Lance-Byrne
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Yingleong Chan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - David Menn
- School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA
| | - Denitsa Milanova
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chih-Chung Kuo
- Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, San Diego, CA, USA
| | - Xiaoge Guo
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sumana Sharma
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Angela Tung
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Ryan J Cecchi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Marcelle Tuttle
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Swechchha Pradhan
- School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA
| | - Elaine T Lim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Noah Davidsohn
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mo R Ebrahimkhani
- School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA
- Division of Gastroenterology and Hematology, Mayo Clinic College of Medicine and Science, Phoenix, AZ, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Samira Kiani
- School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA.
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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37
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Wu GJ, Pen J, Huang Y, An S, Liu Y, Yang Y, Hao Q, Guo XX, Xu TR. KAP1 inhibits the Raf-MEK-ERK pathway to promote tumorigenesis in A549 lung cancer cells. Mol Carcinog 2018; 57:1396-1407. [PMID: 29917268 DOI: 10.1002/mc.22853] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 06/02/2018] [Accepted: 06/12/2018] [Indexed: 12/12/2022]
Abstract
Aberrant activation of the Raf-MEK-ERK pathway has frequently been associated with various cancers, especially lung cancer. However, the key regulators of this pathway are largely unknown. Using functional proteomics screening, we found that KAP1 interacts with c-Raf. Knocking out KAP1 decreased c-Raf phosphorylation at serine 259 and increased its phosphorylation at serine 338, which activated MEK and ERK. We detected higher KAP1 expression in lung cancer tissues than in normal peri-tumoral tissues. KAP1 knockdown arrested A549 lung cancer cells in the G0/G1 phase of the cell cycle and attenuated cell growth, metastasis, the epithelial-mesenchymal transition, angiogenesis, stemness, and colony formation. Furthermore, knocking out KAP1 remarkably increased the susceptibility of A549 cells to the anti-cancer drug 5-Fluorouracil, which correlated with increasing ERK phosphorylation. In vivo xenograft experiments suggested that KAP1 deficiency significantly decreases the tumorigenicity of A549 cells. Taken together, our findings indicate that KAP1 acts as a key module in the c-Raf-interactome complex and regulates lung cancer development through the Raf-MEK-ERK pathway. Therefore, KAP1 may represent a potential diagnosis biomarker and new treatment target for lung cancer.
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Affiliation(s)
- Guo-Jin Wu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jun Pen
- The First People's Hospital of Yunnan, Kunming, Yunnan, China
| | - Ying Huang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Su An
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ying Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Qian Hao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xiao-Xi Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Tian-Rui Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
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38
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Borlepawar A, Frey N, Rangrez AY. A systematic view on E3 ligase Ring TRIMmers with a focus on cardiac function and disease. Trends Cardiovasc Med 2018; 29:1-8. [PMID: 29880235 DOI: 10.1016/j.tcm.2018.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/05/2018] [Accepted: 05/22/2018] [Indexed: 01/01/2023]
Abstract
Ubiquitination, a post-translational modification via ubiquitin-proteasome-system, is one of the vital cellular processes involved in intracellular signaling, cell death, transcriptional control, etc. Importantly, it prevents the aggregation of non-functional, misfolded or unfolded, potentially toxic proteins to maintain cellular protein homeostasis. Ubiquitination is accomplished by the concerted action of three enzymatic steps involving E1 activating enzymes, E2 conjugating enzymes, and E3 ligases. Tripartite motif-containing (TRIM) proteins are one of the integral members of E3 ubiquitin ligases in metazoans modulating essential cellular pathways. For long, MuRFs (Muscle ring finger proteins) were the most extensively studied TRIMs for their cardiac function. Recent research advances in the field and our analysis presented here, however, demonstrated broader and ever increasing involvement of additional TRIM E3 ligases in the pathophysiology of heart. In this review, we summarize the known cardiac E3 ligases and their targets, and discuss their role and importance in cardiac proteostasis, pathophysiology and potential therapeutic implications with specific focus on TRIM E3 ligases.
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Affiliation(s)
- Ankush Borlepawar
- Department of Internal Medicine III, University of Kiel, Arnold-Heller-Str. 3, 24105, Kiel, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Germany
| | - Norbert Frey
- Department of Internal Medicine III, University of Kiel, Arnold-Heller-Str. 3, 24105, Kiel, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Germany
| | - Ashraf Yusuf Rangrez
- Department of Internal Medicine III, University of Kiel, Arnold-Heller-Str. 3, 24105, Kiel, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Germany.
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39
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology , San Francisco, California 94158, United States.,University of California, San Francisco , Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J Conrad
- Gladstone Institute of Virology and Immunology , San Francisco, California 94158, United States.,University of California, San Francisco , Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging , Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology , San Francisco, California 94158, United States.,University of California, San Francisco , Department of Medicine, San Francisco, California 94158, United States
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40
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Czerwińska P, Mazurek S, Wiznerowicz M. The complexity of TRIM28 contribution to cancer. J Biomed Sci 2017; 24:63. [PMID: 28851455 PMCID: PMC5574234 DOI: 10.1186/s12929-017-0374-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/24/2017] [Indexed: 01/07/2023] Open
Abstract
Since the first discovery in 1996, the engagement of TRIM28 in distinct aspects of cellular biology has been extensively studied resulting in identification of a complex nature of TRIM28 protein. In this review, we summarize core biological functions of TRIM28 that emerge from TRIM28 multi-domain structure and possessed enzymatic activities. Moreover, we will discuss whether the complexity of TRIM28 engagement in cancer biology makes TRIM28 a possible candidate for targeted anti-cancer therapy. Briefly, we will demonstrate the role of TRIM28 in regulation of target gene transcription, response to DNA damage, downregulation of p53 activity, stimulation of epithelial-to-mesenchymal transition, stemness sustainability, induction of autophagy and regulation of retrotransposition, to provide the answer whether TRIM28 functions as a stimulator or inhibitor of tumorigenesis. To date, number of studies demonstrate significant upregulation of TRIM28 expression in cancer tissues which correlates with worse overall patient survival, suggesting that TRIM28 supports cancer progression. Here, we present distinct aspects of TRIM28 involvement in regulation of cancer cell homeostasis which collectively imply pro-tumorigenic character of TRIM28. Thorough analyses are further needed to verify whether TRIM28 possess the potential to become a new anti-cancer target.
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Affiliation(s)
- Patrycja Czerwińska
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866, Poznan, Poland. .,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.
| | - Sylwia Mazurek
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Wiznerowicz
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
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41
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Yan FJ, Fan J, Huang Z, Zhang JJ. ZNF300 tight self-regulation and functioning through DNA methylation and histone acetylation. Cell Biosci 2017; 7:33. [PMID: 28670441 PMCID: PMC5490171 DOI: 10.1186/s13578-017-0160-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/20/2017] [Indexed: 11/26/2022] Open
Abstract
Background Accumulating evidence demonstrates that the KRAB-ZNFs involve in various biological processes. As a typical member of KRAB-ZNFs, dysregulation of ZNF300 contributes to multiple pathologies such as leukemia and cancer. However, mechanisms underlying ZNF300 tight regulation and its pathophysiological function remain largely unknown. Methods The effect of ZNF300ZFR on gene transcriptional activity was measured by Dual luciferase reporter system. ChIP-PCR assay were performed to detect the enrichment of ZNF300 protein and H3K9Ac in the ZNF300 gene. Co-immunoprecipitation assays followed by western blot were performed to detect the interaction between ZNF300 and KAP1. The DNA methylation in the ZNF300 gene promoter was analyzed by BSP. ZNF300 function on K562 cell differentiation was analyzed by flow cytometry. Results In this study, we found that the zinc finger domain-encoding region (ZFR) of ZNF300 functioned as a repressor possibly by mediating DNA methylation and ZNF300 bound to its ZNF300ZFR, suggesting a potential auto-inhibition mechanism. To support this, DNA methylation inhibition upregulated ZNF300 expression and ZNF300 overexpression inhibited endogenous ZNF300 expression. More importantly, DNA methylation inhibition restored megakaryocyte differentiation in K562 cells suppressed by ZNF300 downregulation, suggesting an important role of DNA methylation in ZNF300 function. Interestingly, ZNF300 knockdown restored global H3K9Ac that was reduced in K562 cells undergoing megakaryocyte differentiation. Conclusions Our study revealed novel features of ZNF300 that possibly mediate its regulation and function by modulating epigenetic modifications.
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Affiliation(s)
- Feng-Juan Yan
- College of Life Science, Wuhan University, Wuhan, 430072 Hubei People's Republic of China
| | - Jingyi Fan
- Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, 430072 Hubei People's Republic of China
| | - Zan Huang
- College of Life Science, Wuhan University, Wuhan, 430072 Hubei People's Republic of China
| | - Jun-Jian Zhang
- Department of Neurology, Zhongnan Hospital of Wuhan University, Wuhan, 430072 Hubei People's Republic of China
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42
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Imai Y, Baudat F, Taillepierre M, Stanzione M, Toth A, de Massy B. The PRDM9 KRAB domain is required for meiosis and involved in protein interactions. Chromosoma 2017; 126:681-695. [PMID: 28527011 PMCID: PMC5688218 DOI: 10.1007/s00412-017-0631-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 12/31/2022]
Abstract
PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. This role involves its DNA-binding domain, which is composed of a tandem array of zinc fingers, and PRDM9-dependent trimethylation of histone H3 at lysine 4. PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain. Here, we show that truncation of the KRAB domain of mouse PRDM9 leads to loss of PRDM9 function and altered meiotic prophase and gametogenesis. In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. We also show that CXXC1 interacts with IHO1, an essential component of the meiotic double-strand break (DSB) machinery. As CXXC1 is orthologous to Saccharomyces cerevisiae Spp1 that links DSB sites to the DSB machinery on the chromosome axis, we propose that these molecular interactions involved in the regulation of meiotic DSB formation are conserved in mouse meiosis.
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Affiliation(s)
- Yukiko Imai
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 141 rue de la cardonille, 34396, Montpellier cedex 05, France
| | - Frédéric Baudat
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 141 rue de la cardonille, 34396, Montpellier cedex 05, France
| | | | - Marcello Stanzione
- Faculty of Medicine at the TU Dresden, Institute of Physiological Chemistry, Fetscherstraße 74, 01307, Dresden, Germany
| | - Attila Toth
- Faculty of Medicine at the TU Dresden, Institute of Physiological Chemistry, Fetscherstraße 74, 01307, Dresden, Germany
| | - Bernard de Massy
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 141 rue de la cardonille, 34396, Montpellier cedex 05, France.
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43
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Discovery of a novel oocyte-specific Krüppel-associated box domain-containing zinc finger protein required for early embryogenesis in cattle. Mech Dev 2017; 144:103-112. [PMID: 28263788 DOI: 10.1016/j.mod.2017.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/09/2017] [Accepted: 02/20/2017] [Indexed: 12/17/2022]
Abstract
Zinc finger (ZNF) transcription factors interact with DNA through zinc finger motifs and play important roles in a variety of cellular functions including cell growth, proliferation, development, apoptosis, and intracellular signal transduction. One-third of ZNF proteins in metazoans contain a highly conserved N-terminal motif known as the Krüppel-associated box (KRAB) domain, which acts as a potent, DNA-binding dependent transcriptional repression module. Analysis of RNA-Seq data generated from a bovine oocyte cDNA library identified a novel transcript, which encodes a KRAB-containing ZNF transcription factor (named ZNFO). Characterization of ZNFO mRNA expression revealed that it is exclusively expressed in bovine oocytes and early embryos. A GFP reporter assay demonstrated that ZNFO protein localizes specifically to the nucleus, supporting its role in transcriptional regulation. To test the role of ZNFO in early embryonic development, zygotes were generated by in vitro maturation and fertilization of oocytes, and injected with small interfering RNA (siRNA) designed to knockdown ZNFO. Cleavage rates were not affected by ZNFO siRNA injection. However, embryonic development to 8- to 16-cell stage and blastocyst stage was significantly reduced relative to the uninjected and negative control siRNA-injected embryos. Further, interaction of ZNFO with the highly conserved co-factor, KRAB-associated protein-1 (KAP1), was demonstrated, and evidence supporting transcriptional repression by ZNFO was demonstrated using a GAL4-luciferase reporter system. Results of described studies demonstrate that ZNFO is a maternally-derived oocyte-specific nuclear factor required for early embryonic development in cattle, presumably functioning by repressing transcription.
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Huang T, Ji Y, Hu D, Chen B, Zhang H, Li C, Chen G, Luo X, Zheng XW, Lin X. SNHG8 is identified as a key regulator of epstein-barr virus(EBV)-associated gastric cancer by an integrative analysis of lncRNA and mRNA expression. Oncotarget 2016; 7:80990-81002. [PMID: 27835598 PMCID: PMC5348371 DOI: 10.18632/oncotarget.13167] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 10/31/2016] [Indexed: 12/26/2022] Open
Abstract
The Epstein-Barr virus (EBV) is associated with a variety of cancers, including gastric cancer, which has one of the highest mortality rates of all human cancers. Long non-coding RNAs (lncRNAs) have been suggested to have important causal roles in gastric cancer. However, the interaction between lncRNAs and EBV has not yet been studied. To this end, we sequenced 11,311 lncRNAs and 144,826 protein-coding transcripts from four types of tissue: one non-EBV-infected gastric carcinoma (EBVnGC) and its adjacent normal tissue, and one EBV-associated gastric carcinoma (EBVaGC) and its adjacent normal tissue. Five lncRNAs showed EBVaGC-specific expression; of those, one (SNHG8) was validated using real-time PCR in an independent cohort with 88 paired gastric cancer and adjacent tissue samples. To explore the functions of SNHG8, we identified its mRNA targets on the lncRNA-mRNA co-expression network of the Illumina Body Map, which contains the RNA sequencing data of mRNAs and lncRNAs from 16 normal human tissues. SNHG8 lncRNA was found to affect several gastric cancer-specific pathways and target genes of EBV. Our results reveal the intertwined tumorigenesis mechanisms of lncRNA and EBV and identify SNHG8 as a highly possible candidate biomarker and drug target of gastric cancer.
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Affiliation(s)
- Tao Huang
- Department of Pathology, Fujian Provincial Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Ji
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dan Hu
- Department of Pathology, Fujian Provincial Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Baozheng Chen
- Department of Pathology, Fujian Provincial Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Hejun Zhang
- Department of Pathology, Fujian Provincial Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Chao Li
- Department of Pathology, Fujian Provincial Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Gang Chen
- Department of Pathology, Fujian Provincial Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Xiong-wei Zheng
- Department of Pathology, Fujian Provincial Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, China
| | - Xiandong Lin
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, China
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Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals. J Biosci 2016; 41:759-786. [DOI: 10.1007/s12038-016-9650-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Murphy KE, Shylo NA, Alexander KA, Churchill AJ, Copperman C, García-García MJ. The Transcriptional Repressive Activity of KRAB Zinc Finger Proteins Does Not Correlate with Their Ability to Recruit TRIM28. PLoS One 2016; 11:e0163555. [PMID: 27658112 PMCID: PMC5033580 DOI: 10.1371/journal.pone.0163555] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/23/2016] [Indexed: 12/27/2022] Open
Abstract
KRAB domain Zinc finger proteins are one of the most abundant families of transcriptional regulators in higher vertebrates. The prevailing view is that KRAB domain proteins function as potent transcriptional repressors by recruiting TRIM28 and promoting heterochromatin spreading. However, the extent to which all KRAB domain proteins are TRIM28-dependent transcriptional repressors is currently unclear. Our studies on mouse ZFP568 revealed that TRIM28 recruitment by KRAB domain proteins is not sufficient to warrant transcriptional repressive activity. By using luciferase reporter assays and yeast two-hybrid experiments, we tested the ability of ZFP568 and other mouse KRAB domain proteins to repress transcription and bind TRIM28. We found that some mouse KRAB domain proteins are poor transcriptional repressors despite their ability to recruit TRIM28, while others showed strong KRAB-dependent transcriptional repression, but no TRIM28 binding. Together, our results show that the transcriptional repressive activity of KRAB-ZNF proteins does not correlate with their ability to recruit TRIM28, and provide evidence that KRAB domains can regulate transcription in a TRIM28-independent fashion. Our findings challenge the current understanding of the molecular mechanisms used by KRAB domain proteins to control gene expression and highlight that a high percentage of KRAB domain proteins in the mouse genome differ from the consensus KRAB sequence at amino acid residues that are critical for TRIM28 binding and/or repressive activity.
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Affiliation(s)
- Kristin E. Murphy
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Natalia A. Shylo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Katherine A. Alexander
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Angela J. Churchill
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Cecilia Copperman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - María J. García-García
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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Yeh CM, Chen PC, Hsieh HY, Jou YC, Lin CT, Tsai MH, Huang WY, Wang YT, Lin RI, Chen SS, Tung CL, Wu SF, Chang DC, Shen CH, Hsu CD, Chan MWY. Methylomics analysis identifies ZNF671 as an epigenetically repressed novel tumor suppressor and a potential non-invasive biomarker for the detection of urothelial carcinoma. Oncotarget 2016; 6:29555-72. [PMID: 26320192 PMCID: PMC4745746 DOI: 10.18632/oncotarget.4986] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/16/2015] [Indexed: 11/25/2022] Open
Abstract
The molecular mechanism underlying the lethal phenomenon of urothelial carcinoma (UC) tumor recurrence remains unresolved. Here, by methylation microarray, we identified promoter methylation of the zinc-finger protein gene, ZNF671 in bladder UC tumor tissue samples, a finding that was independently validated by bisulphite pyrosequencing in cell lines and tissue samples. Subsequent assays including treatment with epigenetic depressive agents and in vitro methylation showed ZNF671 methylation to result in its transcriptional repression. ZNF671 re-expression in UC cell lines, via ectopic expression, inhibited tumor growth and invasion, in possible conjunction with downregulation of cancer stem cell markers (c-KIT, NANOG, OCT4). Clinically, high ZNF671 methylation in UC tumor tissues (n=96; 63 bladder, 33 upper urinary tract) associated with tumor grade and poor locoregional disease-free survival. Quantitative MSP analysis in a training (n=97) and test (n=61) sets of voided urine samples from bladder UC patients revealed a sensitivity and specificity of 42%-48% and 89%-92.8%, respectively, for UC cancer detection. Moreover, combining DNA methylation of ZNF671 and 2 other genes (IRF8 and sFRP1) further increased the sensitivity to 96.2%, suggesting a possible three-gene UC biomarker. In summary, ZNF671, an epigenetically silenced novel tumor suppressor, represents a potential predictor for UC relapse and non-invasive biomarker that could assist in UC clinical decision-making.
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Affiliation(s)
- Chia-Ming Yeh
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Pi-Che Chen
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Hsiao-Yen Hsieh
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Yeong-Chin Jou
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Chang-Te Lin
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ming-Hsuan Tsai
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Wen-Yu Huang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Yi-Ting Wang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Ru-Inn Lin
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Departments of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Chia Yi, Taiwan
| | - Szu-Shan Chen
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Chun-Liang Tung
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Shu-Fen Wu
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - D Ching Chang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Cheng-Huang Shen
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Cheng-Da Hsu
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Michael W Y Chan
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
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Nishida T, Yamada Y. SUMOylation of the KRAB zinc-finger transcription factor PARIS/ZNF746 regulates its transcriptional activity. Biochem Biophys Res Commun 2016; 473:1261-1267. [PMID: 27086851 DOI: 10.1016/j.bbrc.2016.04.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 04/11/2016] [Indexed: 01/13/2023]
Abstract
Parkin-interacting substrate (PARIS), a member of the family of Krüppel-associated box (KRAB)-containing zinc-finger transcription factors, is a substrate of the ubiquitin E3 ligase parkin. PARIS represses the expression of peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α), although the underlying mechanisms remain largely unknown. In the present study, we demonstrate that PARIS can be SUMOylated, and its SUMOylation plays a role in the repression of PGC-1a promoter activity. Protein inhibitor of activated STAT y (PIASy) was identified as an interacting protein of PARIS and shown to enhance its SUMOylation. PIASy repressed PGC-1a promoter activity, and this effect was attenuated by PARIS in a manner dependent on its SUMOylation status. Co-expression of SUMO-1 with PIASy completely repressed PGC-1a promoter activity independently of PARIS expression. PARIS-mediated PGC-1a promoter repression depended on the activity of histone deacetylases (HDAC), whereas PIASy repressed the PGC-1a promoter in an HDAC-independent manner. Taken together, these results suggest that PARIS and PIASy modulate PGC-1a gene transcription through distinct molecular mechanisms.
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Affiliation(s)
- Tamotsu Nishida
- Department of Human Functional Genomics, Life Science Research Center, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan.
| | - Yoshiji Yamada
- Department of Human Functional Genomics, Life Science Research Center, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
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50
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Marote A, Barroca N, Vitorino R, M. Silva R, H.V. Fernandes M, M. Vilarinho P, A.B. da Cruz e Silva O, I. Vieira S. A proteomic analysis of the interactions between poly(L-lactic acid) nanofibers and SH-SY5Y neuronal-like cells. AIMS MOLECULAR SCIENCE 2016. [DOI: 10.3934/molsci.2016.4.661] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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