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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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Ning T, Zhao M, Zhang N, Wang Z, Zhang S, Liu M, Zhu S. TRIM28 suppresses cancer stem-like characteristics in gastric cancer cells through Wnt/β-catenin signaling pathways. Exp Biol Med (Maywood) 2023; 248:2210-2218. [PMID: 38058023 PMCID: PMC10903244 DOI: 10.1177/15353702231211970] [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: 04/27/2023] [Accepted: 08/23/2023] [Indexed: 12/08/2023] Open
Abstract
The influences of TRIM28 on the gastric tumorigenesis together with potential molecular mechanisms remain to be studied. We aimed at exploring the important effects of TRIM28 on gastric cancer (GC) and uncovering underling molecular mechanisms. Through immunohistochemistry analysis of 20 pairs of GC and the peritumoral tissues, the expression level of TRIM28 was determined. A variety of assays were applied to explore the important roles of TRIM28 in GC. Western blotting and qRT-PCR analyses were used to analyze the association between TRIM28 and the Wnt/β-catenin signaling pathway. TRIM28 was highly expressed in GC tissues than peritumoral tissues. And high expression level of TRIM28 in GC was associated with good prognostic effects. In vitro functional assays suggested TRIM28 knockdown enhanced the proliferation and clone formation of GC cell. Moreover, TRIM28 knockdown enhanced the expression level of stemness markers, strengthened sphere-forming and drug-resistance properties of GC cells, suggesting important effect on GC cell stemness. Besides, our analysis showed that the Wnt/β-catenin signaling was involved in the effect of TRIM28 on GC cell stemness property, and blocking Wnt/β-catenin signaling pathway obviously rescued the promotion influence of TRIM28 knockdown. Overall, TRIM28 has an important influence on regulating the stem-like property of GC cell via Wnt/β-catenin signaling, suggesting TRIM28 a promising drug target and a potential predictor of prognosis.
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Affiliation(s)
- Tingting Ning
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, China
| | - Mengran Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, China
| | - Nan Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, China
| | - Zhaoqing Wang
- Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Shutian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, China
| | - Mo Liu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, China
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Godneeva B, Ninova M, Fejes-Toth K, Aravin A. SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes. eLife 2023; 12:RP89493. [PMID: 37999956 PMCID: PMC10672805 DOI: 10.7554/elife.89493] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. Unlike mammals that have four TIF1 members, Drosophila only encodes one member of the family, Bonus. Bonus has been implicated in embryonic development and organogenesis and shown to regulate several signaling pathways, however, its targets and mechanism of action remained poorly understood. We found that knockdown of Bonus in early oogenesis results in severe defects in ovarian development and in ectopic expression of genes that are normally repressed in the germline, demonstrating its essential function in the ovary. Recruitment of Bonus to chromatin leads to silencing associated with accumulation of the repressive H3K9me3 mark. We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. We further established that Bonus is SUMOylated at a single site at its N-terminus that is conserved among insects and this modification is indispensable for Bonus's repressive activity. SUMOylation influences Bonus's subnuclear localization, its association with chromatin and interaction with SetDB1. Finally, we showed that Bonus SUMOylation is mediated by the SUMO E3-ligase Su(var)2-10, revealing that although SUMOylation of TIF1 proteins is conserved between insects and mammals, both the mechanism and specific site of modification is different in the two taxa. Together, our work identified Bonus as a regulator of tissue-specific gene expression and revealed the importance of SUMOylation as a regulator of complex formation in the context of transcriptional repression.
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Affiliation(s)
- Baira Godneeva
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
- Institute of Gene Biology, Russian Academy of SciencesMoscowRussian Federation
| | - Maria Ninova
- University of California, RiversideRiversideUnited States
| | - Katalin Fejes-Toth
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - Alexei Aravin
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
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4
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Godneeva B, Ninova M, Fejes Tóth K, Aravin AA. SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.14.536936. [PMID: 37645991 PMCID: PMC10461926 DOI: 10.1101/2023.04.14.536936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. Unlike mammals that have four TIF1 members, Drosophila only encodes one member of the family, Bonus. Bonus has been implicated in embryonic development and organogenesis and shown to regulate several signaling pathways, however, its targets and mechanism of action remained poorly understood. We found that knockdown of Bonus in early oogenesis results in severe defects in ovarian development and in ectopic expression of genes that are normally repressed in the germline, demonstrating its essential function in the ovary. Recruitment of Bonus to chromatin leads to silencing associated with accumulation of the repressive H3K9me3 mark. We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. We further established that Bonus is SUMOylated at a single site at its N-terminus that is conserved among insects and this modification is indispensable for Bonus's repressive activity. SUMOylation influences Bonus's subnuclear localization, its association with chromatin and interaction with SetDB1. Finally, we showed that Bonus SUMOylation is mediated by the SUMO E3-ligase Su(var)2-10, revealing that although SUMOylation of TIF1 proteins is conserved between insects and mammals, both the mechanism and specific site of modification is different in the two taxa. Together, our work identified Bonus as a regulator of tissue-specific gene expression and revealed the importance of SUMOylation as a regulator of complex formation in the context of transcriptional repression.
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Affiliation(s)
- Baira Godneeva
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria Ninova
- University of California, Riverside, Riverside, CA 92521, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA
| | - Alexei A. Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA
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Ye Y, Lui VCH, Tam PKH. Pathogenesis of Choledochal Cyst: Insights from Genomics and Transcriptomics. Genes (Basel) 2022; 13:genes13061030. [PMID: 35741793 PMCID: PMC9223186 DOI: 10.3390/genes13061030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 12/10/2022] Open
Abstract
Choledochal cysts (CC) is characterized by extra- and/or intra-hepatic b\ile duct dilations. There are two main theories, “pancreaticobiliary maljunction” and “congenital stenosis of bile ducts” proposed for the pathogenesis of CC. Although family cases or CC associated with other anomalies have been reported, the molecular pathogenesis of CC is still poorly understood. Recent advances in transcriptomics and genomics analysis platforms have unveiled key expression signatures/genes/signaling pathways in the pathogenesis of human diseases including CC. This review summarizes insights from genomics and transcriptomics studies into the pathogenesis of CC, with the aim to improve (i) our understanding of its underlying complex pathomechanisms, and (ii) clinical management of different subtypes of CC, in particular their associated hepatic fibrotic change and their risk of malignancy transformation.
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Affiliation(s)
- Yongqin Ye
- Faculty of Medicine, Macau University of Science and Technology, Macau, China;
- Department of Surgery, School of Clinical Medicine, University of Hong Kong, Hong Kong, China;
| | - Vincent Chi Hang Lui
- Department of Surgery, School of Clinical Medicine, University of Hong Kong, Hong Kong, China;
| | - Paul Kwong Hang Tam
- Faculty of Medicine, Macau University of Science and Technology, Macau, China;
- Correspondence:
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Critical role for TRIM28 and HP1β/γ in the epigenetic control of T cell metabolic reprograming and effector differentiation. Proc Natl Acad Sci U S A 2019; 116:25839-25849. [PMID: 31776254 PMCID: PMC6925996 DOI: 10.1073/pnas.1901639116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
CD4 T cells are major regulators of immune responses against both self and pathogens. Understanding pathways that govern CD4 T cell differentiation and regulation are thus key for the discovery of new immunoregulatory drug targets. Here, we have identified an epigenetic pathway that regulates the expression of a set of proteins that determine T cell responsiveness. By silencing enhancers distal to a set of genes known to be involved in regulatory T cell function, the epigenetic modifiers TRIM28 and HP1β/γ regulate T cell receptor signaling. This leads to defective metabolic reprograming and inefficient effector differentiation of naive T cells. This mechanism provides an exciting opportunity to regulate T cell responsivity in both autoimmunity and T cell-based immunodeficiencies. Naive CD4+ T lymphocytes differentiate into different effector types, including helper and regulatory cells (Th and Treg, respectively). Heritable gene expression programs that define these effector types are established during differentiation, but little is known about the epigenetic mechanisms that install and maintain these programs. Here, we use mice defective for different components of heterochromatin-dependent gene silencing to investigate the epigenetic control of CD4+ T cell plasticity. We show that, upon T cell receptor (TCR) engagement, naive and regulatory T cells defective for TRIM28 (an epigenetic adaptor for histone binding modules) or for heterochromatin protein 1 β and γ isoforms (HP1β/γ, 2 histone-binding factors involved in gene silencing) fail to effectively signal through the PI3K–AKT–mTOR axis and switch to glycolysis. While differentiation of naive TRIM28−/− T cells into cytokine-producing effector T cells is impaired, resulting in reduced induction of autoimmune colitis, TRIM28−/− regulatory T cells also fail to expand in vivo and to suppress autoimmunity effectively. Using a combination of transcriptome and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses for H3K9me3, H3K9Ac, and RNA polymerase II, we show that reduced effector differentiation correlates with impaired transcriptional silencing at distal regulatory regions of a defined set of Treg-associated genes, including, for example, NRP1 or Snai3. We conclude that TRIM28 and HP1β/γ control metabolic reprograming through epigenetic silencing of a defined set of Treg-characteristic genes, thus allowing effective T cell expansion and differentiation into helper and regulatory phenotypes.
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DNA Damage Changes Distribution Pattern and Levels of HP1 Protein Isoforms in the Nucleolus and Increases Phosphorylation of HP1β-Ser88. Cells 2019; 8:cells8091097. [PMID: 31533340 PMCID: PMC6770535 DOI: 10.3390/cells8091097] [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: 06/30/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 12/28/2022] Open
Abstract
The family of heterochromatin protein 1 (HP1) isoforms is essential for chromatin packaging, regulation of gene expression, and repair of damaged DNA. Here we document that γ-radiation reduced the number of HP1α-positive foci, but not HP1β and HP1γ foci, located in the vicinity of the fibrillarin-positive region of the nucleolus. The additional analysis confirmed that γ-radiation has the ability to significantly decrease the level of HP1α in rDNA promoter and rDNA encoding 28S rRNA. By mass spectrometry, we showed that treatment by γ-rays enhanced the HP1β serine 88 phosphorylation (S88ph), but other analyzed modifications of HP1β, including S161ph/Y163ph, S171ph, and S174ph, were not changed in cells exposed to γ-rays or treated by the HDAC inhibitor (HDACi). Interestingly, a combination of HDACi and γ-radiation increased the level of HP1α and HP1γ. The level of HP1β remained identical before and after the HDACi/γ-rays treatment, but HDACi strengthened HP1β interaction with the KRAB-associated protein 1 (KAP1) protein. Conversely, HP1γ did not interact with KAP1, although approximately 40% of HP1γ foci co-localized with accumulated KAP1. Especially HP1γ foci at the periphery of nucleoli were mostly absent of KAP1. Together, DNA damage changed the morphology, levels, and interaction properties of HP1 isoforms. Also, γ-irradiation-induced hyperphosphorylation of the HP1β protein; thus, HP1β-S88ph could be considered as an important marker of DNA damage.
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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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D Urbano V, De Crignis E, Re MC. Host Restriction Factors and Human Immunodeficiency Virus (HIV-1): A Dynamic Interplay Involving All Phases of the Viral Life Cycle. Curr HIV Res 2019; 16:184-207. [PMID: 30117396 DOI: 10.2174/1570162x16666180817115830] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/31/2018] [Accepted: 08/09/2018] [Indexed: 02/08/2023]
Abstract
Mammalian cells have evolved several mechanisms to prevent or block lentiviral infection and spread. Among the innate immune mechanisms, the signaling cascade triggered by type I interferon (IFN) plays a pivotal role in limiting the burden of HIV-1. In the presence of IFN, human cells upregulate the expression of a number of genes, referred to as IFN-stimulated genes (ISGs), many of them acting as antiviral restriction factors (RFs). RFs are dominant proteins that target different essential steps of the viral cycle, thereby providing an early line of defense against the virus. The identification and characterization of RFs have provided unique insights into the molecular biology of HIV-1, further revealing the complex host-pathogen interplay that characterizes the infection. The presence of RFs drove viral evolution, forcing the virus to develop specific proteins to counteract their activity. The knowledge of the mechanisms that prevent viral infection and their viral counterparts may offer new insights to improve current antiviral strategies. This review provides an overview of the RFs targeting HIV-1 replication and the mechanisms that regulate their expression as well as their impact on viral replication and the clinical course of the disease.
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Affiliation(s)
- Vanessa D Urbano
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Elisa De Crignis
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Maria Carla Re
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
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10
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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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11
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Liu H, Wei Q, Huang C, Zhang Y, Guo Z. Potential Roles of Intrinsic Disorder in Maternal-Effect Proteins Involved in the Maintenance of DNA Methylation. Int J Mol Sci 2017; 18:E1898. [PMID: 28869544 PMCID: PMC5618547 DOI: 10.3390/ijms18091898] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/14/2023] Open
Abstract
DNA methylation is an important epigenetic modification that needs to be carefully controlled as a prerequisite for normal early embryogenesis. Compelling evidence now suggests that four maternal-effect proteins, primordial germ cell 7 (PGC7), zinc finger protein 57 (ZFP57), tripartite motif-containing 28 (TRIM28) and DNA methyltransferase (cytosine-5) 1 (DNMT1) are involved in the maintenance of DNA methylation. However, it is still not fully understood how these maternal-effect proteins maintain the DNA methylation imprint. We noticed that a feature common to these proteins is the presence of significant levels of intrinsic disorder so in this study we started from an intrinsic disorder perspective to try to understand these maternal-effect proteins. To do this, we firstly analysed the intrinsic disorder predispositions of PGC7, ZFP57, TRIM28 and DNMT1 by using a set of currently available computational tools and secondly conducted an intensive literature search to collect information on their interacting partners and structural characterization. Finally, we discuss the potential effect of intrinsic disorder on the function of these proteins in maintaining DNA methylation.
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Affiliation(s)
- Hongliang Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Qing Wei
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China.
| | - Chenyang Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
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12
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Wong JKL, Campbell D, Ngo ND, Yeung F, Cheng G, Tang CSM, Chung PHY, Tran NS, So MT, Cherny SS, Sham PC, Tam PK, Garcia-Barcelo MM. Genetic study of congenital bile-duct dilatation identifies de novo and inherited variants in functionally related genes. BMC Med Genomics 2016; 9:75. [PMID: 27955658 PMCID: PMC5154011 DOI: 10.1186/s12920-016-0236-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/07/2016] [Indexed: 12/18/2022] Open
Abstract
Background Congenital dilatation of the bile-duct (CDD) is a rare, mostly sporadic, disorder that results in bile retention with severe associated complications. CDD affects mainly Asians. To our knowledge, no genetic study has ever been conducted. Methods We aim to identify genetic risk factors by a “trio-based” exome-sequencing approach, whereby 31 CDD probands and their unaffected parents were exome-sequenced. Seven-hundred controls from the local population were used to detect gene-sets significantly enriched with rare variants in CDD patients. Results Twenty-one predicted damaging de novo variants (DNVs; 4 protein truncating and 17 missense) were identified in several evolutionarily constrained genes (p < 0.01). Six genes carrying DNVs were associated with human developmental disorders involving epithelial, connective or bone morphologies (PXDN, RTEL1, ANKRD11, MAP2K1, CYLD, ACAN) and four linked with cholangio- and hepatocellular carcinomas (PIK3CA, TLN1 CYLD, MAP2K1). Importantly, CDD patients have an excess of DNVs in cancer-related genes (p < 0.025). Thirteen genes were recurrently mutated at different sites, forming compound heterozygotes or functionally related complexes within patients. Conclusions Our data supports a strong genetic basis for CDD and show that CDD is not only genetically heterogeneous but also non-monogenic, requiring mutations in more than one genes for the disease to develop. The data is consistent with the rarity and sporadic presentation of CDD. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0236-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John K L Wong
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China
| | - Desmond Campbell
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China
| | | | - Fanny Yeung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Guo Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Clara S M Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Patrick H Y Chung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Stacey S Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China.,Center for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Pak C Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China.,Center for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Paul K Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Maria-Mercè Garcia-Barcelo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China. .,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
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13
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Ali SO, Khan FA, Galindo-Campos MA, Yélamos J. Understanding specific functions of PARP-2: new lessons for cancer therapy. Am J Cancer Res 2016; 6:1842-1863. [PMID: 27725894 PMCID: PMC5043098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a widespread and highly conserved post-translational modification catalysed by a large family of enzymes called poly(ADP-ribose) polymerases (PARPs). PARylation plays an essential role in various cardinal processes of cellular physiology and recent approvals and breakthrough therapy designations for PARP inhibitors in cancer therapy have sparked great interest in pharmacological targeting of PARP proteins. Although, many PARP inhibitors have been developed, existing compounds display promiscuous inhibition across the PARP superfamily which could lead to unwanted off-target effects. Thus the prospect of isoform-selective inhibition is being increasingly explored and research is now focusing on understanding specific roles of PARP family members. PARP-2, alongside PARP-1 and PARP-3 are the only known DNA damage-dependent PARPs and play critical roles in the DNA damage response, DNA metabolism and chromatin architecture. However, growing evidence shows that PARP-2 plays specific and diverse regulatory roles in cellular physiology, ranging from genomic stability and epigenetics to proliferative signalling and inflammation. The emerging network of PARP-2 target proteins has uncovered wide-ranging functions of the molecule in many cellular processes commonly dysregulated in carcinogenesis. Here, we review novel PARP-2-specific functions in the hallmarks of cancer and consider the implications for the development of isoform-selective inhibitors in chemotherapy. By considering the roles of PARP-2 through the lens of tumorigenesis, we propose PARP-2-selective inhibition as a potentially multipronged attack on cancer physiology.
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Affiliation(s)
- Syed O Ali
- School of Clinical Medicine, University of CambridgeCambridge, UK
| | - Farhaan A Khan
- School of Clinical Medicine, University of CambridgeCambridge, UK
| | - Miguel A Galindo-Campos
- Department of Immunology, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM)Barcelona, Spain
| | - José Yélamos
- Department of Immunology, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM)Barcelona, Spain
- CIBERehdSpain
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14
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Maeng YS, Kwon JY, Kim EK, Kwon YG. Heterochromatin Protein 1 Alpha (HP1α: CBX5) is a Key Regulator in Differentiation of Endothelial Progenitor Cells to Endothelial Cells. Stem Cells 2016; 33:1512-22. [PMID: 25588582 DOI: 10.1002/stem.1954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 12/23/2014] [Indexed: 11/10/2022]
Abstract
As the ability to control the differentiation of endothelial stem/progenitor cells (EPCs) into vascular endothelial cell lineages could be useful for promoting neovascularization, it is important to obtain a deeper understanding of the epigenetic mechanisms that regulate EPC differentiation and neovascularization. Heterochromatin protein 1α (HP1α) is known to be involved in the epigenetic regulation of gene silencing. However, recent reports demonstrate that HP1α can also activate gene expression during cell differentiation. In this study, microarray analysis revealed that HP1α expression was induced during EPC differentiation and is associated with the expression of outgrowing endothelial cell (OEC)-specific protein markers. To explore the role of HP1α in the differentiation of EPCs to OECs, its expression was knocked-down or over-expressed in differentiating EPCs. Overexpression of HP1α promoted the differentiation and angiogenic activity of EPCs in vitro and in vivo, whereas knockdown of HP1α led to a defect in OEC migration, tube formation, and angiogenic sprouting activity. Gene expression profiling showed increased expression of angiogenic genes, including NOTCH1, cadherin-5, and angiopoietin-like-2, and decreased expression of progenitor cell marker genes, including CD133, CXCR4, and C-KIT, in HP1α-overexpressing EPCs. Also, increased HP1α at an early stage of EPC differentiation may regulate angiogenic gene transcription by interacting with chromatin that modifies epigenetic factors such as the methyl-CpG binding domain, Polycomb group ring finger 2, and DNA methyltransferases. Our findings demonstrate, for the first time, that HP1α plays an important role in the differentiation and angiogenic function of EPCs by regulating endothelial gene expression. Stem Cells 2015;33:1512-1522.
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Affiliation(s)
- Yong-Sun Maeng
- Corneal Dystrophy Research Institute; Department of Ophthalmology, Yonsei University College of Medicine, Seoul, 120-752, Korea; Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Korea
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15
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Venturini L, Stadler M, Manukjan G, Scherr M, Schlegelberger B, Steinemann D, Ganser A. The stem cell zinc finger 1 (SZF1)/ZNF589 protein has a human-specific evolutionary nucleotide DNA change and acts as a regulator of cell viability in the hematopoietic system. Exp Hematol 2015; 44:257-68. [PMID: 26738774 DOI: 10.1016/j.exphem.2015.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/15/2015] [Accepted: 12/19/2015] [Indexed: 01/19/2023]
Abstract
The stem cell zinc finger 1 (SZF1)/ZNF589 protein belongs to the large family of Krüppel-associated box domain-zinc finger (KRAB-ZNF) transcription factors, which are present only in higher vertebrates and epigenetically repress transcription by recruiting chromatin-modifying complexes to the promoter regions of their respective target genes. Although the distinct biological functions of most KRAB-ZNF proteins remain unknown, recent publications indicate their implication in fundamental processes, such as cell proliferation, apoptosis, differentiation, development, and tumorigenesis. SZF1/ZNF589 was first identified as a gene with SZF1-1 isoform specifically expressed in CD34(+) hematopoietic cells, strongly suggesting a role in epigenetic control of gene expression in hematopoietic stem/progenitor cells (HSPCs). However, the function of SZF1/ZNF589 in hematopoiesis has not yet been elucidated. Our study reveals SZF1/ZNF589 as a gene with a human-specific nucleotide DNA-change, conferring potential species-specific functional properties. Through shRNA-mediated loss-of-function experiments, we found that changes in expression of fundamental apoptosis-controlling genes are induced on SZF1/ZNF589 knockdown, resulting in inhibited growth of hematopoietic cell lines and decreased progenitor potential of primary human bone marrow CD34(+) cells. Moreover, we found that the SZF1/ZNF589 gene is differentially regulated during hypoxia in CD34(+) HSPCs in a cytokine-dependent manner, implicating its possible involvement in the maintenance of the hypoxic physiologic status of hematopoietic stem cells. Our results establish the role of SZF1/ZNF589 as a new functional regulator of the hematopoietic system.
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Affiliation(s)
- Letizia Venturini
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany.
| | - Michael Stadler
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Georgi Manukjan
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Michaela Scherr
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | | | - Doris Steinemann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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16
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Dihazi GH, Jahn O, Tampe B, Zeisberg M, Müller C, Müller GA, Dihazi H. Proteomic analysis of embryonic kidney development: Heterochromatin proteins as epigenetic regulators of nephrogenesis. Sci Rep 2015; 5:13951. [PMID: 26359909 PMCID: PMC4566080 DOI: 10.1038/srep13951] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 07/10/2015] [Indexed: 01/18/2023] Open
Abstract
Elucidation of the mechanisms underlying the nephrogenesis will boost enormously the regenerative medicine. Here we performed 2-D gel-based comparative proteome analyses of rat embryonic kidney from different developmental stages. Out of 288 non-redundant identified proteins, 102 were common in all developmental stages. 86% of the proteins found in E14 and E16 were identical, in contrast only 37% of the identified proteins overlap between E14 and P1. Bioinformatics analysis suggests developmental stage-specific pathway activation and highlighted heterochromatin protein 1 (Cbx1, Cbx3, Cbx5) and Trim28 as potential key players in nephrogenesis. These are involved in the epigenetic regulation of gene silencing and were down-regulated in the course of kidney development. Trim28 is a potential epigenetic regulator of the branching inhibitor Bmp4. Silencing of Trim28 in cultured kidneys resulted in branching arrest. In contrast knockdown of Cbx5 was associated with abnormal ureteric bud growth and slight impairment of branching. ChIP analysis showed that the H3K9me3 distribution on Bmp4 promoters at E14 and E19 inversely correlate with mRNA expression levels. The concentrated expression-pattern of heterochromatin proteins and the negative impact of their silencing on kidney development, suggest an important role in reciprocal and inductive signaling between the ureteric bud and the metanephric mesenchyme.
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Affiliation(s)
- Gry H Dihazi
- Department of Nephrology and Rheumatology, Georg-August University Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute of Experimental Medicine, Hermann-Rein-Strasse 3, D-37075 Göttingen, Germany.,Deutsche Forschungsgemeinschaft Research Center for Molecular Physiology of the Brain, Humboldtallee 23, D-37073 Göttingen, Germany
| | - Björn Tampe
- Department of Nephrology and Rheumatology, Georg-August University Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Michael Zeisberg
- Department of Nephrology and Rheumatology, Georg-August University Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Claudia Müller
- Department of Nephrology and Rheumatology, Georg-August University Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany.,Section for Transplantation- Immunology and Immunohematology, ZMF, Eberhard-Karls-University Tübingen, Germany
| | - Gerhard A Müller
- Department of Nephrology and Rheumatology, Georg-August University Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Hassan Dihazi
- Department of Nephrology and Rheumatology, Georg-August University Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
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17
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Bahnassawy L, Perumal TM, Gonzalez-Cano L, Hillje AL, Taher L, Makalowski W, Suzuki Y, Fuellen G, del Sol A, Schwamborn JC. TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability. Sci Rep 2015; 5:13456. [PMID: 26307407 PMCID: PMC4642535 DOI: 10.1038/srep13456] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 07/17/2015] [Indexed: 12/27/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) have revolutionized the world of regenerative medicine; nevertheless, the exact molecular mechanisms underlying their generation and differentiation remain elusive. Here, we investigated the role of the cell fate determinant TRIM32 in modulating such processes. TRIM32 is essential for the induction of neuronal differentiation of neural stem cells by poly-ubiquitinating cMyc to target it for degradation resulting in inhibition of cell proliferation. To elucidate the role of TRIM32 in regulating somatic cell reprogramming we analysed the capacity of TRIM32-knock-out mouse embryonic fibroblasts (MEFs) in generating iPSC colonies. TRIM32 knock-out MEFs produced a higher number of iPSC colonies indicating a role for TRIM32 in inhibiting this cellular transition. Further characterization of the generated iPSCs indicated that the TRIM32 knock-out iPSCs show perturbed differentiation kinetics. Additionally, mathematical modelling of global gene expression data revealed that during differentiation an Oct4 centred network in the wild-type cells is replaced by an E2F1 centred network in the TRIM32 deficient cells. We show here that this might be caused by a TRIM32-dependent downregulation of Oct4. In summary, the data presented here reveal that TRIM32 directly regulates at least two of the four Yamanaka Factors (cMyc and Oct4), to modulate cell fate transitions.
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Affiliation(s)
- Lamia'a Bahnassawy
- Westfälische Wilhelms-Universität Münster, ZMBE, Institute of Cell Biology, Stem Cell Biology and Regeneration Group, Von-Esmarch-Str. 56, 48149 Münster, Germany.,Luxembourg Centre for Systems Biomedicine (LCSB), Developmental and Cellular Biology, University of Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-Belval, Luxembourg
| | - Thanneer M Perumal
- Luxembourg Centre for Systems Biomedicine (LCSB), Computational Biology, University of Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-Belval, Luxembourg
| | - Laura Gonzalez-Cano
- Luxembourg Centre for Systems Biomedicine (LCSB), Developmental and Cellular Biology, University of Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-Belval, Luxembourg
| | - Anna-Lena Hillje
- Luxembourg Centre for Systems Biomedicine (LCSB), Developmental and Cellular Biology, University of Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-Belval, Luxembourg
| | - Leila Taher
- Institute for Biostatistics and Informatics in Medicine und Ageing Research, Rostock University Medical Centre, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany
| | - Wojciech Makalowski
- Westfälische Wilhelms-Universität Münster, Institute of Bioinformatics, Niels-Stensen-Straße 14, 48149 Münster, Germany
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba-ken 227-8561, Japan
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine und Ageing Research, Rostock University Medical Centre, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany
| | - Antonio del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), Computational Biology, University of Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-Belval, Luxembourg
| | - Jens Christian Schwamborn
- Westfälische Wilhelms-Universität Münster, ZMBE, Institute of Cell Biology, Stem Cell Biology and Regeneration Group, Von-Esmarch-Str. 56, 48149 Münster, Germany.,Luxembourg Centre for Systems Biomedicine (LCSB), Developmental and Cellular Biology, University of Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-Belval, Luxembourg
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18
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Identification and characterization of a nuclear localization signal of TRIM28 that overlaps with the HP1 box. Biochem Biophys Res Commun 2015; 462:201-7. [DOI: 10.1016/j.bbrc.2015.04.108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 04/15/2015] [Indexed: 01/06/2023]
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19
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Robbez-Masson L, Rowe HM. Retrotransposons shape species-specific embryonic stem cell gene expression. Retrovirology 2015; 12:45. [PMID: 26021318 PMCID: PMC4448215 DOI: 10.1186/s12977-015-0173-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/07/2015] [Indexed: 01/20/2023] Open
Abstract
Over half of our genome is composed of retrotransposons, which are mobile elements that can readily amplify their copy number by replicating through an RNA intermediate. Most of these elements are no longer mobile but still contain regulatory sequences that can serve as promoters, enhancers or repressors for cellular genes. Despite dominating our genetic content, little is known about the precise functions of retrotransposons, which include both endogenous retroviruses (ERVs) and non-LTR elements like long interspersed nuclear element 1 (LINE-1). However, a few recent cutting-edge publications have illustrated how retrotransposons shape species-specific stem cell gene expression by two opposing mechanisms, involving their recruitment of stem cell-enriched transcription factors (TFs): firstly, they can activate expression of genes linked to naïve pluripotency, and secondly, they can induce repression of proximal genes. The paradox that different retrotransposons are active or silent in embryonic stem cells (ESCs) can be explained by differences between retrotransposon families, between individual copies within the same family, and between subpopulations of ESCs. Since they have coevolved with their host genomes, some of them have been co-opted to perform species-specific beneficial functions, while others have been implicated in genetic disease. In this review, we will discuss retrotransposon functions in ESCs, focusing on recent mechanistic advances of how HERV-H has been adopted to preserve human naïve pluripotency and how particular LINE-1, SVA and ERV family members recruit species-specific transcriptional repressors. This review highlights the fine balance between activation and repression of retrotransposons that exists to harness their ability to drive evolution, while minimizing the risk they pose to genome integrity.
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Affiliation(s)
- Luisa Robbez-Masson
- Division of Infection and Immunity, Medical Research Council Centre for Medical Molecular Virology, University College London, 90 Gower Street, London, WC1E 6BT, UK.
| | - Helen M Rowe
- Division of Infection and Immunity, Medical Research Council Centre for Medical Molecular Virology, University College London, 90 Gower Street, London, WC1E 6BT, UK.
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20
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Wong MM, Xu Q. Stem Cell Therapeutics. Atherosclerosis 2015. [DOI: 10.1002/9781118828533.ch43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Cheng CT, Kuo CY, Ann DK. KAPtain in charge of multiple missions: Emerging roles of KAP1. World J Biol Chem 2014; 5:308-320. [PMID: 25225599 PMCID: PMC4160525 DOI: 10.4331/wjbc.v5.i3.308] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/21/2014] [Accepted: 06/20/2014] [Indexed: 02/05/2023] Open
Abstract
KAP1/TRIM28/TIF1β was identified nearly twenty years ago as a universal transcriptional co-repressor because it interacts with a large KRAB-containing zinc finger protein (KRAB-ZFP) transcription factor family. Many studies demonstrate that KAP1 affects gene expression by regulating the transcription of KRAB-ZFP-specific loci, trans-repressing as a transcriptional co-repressor or epigenetically modulating chromatin structure. Emerging evidence suggests that KAP1 also functions independent of gene regulation by serving as a SUMO/ubiquitin E3 ligase or signaling scaffold protein to mediate signal transduction. KAP1 is subjected to multiple post-translational modifications (PTMs), including serine/tyrosine phosphorylation, SUMOylation, and acetylation, which coordinately regulate KAP1 function and its protein abundance. KAP1 is involved in multiple aspects of cellular activities, including DNA damage response, virus replication, cytokine production and stem cell pluripotency. Moreover, knockout of KAP1 results in embryonic lethality, indicating that KAP1 is crucial for embryonic development and possibly impacts a wide-range of (patho)physiological manifestations. Indeed, studies from conditional knockout mouse models reveal that KAP1-deficiency significantly impairs vital physiological processes, such as immune maturation, stress vulnerability, hepatic metabolism, gamete development and erythropoiesis. In this review, we summarize and evaluate current literatures involving the biochemical and physiological functions of KAP1. In addition, increasing studies on the clinical relevance of KAP1 in cancer will also be discussed.
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22
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Eissenberg JC, Elgin SCR. HP1a: a structural chromosomal protein regulating transcription. Trends Genet 2014; 30:103-10. [PMID: 24555990 DOI: 10.1016/j.tig.2014.01.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/17/2014] [Accepted: 01/17/2014] [Indexed: 01/16/2023]
Abstract
Heterochromatin protein 1 (HP1a in Drosophila) is a conserved eukaryotic chromosomal protein that is prominently associated with pericentric heterochromatin and mediates the concomitant gene silencing. Mechanistic studies implicate HP1 family proteins as 'hub proteins,' able to interact with a variety of chromosomal proteins through the chromo-shadow domain (CSD), as well as to recognize key histone modification sites [primarily histone H3 di/trimethyl Lys9 (H3K9me2/3)] through the chromodomain (CD). Consequently, HP1 has many important roles in chromatin architecture and impacts both gene expression and gene silencing, utilizing a variety of mechanisms. Clearly, HP1 function is altered by context, and potentially by post-translational modifications (PTMs). Here, we report on recent ideas as to how this versatile protein accomplishes its diverse functions.
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Affiliation(s)
- Joel C Eissenberg
- Edward A. Doisy Department of Biochemistry & Molecular Biology, Saint Louis University School of Medicine, Doisy Research Center, 1100 South Grand Boulevard, St Louis, MO 63104, USA
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, Campus Box 1037, One Brookings Drive, St Louis, MO 63130-4899, USA.
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23
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Tan X, Xu X, Elkenani M, Smorag L, Zechner U, Nolte J, Engel W, Pantakani DK. Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells. Stem Cell Res 2013; 11:1045-59. [DOI: 10.1016/j.scr.2013.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 07/09/2013] [Accepted: 07/22/2013] [Indexed: 01/12/2023] Open
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24
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Zeng A, Li YQ, Wang C, Han XS, Li G, Wang JY, Li DS, Qin YW, Shi Y, Brewer G, Jing Q. Heterochromatin protein 1 promotes self-renewal and triggers regenerative proliferation in adult stem cells. ACTA ACUST UNITED AC 2013; 201:409-25. [PMID: 23629965 PMCID: PMC3639387 DOI: 10.1083/jcb.201207172] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Adult stem cells (ASCs) capable of self-renewal and differentiation confer the potential of tissues to regenerate damaged parts. Epigenetic regulation is essential for driving cell fate decisions by rapidly and reversibly modulating gene expression programs. However, it remains unclear how epigenetic factors elicit ASC-driven regeneration. In this paper, we report that an RNA interference screen against 205 chromatin regulators identified 12 proteins essential for ASC function and regeneration in planarians. Surprisingly, the HP1-like protein SMED-HP1-1 (HP1-1) specifically marked self-renewing, pluripotent ASCs, and HP1-1 depletion abrogated self-renewal and promoted differentiation. Upon injury, HP1-1 expression increased and elicited increased ASC expression of Mcm5 through functional association with the FACT (facilitates chromatin transcription) complex, which consequently triggered proliferation of ASCs and initiated blastema formation. Our observations uncover an epigenetic network underlying ASC regulation in planarians and reveal that an HP1 protein is a key chromatin factor controlling stem cell function. These results provide important insights into how epigenetic mechanisms orchestrate stem cell responses during tissue regeneration.
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Affiliation(s)
- An Zeng
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao-Tong University School of Medicine, 200025 Shanghai, China
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25
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Martins MB, Marcello MA, Morari EC, Cunha LL, Soares FA, Vassallo J, Ward LS. Clinical utility of KAP-1 expression in thyroid lesions. Endocr Pathol 2013; 24:77-82. [PMID: 23645532 DOI: 10.1007/s12022-013-9245-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Although there are evidences of the involvement of KAP-1 in other tumors, data on differentiated thyroid carcinomas (DTC) are still lacking. We aimed to evaluate KAP-1 clinical utility in the diagnosis and prognosis of DTC. We used both visual immunohistochemistry and a semiquantitative analysis to evaluate KAP-1 expression in 230 thyroid carcinomas and 131 noncancerous thyroid nodules. There were 43 follicular carcinomas (FC) and 187 papillary thyroid carcinomas (PTC), including 130 classic (CPTC), 4 tall cells (TCPTC), and 53 follicular variants (FVPTC). Patients were followed up for 53.8 ± 41 months. They were classified as free-of-disease (142 cases) or poor outcome (25 cases--10 deaths), according to their serum Tg levels and image evidences. KAP-1 was identified in 78 % PTC, 75 % TCPTC, 74 % FC, 72 % FVPTC, 55 % FA, 44 % hyperplasia, and 11 % normal thyroid tissues. A ROC analysis identified malignant nodules with 69 % sensitivity and 75 % specificity, using a cutoff of 73.19. In addition to distinguishing benign from malignant thyroid tissues (p < 0.0001), KAP-1 expression differentiated CPTC from nodular hyperplasia (p < 0.0001), CPTC from FA (p = 0.0028), FVPTC from hyperplasia (p = 0.0039), and FC from hyperplasia (p = 0.0025). Furthermore, KAP-1 was more expressed in larger tumors (>4 cm; p = 0.0038) and in individuals who presented recurrences/metastases (p = 0.0130). We suggest that KAP-1 may help diagnose thyroid nodules, characterize follicular-patterned thyroid lesions, and identify individuals with poor prognosis.
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MESH Headings
- Adenocarcinoma, Papillary/metabolism
- Adenocarcinoma, Papillary/mortality
- Adenocarcinoma, Papillary/pathology
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/metabolism
- Carcinoma, Papillary, Follicular/metabolism
- Carcinoma, Papillary, Follicular/mortality
- Carcinoma, Papillary, Follicular/pathology
- Female
- Humans
- Hyperplasia
- Male
- Middle Aged
- Prognosis
- Repressor Proteins/metabolism
- Survival Rate
- Thyroid Gland/metabolism
- Thyroid Gland/pathology
- Thyroid Neoplasms/metabolism
- Thyroid Neoplasms/mortality
- Thyroid Neoplasms/pathology
- Thyroid Nodule/metabolism
- Thyroid Nodule/mortality
- Thyroid Nodule/pathology
- Tripartite Motif-Containing Protein 28
- Young Adult
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Affiliation(s)
- Mariana Bonjiorno Martins
- Laboratory of Cancer Molecular Genetics, Faculty of Medical Sciences (FCM), University of Campinas (Unicamp), 126, Tessalia Vieira de Camargo St., Barão Geraldo, Campinas, 13083-970, São Paulo, Brazil
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Kubota S, Fukumoto Y, Aoyama K, Ishibashi K, Yuki R, Morinaga T, Honda T, Yamaguchi N, Kuga T, Tomonaga T, Yamaguchi N. Phosphorylation of KRAB-associated protein 1 (KAP1) at Tyr-449, Tyr-458, and Tyr-517 by nuclear tyrosine kinases inhibits the association of KAP1 and heterochromatin protein 1α (HP1α) with heterochromatin. J Biol Chem 2013; 288:17871-83. [PMID: 23645696 DOI: 10.1074/jbc.m112.437756] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Protein tyrosine phosphorylation regulates a wide range of cellular processes at the plasma membrane. Recently, we showed that nuclear tyrosine phosphorylation by Src family kinases (SFKs) induces chromatin structural changes. In this study, we identify KRAB-associated protein 1 (KAP1/TIF1β/TRIM28), a component of heterochromatin, as a nuclear tyrosine-phosphorylated protein. Tyrosine phosphorylation of KAP1 is induced by several tyrosine kinases, such as Src, Lyn, Abl, and Brk. Among SFKs, Src strongly induces tyrosine phosphorylation of KAP1. Nucleus-targeted Lyn potentiates tyrosine phosphorylation of KAP1 compared with intact Lyn, but neither intact Fyn nor nucleus-targeted Fyn phosphorylates KAP1. Substitution of the three tyrosine residues Tyr-449/Tyr-458/Tyr-517, located close to the HP1 binding-motif, into phenylalanine ablates tyrosine phosphorylation of KAP1. Immunostaining and chromatin fractionation show that Src and Lyn decrease the association of KAP1 with heterochromatin in a kinase activity-dependent manner. KAP1 knockdown impairs the association of HP1α with heterochromatin, because HP1α associates with KAP1 in heterochromatin. Intriguingly, tyrosine phosphorylation of KAP1 decreases the association of HP1α with heterochromatin, which is inhibited by replacement of endogenous KAP1 with its phenylalanine mutant (KAP1-Y449F/Y458F/Y517F, KAP1-3YF). In DNA damage, KAP1-3YF repressed transcription of p21. These results suggest that nucleus-localized tyrosine kinases, including SFKs, phosphorylate KAP1 at Tyr-449/Tyr-458/Tyr-517 and inhibit the association of KAP1 and HP1α with heterochromatin.
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Affiliation(s)
- Sho Kubota
- Department of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
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Jiang JX, Zhan L, Huang Y, He YZ, Sun CY. Clinical significance of expression of KAP-1 in pancreatic carcinoma. Shijie Huaren Xiaohua Zazhi 2013; 21:829-834. [DOI: 10.11569/wcjd.v21.i9.829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the expression of KAP-1 in pancreatic carcinoma.
METHODS: The expression of KAP-1 protein in 46 pancreatic cancer specimens (including 15 cases of highly differentiated cancer, 17 cases of moderately differentiated cancer, and 14 cases of poorly differentiated cancer) and 9 normal pancreas specimens was detected by immunohistochemistry. The mRNA and protein expression of KAP-1 in 8 cases of pancreatic cancer and matched tumor-adjacent pancreatic tissue and in pancreatic carcinoma cell lines (BxPC3, CAPAN-1, PANC-1, AsPC-1, SW1990, MiaPaCa-2 and CFPAC-1) was also detected by RT-qPCR and Western blot.
RESULTS: The positive rate of KAP-1 expression was 45.6% (21/46) in pancreatic cancer and 11.1% (1/9) in normal pancreatic tissue, and was 78.6% (11/14) in poorly differentiated pancreatic cancer, 47.1% (8/17) in moderately differentiated pancreatic cancer, and 13.3% (2/15) in highly differentiated pancreatic cancer. The mRNA and protein expression of KAP-1 was higher in pancreatic cancer than in matched tumor-adjacent pancreatic tissue. The mRNA expression of KAP-1 was highest in poorly differentiated pancreatic cancer line Panc-1, higher in BXPC-3 and CFPAC-1, lower in SW1990, Capan-1 and MIAPaCa-2, and lowest in AsPC-1 and Capan-2. The protein expression of KAP-1 was highest in poorly differentiated pancreatic cancer line MIAPaCa-2 and Panc-1, higher in CFPAC-1 which is derived from liver metastases of pancreatic cancer cell, and was undetectable in other cell lines.
CONCLUSION: The expression of KAP-1 in human pancreatic cancer tissue is significantly higher than that in normal pancreatic tissue, and KAP-1 expression is involved in pancreatic cancer cell differentiation. KAP-1 may play an important role in the development of pancreatic cancer.
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Sdek P, Oyama K, Angelis E, Chan SS, Schenke-Layland K, MacLellan WR. Epigenetic regulation of myogenic gene expression by heterochromatin protein 1 alpha. PLoS One 2013; 8:e58319. [PMID: 23505487 PMCID: PMC3594309 DOI: 10.1371/journal.pone.0058319] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 02/02/2013] [Indexed: 12/17/2022] Open
Abstract
Heterochromatin protein 1 (HP1) is an essential heterochromatin-associated protein typically involved in the epigenetic regulation of gene silencing. However, recent reports have demonstrated that HP1 can also activate gene expression in certain contexts including differentiation. To explore the role of each of the three mammalian HP1 family members (α, β and γ) in skeletal muscle, their expression was individually disrupted in differentiating skeletal myocytes. Among the three isoforms of HP1, HP1α was specifically required for myogenic gene expression in myoblasts only. Knockdown of HP1α led to a defect in transcription of skeletal muscle-specific genes including Lbx1, MyoD and myogenin. HP1α binds to the genomic region of myogenic genes and depletion of HP1α results in a paradoxical increase in histone H3 lysine 9 trimethylation (H3K9me3) at these sites. JHDM3A, a H3K9 demethylase also binds to myogenic gene's genomic regions in myoblasts in a HP1α-dependent manner. JHDM3A interacts with HP1α and knockdown of JHDM3A in myoblasts recapitulates the decreased myogenic gene transcription seen with HP1α depletion. These results propose a novel mechanism for HP1α-dependent gene activation by interacting with the demethylase JHDM3A and that HP1α is required for maintenance of myogenic gene expression in myoblasts.
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Affiliation(s)
- Patima Sdek
- Departments of Medicine/Cardiology, Center for Cardiovascular Biology, Institute for Stem Cell Research, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kyohei Oyama
- Departments of Medicine/Cardiology, Center for Cardiovascular Biology, Institute for Stem Cell Research, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Ekaterini Angelis
- Departments of Medicine/Cardiology, Center for Cardiovascular Biology, Institute for Stem Cell Research, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Shing S. Chan
- Departments of Medicine/Cardiology, Center for Cardiovascular Biology, Institute for Stem Cell Research, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Katja Schenke-Layland
- Departments of Medicine/Cardiology, Center for Cardiovascular Biology, Institute for Stem Cell Research, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - W. Robb MacLellan
- Departments of Medicine/Cardiology, Center for Cardiovascular Biology, Institute for Stem Cell Research, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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Global and stage specific patterns of Krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells. PLoS One 2013; 8:e56721. [PMID: 23451074 PMCID: PMC3579818 DOI: 10.1371/journal.pone.0056721] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/14/2013] [Indexed: 01/24/2023] Open
Abstract
Highly coordinated transcription networks orchestrate the self-renewal of pluripotent stem cell and the earliest steps of mammalian development. KRAB-containing zinc finger proteins represent the largest group of transcription factors encoded by the genomes of higher vertebrates including mice and humans. Together with their putatively universal cofactor KAP1, they have been implicated in events as diverse as the silencing of endogenous retroelements, the maintenance of imprinting and the pluripotent self-renewal of embryonic stem cells, although the genomic targets and specific functions of individual members of this gene family remain largely undefined. Here, we first generated a list of Ensembl-annotated KRAB-containing genes encoding the mouse and human genomes. We then defined the transcription levels of these genes in murine early embryonic cells. We found that the majority of KRAB-ZFP genes are expressed in mouse pluripotent stem cells and other early progenitors. However, we also identified distinctively cell- or stage-specific patterns of expression, some of which are pluripotency-restricted. Finally, we determined that individual KRAB-ZFP genes exhibit highly distinctive modes of expression, even when grouped in genomic clusters, and that these cannot be correlated with the presence of prototypic repressive or activating chromatin marks. These results pave the way to delineating the role of specific KRAB-ZFPs in early embryogenesis.
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Jiang JX, Gao S, Pan YZ, Sun CY. Quantitative proteomic analysis of differentially expressed proteins in pancreatic cancer stem cells. Shijie Huaren Xiaohua Zazhi 2013; 21:145-152. [DOI: 10.11569/wcjd.v21.i2.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To screen and identify differentially expressed proteins in pancreatic cancer stem cells.
METHODS: MIA-PaCa2 (TIChigh) and BxPc-3 (TIClow) were used in the study. Differentially expressed proteins between MIA-PaCa2 (TIChigh) and BxPc-3 (TIClow) cells were isolated and screened by 2D-DIGE analysis. Protein identification was performed by peptide mass fingerprinting with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF). Western blot was performed to verify the differential expression of TRIM28.
RESULTS: Fluorescent differential protein expression patterns were obtained between MIA-PaCa2 (TIChigh) and BxPc-3 (TIClow) cells. Analyses with DeCyder v6.5 software showed a total of 23 differentially expressed protein spots (>1.5 folds), and these protein spots were identified by mass spectrometry as 19 proteins, which are involved in cell communication and signal transduction, immune response, transcription and cell cycle regulation, adipocyte differentiation and lipid droplet formation, cytoskeletal formation, cell adhesion, transport, and translation. Western blot analysis revealed that TRIM28 was highly expressed in MIA-PaCa2 (TIChigh) cells but not expressed in BxPc-3 (TIClow) cells. Among the 19 identified proteins, 8 were up-regulated and 11 down-regulated in MIA-PaCa2 (TIChigh) cells.
CONCLUSION: The identified differentially expressed proteins, such as TRIM28, are associated with the genesis, development and regulation of pancreatic cancer stem cells. They may become new therapeutic targets for pancreatic cancer.
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Morikawa K, Ikeda N, Hisatome I, Shirayoshi Y. Heterochromatin protein 1γ overexpression in P19 embryonal carcinoma cells elicits spontaneous differentiation into the three germ layers. Biochem Biophys Res Commun 2013; 431:225-31. [PMID: 23313480 DOI: 10.1016/j.bbrc.2012.12.128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 12/30/2012] [Indexed: 11/15/2022]
Abstract
P19 embryonal carcinoma (EC) cells are pluripotent stem cells and have numerous morphological and biochemical properties in common with embryonic stem (ES) cells. However, P19 cells differentiate very ineffectively as embryoid bodies (EBs) without the specific chemical inducers whereas ES cells exhibit spontaneous differentiation to the three germ layers. Recently the heterochromatin protein 1 (HP1) family protein HP1γ, which is an epigenetic modulator that binds histone H3 methylated at lysine 9, is shown to be associated with the progression from pluripotent to differentiated status in ES cells. Therefore, to study the role of HP1γ in the differentiation capacity of P19 cells, we have established a HP1γ-overexpressing P19 cell line (HPlγ-P19). Similar to the parental P19 cells, undifferentiated HP1γ-P19 cells continued to express pluripotency marker genes. However, HP1γ-P19 cells exhibited significant morphological differentiation including beating cardiomyocytes, as well as Tuj1-positive neuronal cells and Sox17-positive endodermal cells after EB formation under a normal culture condition. Moreover, real-time RT-qPCR analysis revealed that HP1γ-P19 EB cells expressed various differentiation marker genes. Thus, HP1γ-P19 cells could give rise to all three germ layers in EBs without any drug treatment. Therefore, HP1γ affects the spontaneous differentiation potential of P19 cells, and might play major roles in the decision of cell fates in pluripotent stem cells.
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Affiliation(s)
- Kumi Morikawa
- Division of Regenerative Medicine and Therapeutics, Institute of Regenerative Medicine and Biofunction, Tottori University Graduate School of Medical Science, 86 Nishimachi, Yonago, Tottori 683-8503, Japan.
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32
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Identification of KAP-1-associated complexes negatively regulating the Ey and β-major globin genes in the β-globin locus. J Proteomics 2013; 80:132-44. [PMID: 23291531 DOI: 10.1016/j.jprot.2012.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 12/11/2012] [Accepted: 12/22/2012] [Indexed: 10/27/2022]
Abstract
Deregulations of erythroid differentiation may lead to erythroleukemia and other hemoglobinopathies, yet the molecular mechanisms underlying these events are not fully understood. Here, we found that KAP-1-associated complexes contribute to the regulation of the β-globin locus, the key events of erythroid differentiation. We show that RNAi-mediated knockdown of KAP-1 in mouse erythroleukemia (MEL) cells increases expression of the Ey and β-major globin genes during hexamethylenebisacetamide (HMBA) induced differentiation process. This indicates that at least part of KAP-1-associated complexes negatively regulates β-globin gene expression during definitive erythroid differentiation. ChIP-PCR analysis revealed that one or more KAP-1-associated complexes are targeted to the promoter region of the Ey and beta-major globin genes. Since KAP-1 is only a scaffold molecule, there must be some transcriptional regulators allowing its targeted recruitment to the β-globin locus. To further discover these novel regulators, proteins interacting with KAP-1 were isolated by endogenous immunoprecipitation and identified by LC-ESI-MS/MS. Among the proteins identified, MafK and Zfp445 were studied further. We found that KAP-1 may contribute to the repression of Ey and β-major globin gene transcription through recruitment to the promoters of these two genes, mediated by the interaction of KAP-1 with either Zfp445 or MafK, respectively.
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33
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Silencing of proviruses in embryonic cells: efficiency, stability and chromatin modifications. EMBO Rep 2012; 14:73-9. [PMID: 23154467 DOI: 10.1038/embor.2012.182] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 10/15/2012] [Accepted: 10/22/2012] [Indexed: 12/16/2022] Open
Abstract
Embryonic stem cells repress retroviral infection through transcriptional silencing of proviral DNAs. We characterized two distinct mechanisms of silencing in embryonic mouse cells infected by Moloney murine leukaemia virus (MLV): a highly efficient one targeting the proline transfer RNA primer-binding site (PBSpro), and a less efficient one operating independently of the PBS. Rare virus-expressing populations were isolated, and the timing and efficiency of establishment of silencing were determined. Superinfection of the selected virus-expressing cells with a second virus carrying a distinguishable reporter revealed that the PBSpro-directed silencing was still largely intact, whereas the PBS-independent silencing was partially reduced. The timing and stability of silencing, and the associated chromatin modifications on newly established and endogenous proviruses were determined. The results indicate that epigenetic mechanisms with different specificity and efficiency are used to silence the exogenous retroviral sequences in embryonic cells.
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Strogantsev R, Ferguson-Smith AC. Proteins involved in establishment and maintenance of imprinted methylation marks. Brief Funct Genomics 2012; 11:227-39. [PMID: 22760206 DOI: 10.1093/bfgp/els018] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Epigenetic phenomena are being increasingly recognized to play key roles in normal mammalian development and disease. This is exemplified by the process of genomic imprinting whereby despite identical DNA sequence, the two parental chromosomes are not equivalent and show either maternal- or paternal-specific expression at a subset of genes in the genome. These patterns are set up by differential DNA methylation marking at the imprinting control regions in male and female germ line. In this review, we discuss the specific mechanisms by which these methyl marks are established and then selectively maintained throughout pre-implantation development. Specifically, we discuss the recent findings of a critical role played by a KRAB zinc-finger protein ZFP57 and its co-factor KAP1/TRIM28 in mediating both processes.
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Affiliation(s)
- Ruslan Strogantsev
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3EG, UK
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Chen L, Chen DT, Kurtyka C, Rawal B, Fulp WJ, Haura EB, Cress WD. Tripartite motif containing 28 (Trim28) can regulate cell proliferation by bridging HDAC1/E2F interactions. J Biol Chem 2012; 287:40106-18. [PMID: 23060449 DOI: 10.1074/jbc.m112.380865] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Trim28 appears up-regulated in many cancers. RESULTS In early stage lung tumors high Trim28 correlates with increased overall survival and Trim28 reduces cell proliferation in model lung cancer cell lines through E2F interactions. CONCLUSION Trim28 may have a tumor suppressing role in the early stages of lung cancer. SIGNIFICANCE These results suggest a complex role for Trim28 in lung cancer. Trim28 is a poorly understood transcriptional co-factor with pleiotropic biological activities. Although Trim28 mRNA is found in many studies to be up-regulated in both lung and breast cancer tissues relative to normal adjacent tissue, we found that within a panel of early-stage lung adenocarcinomas high levels of Trim28 protein correlate with better overall survival. This surprising observation suggests that Trim 28 may have anti-proliferative activity within tumors. To test this hypothesis, we used shRNAi to generate Trim28-knockdown breast and lung cancer cell lines and found that Trim28 depletion led to increased cell proliferation. Likewise, overexpression of Trim28 led to decreased cell proliferation. Confocal microscopy indicated co-localization of E2F3 and E2F4 with Trim28 within the cell nucleus, and co-immunoprecipitation assays demonstrated that Trim28 can bind both E2F3 and E2F4. Trim28 overexpression inhibited the transcriptional activity of E2F3 and E2F4, whereas Trim28 deficiency enhanced their activity. Co-immunoprecipitations further indicated that Trim28 bridges an interaction between E2Fs 3 and 4 and HDAC1. Promoter-reporter assays demonstrated that the ability of HDAC1 to repress E2F3 and E2F4-driven transcription is dependent on Trim28. Trim28 depletion increased E2F3 and E2F4 DNA binding activity, as measured by chromatin-immunoprecipitation (ChIP) assays while simultaneously reducing HDAC1 binding. Finally, ChIP-ReChIP experiments demonstrated that Trim/E2F complexes exist on several E2F-regulated promoters. Taken together, these results suggest that Trim28 has anti-proliferative activity in lung cancers via repression of members of the E2F family that are critical for cell proliferation.
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Affiliation(s)
- Lu Chen
- Molecular Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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36
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Argonaute proteins couple chromatin silencing to alternative splicing. Nat Struct Mol Biol 2012; 19:998-1004. [PMID: 22961379 DOI: 10.1038/nsmb.2373] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 08/02/2012] [Indexed: 12/29/2022]
Abstract
Argonaute proteins play a major part in transcriptional gene silencing in many organisms, but their role in the nucleus of somatic mammalian cells remains elusive. Here, we have immunopurified human Argonaute-1 and Argonaute-2 (AGO1 and AGO2) chromatin-embedded proteins and found them associated with chromatin modifiers and, notably, with splicing factors. Using the CD44 gene as a model, we show that AGO1 and AGO2 facilitate spliceosome recruitment and modulate RNA polymerase II elongation rate, thereby affecting alternative splicing. Proper AGO1 and AGO2 recruitment to CD44 transcribed regions required the endonuclease Dicer and the chromobox protein HP1γ, and resulted in increased histone H3 lysine 9 methylation on variant exons. Our data thus uncover a new model for the regulation of alternative splicing, in which Argonaute proteins couple RNA polymerase II elongation to chromatin modification.
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Zhang L, Zhou Y, Zhu J, Xu Q. An updated view on stem cell differentiation into smooth muscle cells. Vascul Pharmacol 2012; 56:280-7. [PMID: 22421140 DOI: 10.1016/j.vph.2012.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 02/17/2012] [Accepted: 02/28/2012] [Indexed: 12/16/2022]
Abstract
Stem cells possess the ability of self-renewal and give rise to specific cell types. The differentiation of stem cells involves environmental factors, transduction of extra and intra-cellular signals, regulation of gene expression by transcriptional factors, microRNAs and chromosome structural modifiers. Vascular SMCs play a profound role in blood vessel physiology and participate in a number of cardiovascular diseases such as atherosclerosis, hypertension and restenosis. In addition, SMCs could be a crucial cell component for vascular tissue engineering. In this review, we aim to update the recent progress on the mechanisms of SMC differentiation from stem cells, which involve reactive oxygen species, epigenetic modifiers, transcription factors and microRNAs coordinately regulated during stem cell differentiation. We will also discuss the potential application of stem cell therapy for patients with cardiovascular diseases.
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Affiliation(s)
- Li Zhang
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University, School of Medicine, Hangzhou 310003, PR China
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Shibata M, Blauvelt KE, Liem KF, García-García MJ. TRIM28 is required by the mouse KRAB domain protein ZFP568 to control convergent extension and morphogenesis of extra-embryonic tissues. Development 2012; 138:5333-43. [PMID: 22110054 DOI: 10.1242/dev.072546] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
TRIM28 is a transcriptional regulator that is essential for embryonic development and is implicated in a variety of human diseases. The roles of TRIM28 in distinct biological processes are thought to depend on its interaction with factors that determine its DNA target specificity. However, functional evidence linking TRIM28 to specific co-factors is scarce. chatwo, a hypomorphic allele of Trim28, causes embryonic lethality and defects in convergent extension and morphogenesis of extra-embryonic tissues. These phenotypes are remarkably similar to those of mutants in the Krüppel-associated box (KRAB) zinc finger protein ZFP568, providing strong genetic evidence that ZFP568 and TRIM28 control morphogenesis through a common molecular mechanism. We determined that chatwo mutations decrease TRIM28 protein stability and repressive activity, disrupting both ZFP568-dependent and ZFP568-independent roles of TRIM28. These results, together with the analysis of embryos bearing a conditional inactivation of Trim28 in embryonic-derived tissues, revealed that TRIM28 is differentially required by ZFP568 and other factors during the early stages of mouse embryogenesis. In addition to uncovering novel roles of TRIM28 in convergent extension and morphogenesis of extra-embryonic tissues, our characterization of chatwo mutants demonstrates that KRAB domain proteins are essential to determine some of the biological functions of TRIM28.
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Affiliation(s)
- Maho Shibata
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853, USA
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TRIM involvement in transcriptional regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 770:59-76. [PMID: 23631000 DOI: 10.1007/978-1-4614-5398-7_5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Members of the tripartite motif (TRIM) protein family are found in all multicellular eukaryotes and function in a wide range of cellular processes such as cell cycle regulation, differentiation, development, oncogenesis and viral response. Over the past few years, several TRIM proteins have been reported to control gene expression through regulation of the transcriptional activity of numerous sequence-specific transcription factors. These proteins include the transcriptional intermediary factor 1 (TIF1) regulators, the promyelocytic leukemia tumor suppressor PML and the RET finger protein (RFP). In this chapter, we will consider the molecular interactions made by these TRIM proteins and will attempt to clarify some of the molecular mechanisms underlying their regulatory effect on transcription.
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40
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White D, Rafalska-Metcalf IU, Ivanov AV, Corsinotti A, Peng H, Lee SC, Trono D, Janicki SM, Rauscher FJ. The ATM substrate KAP1 controls DNA repair in heterochromatin: regulation by HP1 proteins and serine 473/824 phosphorylation. Mol Cancer Res 2011; 10:401-14. [PMID: 22205726 DOI: 10.1158/1541-7786.mcr-11-0134] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The repair of DNA damage in highly compact, transcriptionally silent heterochromatin requires that repair and chromatin packaging machineries be tightly coupled and regulated. KAP1 is a heterochromatin protein and co-repressor that binds to HP1 during gene silencing but is also robustly phosphorylated by Ataxia telangiectasia mutated (ATM) at serine 824 in response to DNA damage. The interplay between HP1-KAP1 binding/ATM phosphorylation during DNA repair is not known. We show that HP1α and unmodified KAP1 are enriched in endogenous heterochromatic loci and at a silent transgene prior to damage. Following damage, γH2AX and pKAP1-s824 rapidly increase and persist at these loci. Cells that lack HP1 fail to form discreet pKAP1-s824 foci after damage but levels are higher and more persistent. KAP1 is phosphorylated at serine 473 in response to DNA damage and its levels are also modulated by HP1. Unlike pKAP1-s824, pKAP1-s473 does not accumulate at damage foci but is diffusely localized in the nucleus. While HP1 association tempers KAP1 phosphorylation, this interaction also slows the resolution of γH2AX foci. Thus, HP1-dependent regulation of KAP1 influences DNA repair in heterochromatin.
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Affiliation(s)
- David White
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
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Zuo X, Sheng J, Lau HT, McDonald CM, Andrade M, Cullen DE, Bell FT, Iacovino M, Kyba M, Xu G, Li X. Zinc finger protein ZFP57 requires its co-factor to recruit DNA methyltransferases and maintains DNA methylation imprint in embryonic stem cells via its transcriptional repression domain. J Biol Chem 2011; 287:2107-18. [PMID: 22144682 DOI: 10.1074/jbc.m111.322644] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Previously, we discovered that ZFP57 is a maternal-zygotic effect gene, and it maintains DNA methylation genomic imprint at multiple imprinted regions in mouse embryos. Despite these findings, it remains elusive how DNA methyltransferases are targeted to the imprinting control regions to initiate and maintain DNA methylation imprint. To gain insights into these essential processes in genomic imprinting, we examined how ZFP57 maintains genomic DNA methylation imprint in mouse embryonic stem (ES) cells. Here we demonstrate that the loss of ZFP57 in mouse ES cells led to a complete loss of genomic DNA methylation imprint at multiple imprinted regions, similar to its role in mouse embryos. However, reintroduction of ZFP57 into Zfp57-null ES cells did not result in reacquisition of DNA methylation imprint, suggesting that the memory for genomic imprinting had been lost or altered in Zfp57-null ES cells in culture. Interestingly, ZFP57 and DNA methyltransferases could form complexes in the presence of KAP1/TRIM28/TIF1β when co-expressed in COS cells. We also found that the wild-type exogenous ZFP57 but not the mutant ZFP57 lacking the KRAB box that interacts with its co-factor KAP1/TRIM28/TIF1β could substitute for the endogenous ZFP57 in maintaining the DNA methylation imprint in ES cells. These results suggest that ZFP57 may recruit DNA methyltransferases to its target regions to maintain DNA methylation imprint, and this interaction is likely facilitated by KAP1/TRIM28/TIF1β.
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Affiliation(s)
- Xiaopan Zuo
- Black Family Stem Cell Institute, Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York 10029, USA
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Sdek P, Zhao P, Wang Y, Huang CJ, Ko CY, Butler PC, Weiss JN, Maclellan WR. Rb and p130 control cell cycle gene silencing to maintain the postmitotic phenotype in cardiac myocytes. ACTA ACUST UNITED AC 2011; 194:407-23. [PMID: 21825075 PMCID: PMC3153646 DOI: 10.1083/jcb.201012049] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The mammalian heart loses its regenerative potential soon after birth. Adult cardiac myocytes (ACMs) permanently exit the cell cycle, and E2F-dependent genes are stably silenced, although the underlying mechanism is unclear. Heterochromatin, which silences genes in many biological contexts, accumulates with cardiac differentiation. H3K9me3, a histone methylation characteristic of heterochromatin, also increases in ACMs and at E2F-dependent promoters. We hypothesize that genes relevant for cardiac proliferation are targeted to heterochromatin by retinoblastoma (Rb) family members interacting with E2F transcription factors and recruiting heterochromatin protein 1 (HP1) proteins. To test this hypothesis, we created cardiac-specific Rb and p130 inducible double knockout (IDKO) mice. IDKO ACMs showed a decrease in total heterochromatin, and cell cycle genes were derepressed, leading to proliferation of ACMs. Although Rb/p130 deficiency had no effect on total H3K9me3 levels, recruitment of HP1-γ to promoters was lost. Depleting HP1-γ up-regulated proliferation-promoting genes in ACMs. Thus, Rb and p130 have overlapping roles in maintaining the postmitotic state of ACMs through their interaction with HP1-γ to direct heterochromatin formation and silencing of proliferation-promoting genes.
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Affiliation(s)
- Patima Sdek
- Cardiovascular Research Laboratory, Department of Medicine and Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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Abstract
Acetylation of lysine residues is a post-translational modification with broad relevance
to cellular signalling and disease biology. Enzymes that ‘write’
(histone acetyltransferases, HATs) and ‘erase’ (histone deacetylases,
HDACs) acetylation sites are an area of extensive research in current drug development,
but very few potent inhibitors that modulate the ‘reading process’
mediated by acetyl lysines have been described. The principal readers of
ɛ-N-acetyl lysine (Kac) marks are
bromodomains (BRDs), which are a diverse family of evolutionary conserved
protein-interaction modules. The conserved BRD fold contains a deep, largely hydrophobic
acetyl lysine binding site, which represents an attractive pocket for the development of
small, pharmaceutically active molecules. Proteins that contain BRDs have been implicated
in the development of a large variety of diseases. Recently, two highly potent and
selective inhibitors that target BRDs of the BET (bromodomains and extra-terminal) family
provided compelling data supporting targeting of these BRDs in inflammation and in an
aggressive type of squamous cell carcinoma. It is likely that BRDs will emerge alongside
HATs and HDACs as interesting targets for drug development for the large number of
diseases that are caused by aberrant acetylation of lysine residues.
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Xiao Q, Wang G, Yin X, Luo Z, Margariti A, Zeng L, Mayr M, Ye S, Xu Q. Chromobox Protein Homolog 3 Is Essential for Stem Cell Differentiation to Smooth Muscles In Vitro and in Embryonic Arteriogenesis. Arterioscler Thromb Vasc Biol 2011; 31:1842-52. [DOI: 10.1161/atvbaha.111.230110] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Qingzhong Xiao
- From the Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (Q. Xiao, S.Y.); Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (G.W., X.Y., Z.L., A.M., L.Z., M.M., Q. Xu)
| | - Gang Wang
- From the Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (Q. Xiao, S.Y.); Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (G.W., X.Y., Z.L., A.M., L.Z., M.M., Q. Xu)
| | - Xiaoke Yin
- From the Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (Q. Xiao, S.Y.); Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (G.W., X.Y., Z.L., A.M., L.Z., M.M., Q. Xu)
| | - Zhenling Luo
- From the Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (Q. Xiao, S.Y.); Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (G.W., X.Y., Z.L., A.M., L.Z., M.M., Q. Xu)
| | - Andriani Margariti
- From the Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (Q. Xiao, S.Y.); Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (G.W., X.Y., Z.L., A.M., L.Z., M.M., Q. Xu)
| | - Lingfang Zeng
- From the Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (Q. Xiao, S.Y.); Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (G.W., X.Y., Z.L., A.M., L.Z., M.M., Q. Xu)
| | - Manuel Mayr
- From the Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (Q. Xiao, S.Y.); Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (G.W., X.Y., Z.L., A.M., L.Z., M.M., Q. Xu)
| | - Shu Ye
- From the Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (Q. Xiao, S.Y.); Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (G.W., X.Y., Z.L., A.M., L.Z., M.M., Q. Xu)
| | - Qingbo Xu
- From the Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (Q. Xiao, S.Y.); Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (G.W., X.Y., Z.L., A.M., L.Z., M.M., Q. Xu)
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Meylan S, Groner AC, Ambrosini G, Malani N, Quenneville S, Zangger N, Kapopoulou A, Kauzlaric A, Rougemont J, Ciuffi A, Bushman FD, Bucher P, Trono D. A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing. BMC Genomics 2011; 12:378. [PMID: 21791101 PMCID: PMC3199781 DOI: 10.1186/1471-2164-12-378] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/26/2011] [Indexed: 01/20/2023] Open
Abstract
Background KRAB-ZFPs (Krüppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by the mouse and human genomes. They act via an essential cofactor, KAP1, which recruits effectors responsible for the formation of facultative heterochromatin. We have recently shown that KRAB/KAP1 can mediate long-range transcriptional repression through heterochromatin spreading, but also demonstrated that this process is at times countered by endogenous influences. Method To investigate this issue further we used an ectopic KRAB-based repressor. This system allowed us to tether KRAB/KAP1 to hundreds of euchromatic sites within genes, and to record its impact on gene expression. We then correlated this KRAB/KAP1-mediated transcriptional effect to pre-existing genomic and chromatin structures to identify specific characteristics making a gene susceptible to repression. Results We found that genes that were susceptible to KRAB/KAP1-mediated silencing carried higher levels of repressive histone marks both at the promoter and over the transcribed region than genes that were insensitive. In parallel, we found a high enrichment in euchromatic marks within both the close and more distant environment of these genes. Conclusion Together, these data indicate that high levels of gene activity in the genomic environment and the pre-deposition of repressive histone marks within a gene increase its susceptibility to KRAB/KAP1-mediated repression.
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Affiliation(s)
- Sylvain Meylan
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Jeevan-Raj BP, Robert I, Heyer V, Page A, Wang JH, Cammas F, Alt FW, Losson R, Reina-San-Martin B. Epigenetic tethering of AID to the donor switch region during immunoglobulin class switch recombination. ACTA ACUST UNITED AC 2011; 208:1649-60. [PMID: 21746811 PMCID: PMC3149220 DOI: 10.1084/jem.20110118] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Immunoglobulin class switch recombination (CSR) is initiated by double-stranded DNA breaks (DSBs) in switch regions triggered by activation-induced cytidine deaminase (AID). Although CSR correlates with epigenetic modifications at the IgH locus, the relationship between these modifications and AID remains unknown. In this study, we show that during CSR, AID forms a complex with KAP1 (KRAB domain-associated protein 1) and HP1 (heterochromatin protein 1) that is tethered to the donor switch region (Sμ) bearing H3K9me3 (trimethylated histone H3 at lysine 9) in vivo. Furthermore, in vivo disruption of this complex results in impaired AID recruitment to Sμ, inefficient DSB formation, and a concomitant defect in CSR but not in somatic hypermutation. We propose that KAP1 and HP1 tether AID to H3K9me3 residues at the donor switch region, thus providing a mechanism linking AID to epigenetic modifications during CSR.
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Affiliation(s)
- Beena Patricia Jeevan-Raj
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de Santé et de Recherche Médicale Unité 964/Centre National de Recherche Scientifique Unité Mixte de Recherche 7104, Université de Strasbourg, 67404 Illkirch, France
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47
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Abstract
In mammalian cells, multiple cellular processes, including gene silencing, cell growth and differentiation, pluripotency, neoplastic transformation, apoptosis, DNA repair, and maintenance of genomic integrity, converge on the evolutionarily conserved protein KAP1, which is thought to regulate the dynamic organization of chromatin structure via its ability to influence epigenetic patterns and chromatin compaction. In this minireview, we discuss how KAP1 might execute such pleiotropic effects, focusing on genomic targeting mechanisms, protein-protein interactions, specific post-translational modifications of both KAP1 and associated histones, and transcriptome analyses of cells deficient in KAP1.
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Affiliation(s)
- Sushma Iyengar
- From the Genetics Graduate Group, University of California, Davis, California 95616, USA
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48
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Young RA. Control of the embryonic stem cell state. Cell 2011; 144:940-54. [PMID: 21414485 DOI: 10.1016/j.cell.2011.01.032] [Citation(s) in RCA: 865] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/23/2010] [Accepted: 01/03/2011] [Indexed: 12/25/2022]
Abstract
Embryonic stem cells and induced pluripotent stem cells hold great promise for regenerative medicine. These cells can be propagated in culture in an undifferentiated state but can be induced to differentiate into specialized cell types. Moreover, these cells provide a powerful model system for studies of cellular identity and early mammalian development. Recent studies have provided insights into the transcriptional control of embryonic stem cell state, including the regulatory circuitry underlying pluripotency. These studies have, as a consequence, uncovered fundamental mechanisms that control mammalian gene expression, connect gene expression to chromosome structure, and contribute to human disease.
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Affiliation(s)
- Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
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49
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Transcription cofactors TRIM24, TRIM28, and TRIM33 associate to form regulatory complexes that suppress murine hepatocellular carcinoma. Proc Natl Acad Sci U S A 2011; 108:8212-7. [PMID: 21531907 DOI: 10.1073/pnas.1101544108] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
TRIM24 (TIF1α), TRIM28 (TIF1β), and TRIM33 (TIF1γ) are three related cofactors belonging to the tripartite motif superfamily that interact with distinct transcription factors. TRIM24 interacts with the liganded retinoic acid (RA) receptor to repress its transcriptional activity. Germ line inactivation of TRIM24 in mice deregulates RA-signaling in hepatocytes leading to the development of hepatocellular carcinoma (HCC). Here we show that TRIM24 can be purified as at least two macromolecular complexes comprising either TRIM33 or TRIM33 and TRIM28. Somatic hepatocyte-specific inactivation of TRIM24, TRIM28, or TRIM33 all promote HCC in a cell-autonomous manner in mice. Moreover, HCC formation upon TRIM24 inactivation is strongly potentiated by further loss of TRIM33. These results demonstrate that the TIF1-related subfamily of TRIM proteins interact both physically and functionally to modulate HCC formation in mice.
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50
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Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res 2011; 21:147-63. [PMID: 21177972 PMCID: PMC3032919 DOI: 10.1101/gr.110098.110] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Accepted: 12/08/2010] [Indexed: 12/18/2022]
Abstract
Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in different cell types using ChIP-array analysis of histone modifications and chromosomal proteins. As anticipated, the pericentric heterochromatin and chromosome 4 are on average enriched for the "silencing" marks H3K9me2, H3K9me3, HP1a, and SU(VAR)3-9, and are generally depleted for marks associated with active transcription. The locations of the euchromatin-heterochromatin borders identified by these marks are similar in animal tissues and most cell lines, although the amount of heterochromatin is variable in some cell lines. Combinatorial analysis of chromatin patterns reveals distinct profiles for euchromatin, pericentric heterochromatin, and the 4th chromosome. Both silent and active protein-coding genes in heterochromatin display complex patterns of chromosomal proteins and histone modifications; a majority of the active genes exhibit both "activation" marks (e.g., H3K4me3 and H3K36me3) and "silencing" marks (e.g., H3K9me2 and HP1a). The hallmark of active genes in heterochromatic domains appears to be a loss of H3K9 methylation at the transcription start site. We also observe complex epigenomic profiles of intergenic regions, repeated transposable element (TE) sequences, and genes in the heterochromatic extensions. An unexpectedly large fraction of sequences in the euchromatic chromosome arms exhibits a heterochromatic chromatin signature, which differs in size, position, and impact on gene expression among cell types. We conclude that patterns of heterochromatin/euchromatin packaging show greater complexity and plasticity than anticipated. This comprehensive analysis provides a foundation for future studies of gene activity and chromosomal functions that are influenced by or dependent upon heterochromatin.
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Affiliation(s)
- Nicole C. Riddle
- Department of Biology, Washington University St. Louis, Missouri 63130, USA
| | - Aki Minoda
- Department of Molecular and Cell Biology, University of California at Berkeley and Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
| | - Peter V. Kharchenko
- Center for Biomedical Informatics, Harvard Medical School and Informatics Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Artyom A. Alekseyenko
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yuri B. Schwartz
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
- Department of Molecular Biology, Umea University, 90187 Umea, Sweden
| | - Michael Y. Tolstorukov
- Center for Biomedical Informatics, Harvard Medical School and Informatics Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Andrey A. Gorchakov
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jacob D. Jaffe
- Proteomics Group, The Broad Institute, Cambridge, Massachusetts 02139, USA
| | - Cameron Kennedy
- Department of Molecular and Cell Biology, University of California at Berkeley and Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
| | - Daniela Linder-Basso
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
| | - Sally E. Peach
- Proteomics Group, The Broad Institute, Cambridge, Massachusetts 02139, USA
| | - Gregory Shanower
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Resource, Center for Advanced Biotechnology and Medicine, University of Dentistry and Medicine of New Jersey, Piscataway, New Jersey 08854, USA
| | - Mitzi I. Kuroda
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Vincenzo Pirrotta
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
| | - Peter J. Park
- Center for Biomedical Informatics, Harvard Medical School and Informatics Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Sarah C.R. Elgin
- Department of Biology, Washington University St. Louis, Missouri 63130, USA
| | - Gary H. Karpen
- Department of Molecular and Cell Biology, University of California at Berkeley and Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
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