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Wilhelm E, Poirier M, Da Rocha M, Bédard M, McDonald PP, Lavigne P, Hunter CL, Bell B. Mitotic deacetylase complex (MiDAC) recognizes the HIV-1 core promoter to control activated viral gene expression. PLoS Pathog 2024; 20:e1011821. [PMID: 38781120 PMCID: PMC11115230 DOI: 10.1371/journal.ppat.1011821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
The human immunodeficiency virus (HIV) integrates into the host genome forming latent cellular reservoirs that are an obstacle for cure or remission strategies. Viral transcription is the first step in the control of latency and depends upon the hijacking of the host cell RNA polymerase II (Pol II) machinery by the 5' HIV LTR. Consequently, "block and lock" or "shock and kill" strategies for an HIV cure depend upon a full understanding of HIV transcriptional control. The HIV trans-activating protein, Tat, controls HIV latency as part of a positive feed-forward loop that strongly activates HIV transcription. The recognition of the TATA box and adjacent sequences of HIV essential for Tat trans-activation (TASHET) of the core promoter by host cell pre-initiation complexes of HIV (PICH) has been shown to be necessary for Tat trans-activation, yet the protein composition of PICH has remained obscure. Here, DNA-affinity chromatography was employed to identify the mitotic deacetylase complex (MiDAC) as selectively recognizing TASHET. Using biophysical techniques, we show that the MiDAC subunit DNTTIP1 binds directly to TASHET, in part via its CTGC DNA motifs. Using co-immunoprecipitation assays, we show that DNTTIP1 interacts with MiDAC subunits MIDEAS and HDAC1/2. The Tat-interacting protein, NAT10, is also present in HIV-bound MiDAC. Gene silencing revealed a functional role for DNTTIP1, MIDEAS, and NAT10 in HIV expression in cellulo. Furthermore, point mutations in TASHET that prevent DNTTIP1 binding block the reactivation of HIV by latency reversing agents (LRA) that act via the P-TEFb/7SK axis. Our data reveal a key role for MiDAC subunits DNTTIP1, MIDEAS, as well as NAT10, in Tat-activated HIV transcription and latency. DNTTIP1, MIDEAS and NAT10 emerge as cell cycle-regulated host cell transcription factors that can control activated HIV gene expression, and as new drug targets for HIV cure strategies.
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Affiliation(s)
| | | | - Morgane Da Rocha
- Département de microbiologie et d’infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Mikaël Bédard
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Patrick P. McDonald
- Pulmonary Division, Medicine Faculty, Université de Sherbrooke; and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Pierre Lavigne
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | | | - Brendan Bell
- Département de microbiologie et d’infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
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2
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Xiao H, Wang S, Tang Y, Li S, Jiang Y, Yang Y, Zhang Y, Han Y, Wu X, Zheng L, Li Y, Gao Y. Absence of terminal deoxynucleotidyl transferase expression in T-ALL/LBL accumulates chromosomal abnormalities to induce drug resistance. Int J Cancer 2023; 152:2383-2395. [PMID: 36757202 DOI: 10.1002/ijc.34465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/21/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023]
Abstract
T-acute lymphoblastic leukemia/lymphoma (T-ALL/LBL) is a malignant neoplasm of immature lymphoblasts. Terminal deoxynucleotidyl transferase (TDT) is a template-independent DNA polymerase that plays an essential role in generating diversity for immunoglobulin genes. T-ALL/LBL patients with TDT- have a worse prognosis. However, how TDT- promotes the disease progression of T-ALL/LBL remains unknown. Here we analyzed the prognosis of T-ALL/LBL patients in Shanghai Children's Medical Center (SCMC) and confirmed that TDT- patients had a higher rate of recurrence and remission failure and worse outcomes. Cellular experiments demonstrated that TDT was involved in DNA damage repair. TDT knockout delayed DNA repair, arrested the cell cycle and decreased apoptosis to induce the accumulation of chromosomal abnormalities and tolerance to abnormal karyotypes. Our study demonstrated that the poor outcomes in TDT- T-ALL/LBL might be due to the drug resistance (VP16 and MTX) induced by chromosomal abnormalities. Our findings revealed novel functions and mechanisms of TDT in T-ALL/LBL and supported that hematopoietic stem cell transplantation (HSCT) might be a better choice for these patients.
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Affiliation(s)
- Hui Xiao
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Siqi Wang
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yuejia Tang
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Shanshan Li
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yufeng Jiang
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yi Yang
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yinwen Zhang
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yali Han
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Xiaoyu Wu
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Liang Zheng
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yanxin Li
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yijin Gao
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
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3
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Zhang Y, Wang Z, Huang Y, Ying M, Wang Y, Xiong J, Liu Q, Cao F, Joshi R, Liu Y, Xu D, Zhang M, Yuan K, Zhou N, Koropatnick J, Min W. TdIF1: a putative oncogene in NSCLC tumor progression. Signal Transduct Target Ther 2018; 3:28. [PMID: 30345081 PMCID: PMC6194072 DOI: 10.1038/s41392-018-0030-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 12/17/2022] Open
Abstract
TdT-interacting factor 1 (TdIF1) is a ubiquitously expressed DNA- and protein-binding protein that directly binds to terminal deoxynucleotidyl transferase (TdT) polymerase. Little is known about the functional role of TdIF1 in cancer cellular signaling, nor has it previously been identified as aberrant in any type of cancer. We report here for the first time that TdIF1 is abundantly expressed in clinical lung cancer patients and that high expression of TdIF1 is associated with poor patient prognosis. We further established that TdIF1 is highly expressed in human non-small cell lung cancer (NSCLC) cell lines compared to a normal lung cell line. shRNA-mediated gene silencing of TdIF1 resulted in the suppression of proliferation and anchorage-independent colony formation of the A549 adenocarcinoma cell line. Moreover, when these TdIF1-silenced cells were used to establish a mouse xenograft model of human NSCLC, tumor size was greatly reduced. These data suggest that TdIF1 is a potent regulator of lung tumor development. Several cell cycle-related and tumor growth signaling pathways, including the p53 and HDAC1/2 pathways, were identified as participating in the TdIF1 signaling network by in silico analysis. Microarray, transcriptome and protein-level analyses validated p53 and HDAC1/2 modulation upon TdIF1 downregulation in an NSCLC cellular model. Moreover, several other cell cycle regulators were affected at the transcript level by TdIF1 silencing, including an increase in CDKN1A/p21 transcripts. Taken together, these results indicate that TdIF1 is a bona fide tumor-promoting factor in NSCLC and a potential target for therapy. A protein involved in the immune system also plays a role in the most common type of lung cancer. Weiping Min, of the University of Western Ontario in Canada, and international colleagues found, for the first time, that the protein TdIF1 is significantly upregulated in non-small cell lung cancer (NSCLC) tissues in patients. High expression levels of this protein were correlated with poor prognosis. NSCLC tumor tissues grown in mice where TdIF1 expression was ‘knocked down’ were significantly smaller than in those without TdIF1 knockdown. Further analyses showed the protein was involved in known cell signaling pathways with roles in NSCLC progression. The findings indicate TdIF1 should be further investigated as a biomarker of NSCLC or as a molecular target for its treatment.
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Affiliation(s)
- Yujuan Zhang
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China.,3Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Zhigang Wang
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Yanqing Huang
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Muying Ying
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Yifan Wang
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China.,4Department of Surgery, Pathology and Oncology, University of Western Ontario, London, Canada
| | - Juan Xiong
- 5Department of Preventive Medicine, School of Medicine, Shenzhen University, Shenzhen, China
| | - Qi Liu
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Fan Cao
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Rakesh Joshi
- 4Department of Surgery, Pathology and Oncology, University of Western Ontario, London, Canada
| | - Yanling Liu
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Derong Xu
- 6Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Meng Zhang
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China.,4Department of Surgery, Pathology and Oncology, University of Western Ontario, London, Canada
| | - Keng Yuan
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Nanjin Zhou
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - James Koropatnick
- 4Department of Surgery, Pathology and Oncology, University of Western Ontario, London, Canada
| | - Weiping Min
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China.,4Department of Surgery, Pathology and Oncology, University of Western Ontario, London, Canada
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4
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Yu H, Waddell JN, Kuang S, Tellam RL, Cockett NE, Bidwell CA. Identification of genes directly responding to DLK1 signaling in Callipyge sheep. BMC Genomics 2018; 19:283. [PMID: 29690867 PMCID: PMC5937834 DOI: 10.1186/s12864-018-4682-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/16/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In food animal agriculture, there is a need to identify the mechanisms that can improve the efficiency of muscle growth and protein accretion. Callipyge sheep provide excellent machinery since the up-regulation of DLK1 and RTL1 results in extreme postnatal muscle hypertrophy in distinct muscles. The aim of this study is to distinguish the genes that directly respond to DLK1 and RTL1 signaling from the genes that change as the result of muscle specific effects. RESULTS The quantitative PCR results indicated that DLK1 expression was significantly increased in hypertrophied muscles but not in non-hypertrophied muscles. However, RTL1 was up-regulated in both hypertrophied and non-hypertrophied muscles. Five genes, including PARK7, DNTTIP1, SLC22A3, METTL21E and PDE4D, were consistently co-expressed with DLK1, and therefore were possible transcriptional target genes responding to DLK1 signaling. Treatment of myoblast and myotubes with DLK1 protein induced an average of 1.6-fold and 1.4-fold increase in Dnttip1 and Pde4d expression respectively. Myh4 expression was significantly elevated in DLK1-treated myotubes, whereas the expression of Mettl21e was significantly increased in the DLK1-treated myoblasts but reduced in DLK1-treated myotubes. DLK1 treatment had no impact on Park7 expression. In addition, Park7 and Dnttip1 increased Myh4 and decreased Myh7 promoter activity, resemble to the effects of Dlk1. In contrast, expression of Mettl21e increased Myh7 and decreased Myh4 luciferase activity. CONCLUSION The study provided additional supports that RTL1 alone was insufficient to induce muscle hypertrophy and concluded that DLK1 was likely the primary effector of the hypertrophy phenotype. The results also suggested that DNTTIP1 and PDE4D were secondary effector genes responding to DLK1 signaling resulting in muscle fiber switch and muscular hypertrophy in callipyge lamb.
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Affiliation(s)
- Hui Yu
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA. .,Department of Molecular and Integrative Physiology, University of Michigan, 1000 Wall Street, Ann Arbor, MI, 48105, USA.
| | - Jolena N Waddell
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.,Department of Animal Science & Veterinary Technology, Tarleton State University, Stephenville, TX, USA
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.,Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Ross L Tellam
- CSIRO Animal, Food and Health Sciences, St. Lucia, QLD, Australia
| | - Noelle E Cockett
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Christopher A Bidwell
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.
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5
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Loc'h J, Delarue M. Terminal deoxynucleotidyltransferase: the story of an untemplated DNA polymerase capable of DNA bridging and templated synthesis across strands. Curr Opin Struct Biol 2018; 53:22-31. [PMID: 29656238 DOI: 10.1016/j.sbi.2018.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/27/2018] [Accepted: 03/30/2018] [Indexed: 01/08/2023]
Abstract
Terminal deoxynucleotidyltransferase (TdT) is a member of the polX family which is involved in DNA repair. It has been known for years as an untemplated DNA polymerase used during V(D)J recombination to generate diversity at the CDR3 region of immunoglobulins and T-cell receptors. Recently, however, TdT was crystallized in the presence of a complete DNA synapsis made of two double-stranded DNA (dsDNA), each with a 3' protruding end, and overlapping with only one micro-homology base-pair, thus giving structural insight for the first time into DNA synthesis across strands. It was subsequently shown that TdT indeed has an in trans template-dependent activity in the presence of an excess of the downstream DNA duplex. A possible biological role of this dual activity is discussed.
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Affiliation(s)
- Jérôme Loc'h
- Unit of Structural Dynamics of Biological Macromolecules and UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Marc Delarue
- Unit of Structural Dynamics of Biological Macromolecules and UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France.
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6
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Ou R, Huang J, Shen H, Liu Z, Zhu Y, Zhong Q, Zheng L, Yao M, She Y, Zhou S, Chen R, Li C, Zhang Q, Liu S. Transcriptome analysis of CD34+ cells from myelodysplastic syndrome patients. Leuk Res 2017; 62:40-50. [PMID: 28982058 DOI: 10.1016/j.leukres.2017.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 11/15/2022]
Abstract
The myelodysplastic syndrome (MDS) represents a heterogeneous group of clonal hematologic stem cell disorders with the characteristic of ineffective hematopoiesis leading to low blood counts, and a risk of progression to acute myeloid leukemia (AML). To understand specific molecular characteristics of different MDS subtypes with del(5q), we analyzed the gene expression profiles of CD34+ cells from MDS patients of different databases and its enriched pathways. 44 genes, such as MME and RAG1, and eight related pathways were identified to be commonly changed, indicating their conserved roles in MDS development. Additionally, U43604 was identified to be specifically changed in three subtypes with del(5q), including refractory anemia (RA), refractory anemia with ringed sideroblasts (RARS) and refractory anemia with excess blasts (RAEB). C10orf10 and CD79B were specifically changed in RA patients with del(5q), while POU2AF1 were in RARS patients with del(5q). We also analyzed specific pathways of MDS subtypes, such as "Glycosaminoglycan biosynthesis-chondroitin sulfate" which was specific identified in RARS patients. Importantly, those findings can be validated well using another MDS database. Taken together, our analysis identified specific genes and pathways associated with different MDS subtypes with del(5q).
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Affiliation(s)
- Ruiming Ou
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Jing Huang
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Huijuan Shen
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Zhi Liu
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Yangmin Zhu
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Qi Zhong
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Liling Zheng
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Mengdong Yao
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Yanling She
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Shanyao Zhou
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Rui Chen
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Cheng Li
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China
| | - Qing Zhang
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China.
| | - Shuang Liu
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangdong, Guangzhou, 510317, China.
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7
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Filarsky M, Zillner K, Araya I, Villar-Garea A, Merkl R, Längst G, Németh A. The extended AT-hook is a novel RNA binding motif. RNA Biol 2016; 12:864-76. [PMID: 26156556 PMCID: PMC4615771 DOI: 10.1080/15476286.2015.1060394] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The AT-hook has been defined as a DNA binding peptide motif that contains a glycine-arginine-proline (G-R-P) tripeptide core flanked by basic amino acids. Recent reports documented variations in the sequence of AT-hooks and revealed RNA binding activity of some canonical AT-hooks, suggesting a higher structural and functional variability of this protein domain than previously anticipated. Here we describe the discovery and characterization of the extended AT-hook peptide motif (eAT-hook), in which basic amino acids appear symmetrical mainly at a distance of 12-15 amino acids from the G-R-P core. We identified 80 human and 60 mouse eAT-hook proteins and biochemically characterized the eAT-hooks of Tip5/BAZ2A, PTOV1 and GPBP1. Microscale thermophoresis and electrophoretic mobility shift assays reveal the nucleic acid binding features of this peptide motif, and show that eAT-hooks bind RNA with one order of magnitude higher affinity than DNA. In addition, cellular localization studies suggest a role for the N-terminal eAT-hook of PTOV1 in nucleocytoplasmic shuttling. In summary, our findings classify the eAT-hook as a novel nucleic acid binding motif, which potentially mediates various RNA-dependent cellular processes.
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Affiliation(s)
- Michael Filarsky
- a Biochemistry Center Regensburg ; University of Regensburg ; Regensburg , Germany
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8
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Koiwai K, Kubota T, Watanabe N, Hori K, Koiwai O, Masai H. Definition of the transcription factor TdIF1 consensus-binding sequence through genomewide mapping of its binding sites. Genes Cells 2015; 20:242-54. [PMID: 25619743 DOI: 10.1111/gtc.12216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/04/2014] [Indexed: 12/26/2022]
Abstract
TdIF1 was originally identified as a protein that directly binds to terminal deoxynucleotidyltransferase, TdT. Through in vitro selection assays (SELEX), we recently showed that TdIF1 recognizes both AT-tract and a specific DNA sequence motif, 5'-TGCATG-3', and can up-regulate the expression of RAB20 through the latter motif. However, whether TdIF1 binds to these sequences in the cells has not been clear and its other target genes remain to be identified. Here, we determined in vivo TdIF1-binding sequences (TdIF1-invivoBMs) on the human chromosomes through ChIP-seq analyses. The result showed a 160-base pair cassette containing 'AT-tract~palindrome (inverted repeat)~AT-tract' as a likely target sequence of TdIF1. Interestingly, the core sequence of the palindrome in the TdIF1-invivoBMs shares significant similarity to the above 5'-TGCATG-3' motif determined by SELEX in vitro. Furthermore, spacer sequences between AT-tract and the palindrome contain many potential transcription factor binding sites. In luciferase assays, TdIF1 can up-regulate transcription activity of the promoters containing the TdIF1-invivoBM, and this effect is mainly through the palindrome. Clusters of this motif were found in the potential target genes. Gene ontology analysis and RT-qPCR showed the enrichment of some candidate targets of TdIF1 among the genes involved in the regulation of ossification. Potential modes of transcription activation by TdIF1 are discussed.
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Affiliation(s)
- Kotaro Koiwai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
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9
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Natalizio AH, Matera AG. Identification and characterization of Drosophila Snurportin reveals a role for the import receptor Moleskin/importin-7 in snRNP biogenesis. Mol Biol Cell 2013; 24:2932-42. [PMID: 23885126 PMCID: PMC3771954 DOI: 10.1091/mbc.e13-03-0118] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Previous work established Importin-β and Snurportin1 as the vertebrate snRNP import receptor and adaptor proteins, respectively. This study identifies Drosophila Snurportin and shows that it uses an alternative import receptor, Importin7/Moleskin. Moleskin is required for the stability of other snRNP biogenesis factors. Nuclear import is an essential step in small nuclear ribonucleoprotein (snRNP) biogenesis. Snurportin1 (SPN1), the import adaptor, binds to trimethylguanosine (TMG) caps on spliceosomal small nuclear RNAs. Previous studies indicated that vertebrate snRNP import requires importin-β, the transport receptor that binds directly to SPN1. We identify CG42303/snup as the Drosophila orthologue of human snurportin1 (SNUPN). Of interest, the importin-β binding (IBB) domain of SPN1, which is essential for TMG cap–mediated snRNP import in humans, is not well conserved in flies. Consistent with its lack of an IBB domain, we find that Drosophila SNUP (dSNUP) does not interact with Ketel/importin-β. Fruit fly snRNPs also fail to bind Ketel; however, the importin-7 orthologue Moleskin (Msk) physically associates with both dSNUP and spliceosomal snRNPs and localizes to nuclear Cajal bodies. Strikingly, we find that msk-null mutants are depleted of the snRNP assembly factor, survival motor neuron, and the Cajal body marker, coilin. Consistent with a loss of snRNP import function, long-lived msk larvae show an accumulation of TMG cap signal in the cytoplasm. These data indicate that Ketel/importin-β does not play a significant role in Drosophila snRNP import and demonstrate a crucial function for Msk in snRNP biogenesis.
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Affiliation(s)
- Amanda Hicks Natalizio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Departments of Biology, University of North Carolina, Chapel Hill, NC 27599 Departments of Genetics, University of North Carolina, Chapel Hill, NC 27599 Program in Molecular Biology and Biotechnology, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
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Kubota T, Koiwai O, Hori K, Watanabe N, Koiwai K. TdIF1 recognizes a specific DNA sequence through its Helix-Turn-Helix and AT-hook motifs to regulate gene transcription. PLoS One 2013; 8:e66710. [PMID: 23874396 PMCID: PMC3707907 DOI: 10.1371/journal.pone.0066710] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 05/09/2013] [Indexed: 12/27/2022] Open
Abstract
TdIF1 was originally identified as a protein that directly binds to DNA polymerase TdT. TdIF1 is also thought to function in transcription regulation, because it binds directly to the transcriptional factor TReP-132, and to histone deacetylases HDAC1 and HDAC2. Here we show that TdIF1 recognizes a specific DNA sequence and regulates gene transcription. By constructing TdIF1 mutants, we identify amino acid residues essential for its interaction with DNA. An in vitro DNA selection assay, SELEX, reveals that TdIF1 preferentially binds to the sequence 5′-GNTGCATG-3′ following an AT-tract, through its Helix-Turn-Helix and AT-hook motifs. We show that four repeats of this recognition sequence allow TdIF1 to regulate gene transcription in a plasmid-based luciferase reporter assay. We demonstrate that TdIF1 associates with the RAB20 promoter, and RAB20 gene transcription is reduced in TdIF1-knocked-down cells, suggesting that TdIF1 stimulates RAB20 gene transcription.
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Affiliation(s)
- Takashi Kubota
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Osamu Koiwai
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Katsutoshi Hori
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | | | - Kotaro Koiwai
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan
- * E-mail:
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Matsumoto T, Go K, Hyodo M, Koiwai K, Maezawa S, Hayano T, Suzuki M, Koiwai O. BRCT domain of DNA polymerase μ has DNA-binding activity and promotes the DNA polymerization activity. Genes Cells 2012; 17:790-806. [DOI: 10.1111/j.1365-2443.2012.01628.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 06/14/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Takuro Matsumoto
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Kaori Go
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Mariko Hyodo
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Kotaro Koiwai
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - So Maezawa
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Takahide Hayano
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Masahiro Suzuki
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Osamu Koiwai
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
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12
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Coordinate activation of inflammatory gene networks, alveolar destruction and neonatal death in AKNA deficient mice. Cell Res 2011; 21:1564-77. [PMID: 21606955 DOI: 10.1038/cr.2011.84] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Gene expression can be regulated by chromatin modifiers, transcription factors and proteins that modulate DNA architecture. Among the latter, AT-hook transcription factors have emerged as multifaceted regulators that can activate or repress broad A/T-rich gene networks. Thus, alterations of AT-hook genes could affect the transcription of multiple genes causing global cell dysfunction. Here we report that targeted deletions of mouse AKNA, a hypothetical AT-hook-like transcription factor, sensitize mice to pathogen-induced inflammation and cause sudden neonatal death. Compared with wild-type littermates, AKNA KO mice appeared weak, failed to thrive and most died by postnatal day 10. Systemic inflammation, predominantly in the lungs, was accompanied by enhanced leukocyte infiltration and alveolar destruction. Cytologic, immunohistochemical and molecular analyses revealed CD11b(+)Gr1(+) neutrophils as major tissue infiltrators, neutrophilic granule protein, cathelin-related antimicrobial peptide and S100A8/9 as neutrophil-specific chemoattracting factors, interleukin-1β and interferon-γ as proinflammatory mediators, and matrix metalloprotease 9 as a plausible proteolytic trigger of alveolar damage. AKNA KO bone marrow transplants in wild-type recipients reproduced the severe pathogen-induced reactions and confirmed the involvement of neutrophils in acute inflammation. Moreover, promoter/reporter experiments showed that AKNA could act as a gene repressor. Our results support the concept of coordinated pathway-specific gene regulation functions modulating the intensity of inflammatory responses, reveal neutrophils as prominent mediators of acute inflammation and suggest mechanisms underlying the triggering of acute and potentially fatal immune reactions.
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Bantscheff M, Hopf C, Savitski MM, Dittmann A, Grandi P, Michon AM, Schlegl J, Abraham Y, Becher I, Bergamini G, Boesche M, Delling M, Dümpelfeld B, Eberhard D, Huthmacher C, Mathieson T, Poeckel D, Reader V, Strunk K, Sweetman G, Kruse U, Neubauer G, Ramsden NG, Drewes G. Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes. Nat Biotechnol 2011; 29:255-65. [PMID: 21258344 DOI: 10.1038/nbt.1759] [Citation(s) in RCA: 501] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 12/17/2010] [Indexed: 11/09/2022]
Abstract
The development of selective histone deacetylase (HDAC) inhibitors with anti-cancer and anti-inflammatory properties remains challenging in large part owing to the difficulty of probing the interaction of small molecules with megadalton protein complexes. A combination of affinity capture and quantitative mass spectrometry revealed the selectivity with which 16 HDAC inhibitors target multiple HDAC complexes scaffolded by ELM-SANT domain subunits, including a novel mitotic deacetylase complex (MiDAC). Inhibitors clustered according to their target profiles with stronger binding of aminobenzamides to the HDAC NCoR complex than to the HDAC Sin3 complex. We identified several non-HDAC targets for hydroxamate inhibitors. HDAC inhibitors with distinct profiles have correspondingly different effects on downstream targets. We also identified the anti-inflammatory drug bufexamac as a class IIb (HDAC6, HDAC10) HDAC inhibitor. Our approach enables the discovery of novel targets and inhibitors and suggests that the selectivity of HDAC inhibitors should be evaluated in the context of HDAC complexes and not purified catalytic subunits.
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Hayano T, Koiwai K, Ishii H, Maezawa S, Kouda K, Motoyama T, Kubota T, Koiwai O. TdT interacting factor 1 enhances TdT ubiquitylation through recruitment of BPOZ-2 into nucleus from cytoplasm. Genes Cells 2009; 14:1415-27. [PMID: 19930467 DOI: 10.1111/j.1365-2443.2009.01358.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Takahide Hayano
- Faculty of Science & Technology, Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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