1
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Costa JR, Li Y, Anuar NZ, O'Connor D, Rahman S, Rapoz-D'Silva T, Fung KTM, Pocock R, Li Z, Henderson S, Wang L, Krulik ME, Hyseni S, Singh N, Morrow G, Guo Y, Gresham DOF, Herrero J, Jenner RG, Look AT, Kappei D, Mansour MR. Transcription factor cooperativity at a GATA3 tandem DNA sequence determines oncogenic enhancer-mediated activation. Cell Rep 2025; 44:115705. [PMID: 40378042 DOI: 10.1016/j.celrep.2025.115705] [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: 08/13/2024] [Revised: 03/08/2025] [Accepted: 04/25/2025] [Indexed: 05/18/2025] Open
Abstract
The TAL1 oncogene driving T cell lymphoblastic leukemia is frequently activated through mutated cis-regulatory elements, whereby small insertions or deletions (indels) create a binding site for the transcription factor MYB. Unraveling how non-coding mutations create oncogenic enhancers is key to understanding cancer biology and can provide important insights into fundamental mechanisms of gene regulation. Utilizing a CRISPR-Cas9 screening approach, we identify GATA3 as the key transcriptional regulator of enhancer-mediated TAL1 overexpression. CRISPR-Cas9 engineering of the mutant enhancer reveals a tandem GATA3 site that is required for binding of GATA3, chromatin accessibility, and MYB recruitment. Reciprocally, MYB binding to its motif is required for GATA3 recruitment, consistent with a transcription factor cooperativity model. Importantly, we show that GATA3 stabilizes a TAL1-MYB interaction and that complex formation requires GATA3 binding to DNA. Our work sheds light on the mechanisms of enhancer-mediated oncogene activation, where key transcription factors cooperate to achieve maximal transcriptional output, thereby supporting leukemogenesis.
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Affiliation(s)
- Joana R Costa
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - Yang Li
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - Nurkaiyisah Zaal Anuar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - David O'Connor
- Department of Haematology, UCL Cancer Institute, University College London, London, UK; Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Sunniyat Rahman
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Tanya Rapoz-D'Silva
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - Kent T M Fung
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - Rachael Pocock
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - Zhaodong Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Stephen Henderson
- Cancer Institute Bioinformatics Hub, UCL Cancer Institute, University College London, London, UK; CRUK City of London Centre, UCL Cancer Institute, University College London, London, UK
| | - Lingyi Wang
- Department of Haematology, UCL Cancer Institute, University College London, London, UK; Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Mateja E Krulik
- Faculty of Biology, University of Wurzburg, Wurzburg, Germany
| | - Sara Hyseni
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - Nivedita Singh
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - George Morrow
- Flow Cytometry Translational Technology Platform, University College London, London, UK
| | - Yanping Guo
- Flow Cytometry Translational Technology Platform, University College London, London, UK
| | - Daisy O F Gresham
- Department of Haematology, UCL Cancer Institute, University College London, London, UK; Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Javier Herrero
- Cancer Institute Bioinformatics Hub, UCL Cancer Institute, University College London, London, UK; CRUK City of London Centre, UCL Cancer Institute, University College London, London, UK
| | - Richard G Jenner
- CRUK City of London Centre, UCL Cancer Institute, University College London, London, UK; Department of Cancer Biology, UCL Cancer Institute, University College London, London, UK
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Marc R Mansour
- Department of Haematology, UCL Cancer Institute, University College London, London, UK; Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK; University College London Hospitals NHS Foundation Trust, London, UK.
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2
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Chen Y, Wan Y, Pei X, Wei Z, Wang T, Zhang J, Chen L. GATA3 differentially regulates the transcriptome via zinc finger 2-modulated phase separation. Cell Rep 2025; 44:115702. [PMID: 40372915 DOI: 10.1016/j.celrep.2025.115702] [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: 05/05/2023] [Revised: 02/28/2025] [Accepted: 04/24/2025] [Indexed: 05/17/2025] Open
Abstract
Phase separation (PS) underlies gene control by transcription factors. However, little is known about whether and how DNA-binding domains (DBDs) regulate the PS for transcription factors to differentially regulate the transcriptome. The transcription factor GATA3, a master immune regulator, is frequently mutated in breast cancer. Here, we report that GATA3 undergoes DBD-modulated PS to mediate the formation of chromatin condensates. We show that the DBD regulates the GATA3 PS through its zinc finger 2 (ZnF2) domain, which provides positive charges for multivalent electrostatic interactions mainly via two arginine amino acids, R329 and R330. Compared with breast-cancer-associated GATA3 without ZnF2-defective mutations, breast cancer GATA3 with ZnF2-defective mutations causes aberrant ZnF2-modulated PS and condensate formation to remodel the differentially regulated transcriptome, resulting in a favorable prognosis for patients and reduced tumor growth in mice. Therefore, GATA3 demonstrates a principle of how a transcription factor differentially regulates the transcriptome via DBD-modulated PS.
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Affiliation(s)
- Yatao Chen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China; Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Yajie Wan
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiaoying Pei
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ziqi Wei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Tan Wang
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jun Zhang
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Liming Chen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China; Jiangsu Key Laboratory of Innovative Cancer Diagnosis & Therapeutics, Cancer Institute of Jiangsu Province, Nanjing 210009, China.
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3
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Dalal K, McAnany C, Weilert M, McKinney MC, Krueger S, Zeitlinger J. Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model. CELL GENOMICS 2025; 5:100821. [PMID: 40174587 PMCID: PMC12008814 DOI: 10.1016/j.xgen.2025.100821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 09/23/2024] [Accepted: 03/05/2025] [Indexed: 04/04/2025]
Abstract
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of signaling effectors is driven by cell-type-specific sequence rules that can be learned genome wide by deep learning models. Through model interpretation and experimental validation, we show that motifs for the cell-type-specific transcription factor TFAP2C enhance TEAD4/YAP1 binding in a nucleosome-range and distance-dependent manner, driving synergistic enhancer activation. We also discovered that Tead double motifs are widespread, highly active canonical response elements. Molecular dynamics simulations suggest that TEAD4 binds them cooperatively through surprisingly labile protein-protein interactions that depend on the DNA template. These results show that the response to signaling pathways is encoded in the cis-regulatory sequences and that interpreting the rules reveals insights into the mechanisms by which signaling effectors influence cell-type-specific enhancer activity.
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Affiliation(s)
- Khyati Dalal
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, USA
| | - Charles McAnany
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, USA.
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4
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Gharui S, Sengupta D. Molecular Interactions of the Pioneer Transcription Factor GATA3 With DNA. Proteins 2025; 93:555-566. [PMID: 39315643 DOI: 10.1002/prot.26749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/15/2024] [Accepted: 08/30/2024] [Indexed: 09/25/2024]
Abstract
The GATA3 transcription factor is a pioneer transcription factor that is critical in the development, proliferation, and maintenance of several immune cell types. Identifying the detailed conformational dynamics and interactions of this transcription factor, as well as its clinically important population variants will allow us to unravel its mode of action. In this study, we analyze the molecular interactions of the GATA3 transcription factor bound to dsDNA as well as three clinically important population variants by atomistic molecular dynamics simulations. We identify the effect of the variants on the DNA conformational dynamics and delineate the differences compared to the wildtype transcription factor that could be related to impaired function. We highlight the structural plasticity in the binding of the GATA3 transcription factor and identify important DNA-protein contacts. Although the DNA-protein contacts are persistent and appear to be stable, they exhibit nanosecond timescale fluctuations and several binding/unbinding events. Further, we identify differential DNA binding in the three variants and show that the N-terminal binding is reduced in two of the variants. Our results indicate that reduced minor groove width and DNA diameter are important hallmarks for the binding of GATA3. Our work is an important step towards understanding the functional dynamics of the GATA3 protein and its clinically significant population variants.
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Affiliation(s)
- Sowmomita Gharui
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India
| | - Durba Sengupta
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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5
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Lin X, Li S, Shi Y, Ma Y, Li Y, Tan H, Zhang B, Xu C, Chen K. CitGATA7 interact with histone acetyltransferase CitHAG28 to promote citric acid degradation by regulating the glutamine synthetase pathway in citrus. MOLECULAR HORTICULTURE 2025; 5:8. [PMID: 39891226 PMCID: PMC11786515 DOI: 10.1186/s43897-024-00126-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Accepted: 11/03/2024] [Indexed: 02/03/2025]
Abstract
Organic acid is a crucial indicator of fruit quality traits. Citric acid, the predominant organic acid in citrus fruit, directly influences its edible quality and economic value. While the transcriptional regulatory mechanisms of citric acid metabolism have been extensively studied, the understanding about the transcriptional and epigenetic co-regulation mechanisms is limited. This study characterized a transcription factor, CitGATA7, which directly binds to and activates the expression of genes associated with the glutamine synthetase pathway regulating citric acid degradation. These genes include the aconitase encoding gene CitACO3, the isocitrate dehydrogenase encoding gene CitIDH1, and the glutamine synthetase encoding gene CitGS1. Furthermore, CitGATA7 physically interacts with the histone acetyltransferase CitHAG28 to enhance histone 3 acetylation levels near the transcription start site of CitACO3, CitIDH1, and CitGS1, thereby increasing their transcription and promoting citric acid degradation. The findings demonstrate that the CitGATA7-CitHAG28 protein complex transcriptionally regulate the expression of the GS pathway genes, i.e., CitACO3, CitIDH1, and CitGS1, via histone acetylation, thus promoting citric acid catabolism. This study establishes a direct link between transcriptional regulation and histone acetylation regarding citric acid metabolism, providing insights for strategies to manipulate organic acid accumulation in fruit.
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Affiliation(s)
- Xiahui Lin
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Shaojia Li
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Yanna Shi
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Yuchen Ma
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Yinchun Li
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Haohan Tan
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Bo Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Changjie Xu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Kunsong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China.
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China.
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China.
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6
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Groves IJ, O’Connor CM. Loopy virus or controlled contortionist? 3D regulation of HCMV gene expression by CTCF-driven chromatin interactions. J Virol 2024; 98:e0114824. [PMID: 39212383 PMCID: PMC11495066 DOI: 10.1128/jvi.01148-24] [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] [Indexed: 09/04/2024] Open
Abstract
Three-dimensional chromatin control of eukaryotic transcription is pivotal for regulating gene expression. This additional layer of epigenetic regulation is also utilized by DNA viruses, including herpesviruses. Dynamic, spatial genomic organization often involves looping of chromatin anchored by host-encoded CCCTC-binding factor (CTCF) and other factors, which control crosstalk between promoters and enhancers. Herein, we review the contribution of CTCF-mediated looping in regulating transcription during herpesvirus infection, with a specific focus on the betaherpesvirus, human cytomegalovirus (HCMV).
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Affiliation(s)
- Ian J. Groves
- Infection Biology Program, Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, Ohio, USA
| | - Christine M. O’Connor
- Infection Biology Program, Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, Ohio, USA
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7
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Begolli R, Patouna A, Vardakas P, Xagara A, Apostolou K, Kouretas D, Giakountis A. Deciphering the Landscape of GATA-Mediated Transcriptional Regulation in Gastric Cancer. Antioxidants (Basel) 2024; 13:1267. [PMID: 39456519 PMCID: PMC11504088 DOI: 10.3390/antiox13101267] [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: 08/26/2024] [Revised: 10/11/2024] [Accepted: 10/16/2024] [Indexed: 10/28/2024] Open
Abstract
Gastric cancer (GC) is an asymptomatic malignancy in early stages, with an invasive and cost-ineffective diagnostic toolbox that contributes to severe global mortality rates on an annual basis. Ectopic expression of the lineage survival transcription factors (LS-TFs) GATA4 and 6 promotes stomach oncogenesis. However, LS-TFs also govern important physiological roles, hindering their direct therapeutic targeting. Therefore, their downstream target genes are particularly interesting for developing cancer-specific molecular biomarkers or therapeutic agents. In this work, we couple inducible knockdown systems with chromatin immunoprecipitation and RNA-seq to thoroughly detect and characterize direct targets of GATA-mediated transcriptional regulation in gastric cancer cells. Our experimental and computational strategy provides evidence that both factors regulate the expression of several coding and non-coding RNAs that in turn mediate for their cancer-promoting phenotypes, including but not limited to cell cycle, apoptosis, ferroptosis, and oxidative stress response. Finally, the diagnostic and prognostic potential of four metagene signatures consisting of selected GATA4/6 target transcripts is evaluated in a multi-cancer panel of ~7000 biopsies from nineteen tumor types, revealing elevated specificity for gastrointestinal tumors. In conclusion, our integrated strategy uncovers the landscape of GATA-mediated coding and non-coding transcriptional regulation, providing insights regarding their molecular and clinical function in gastric cancer.
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Affiliation(s)
- Rodiola Begolli
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Mezourlo, 41500 Larissa, Greece
| | - Anastasia Patouna
- Laboratory of Animal Physiology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Mezourlo, 41500 Larissa, Greece
| | - Periklis Vardakas
- Laboratory of Animal Physiology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Mezourlo, 41500 Larissa, Greece
| | - Anastasia Xagara
- Laboratory of Oncology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Mezourlo, 41110 Larissa, Greece
| | - Kleanthi Apostolou
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Mezourlo, 41500 Larissa, Greece
| | - Demetrios Kouretas
- Laboratory of Animal Physiology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Mezourlo, 41500 Larissa, Greece
| | - Antonis Giakountis
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Mezourlo, 41500 Larissa, Greece
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8
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Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y. Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4. Mol Cell 2024; 84:3061-3079.e10. [PMID: 39121853 PMCID: PMC11344660 DOI: 10.1016/j.molcel.2024.07.016] [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: 02/12/2024] [Revised: 06/10/2024] [Accepted: 07/16/2024] [Indexed: 08/12/2024]
Abstract
Mouse FOXA1 and GATA4 are prototypes of pioneer factors, initiating liver cell development by binding to the N1 nucleosome in the enhancer of the ALB1 gene. Using cryoelectron microscopy (cryo-EM), we determined the structures of the free N1 nucleosome and its complexes with FOXA1 and GATA4, both individually and in combination. We found that the DNA-binding domains of FOXA1 and GATA4 mainly recognize the linker DNA and an internal site in the nucleosome, respectively, whereas their intrinsically disordered regions interact with the acidic patch on histone H2A-H2B. FOXA1 efficiently enhances GATA4 binding by repositioning the N1 nucleosome. In vivo DNA editing and bioinformatics analyses suggest that the co-binding mode of FOXA1 and GATA4 plays important roles in regulating genes involved in liver cell functions. Our results reveal the mechanism whereby FOXA1 and GATA4 cooperatively bind to the nucleosome through nucleosome repositioning, opening chromatin by bending linker DNA and obstructing nucleosome packing.
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Furong Huang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Iris Zhu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY 10003, USA
| | - Dan Shi
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Development Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qianben Wang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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9
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Saotome M, Poduval D, Grimm SA, Nagornyuk A, Gunarathna S, Shimbo T, Wade P, Takaku M. Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4. Nucleic Acids Res 2024; 52:3607-3622. [PMID: 38281186 PMCID: PMC11039999 DOI: 10.1093/nar/gkae025] [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: 05/27/2023] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Biologically precise enhancer licensing by lineage-determining transcription factors enables activation of transcripts appropriate to biological demand and prevents deleterious gene activation. This essential process is challenged by the millions of matches to most transcription factor binding motifs present in many eukaryotic genomes, leading to questions about how transcription factors achieve the exquisite specificity required. The importance of chromatin remodeling factors to enhancer activation is highlighted by their frequent mutation in developmental disorders and in cancer. Here, we determine the roles of CHD4 in enhancer licensing and maintenance in breast cancer cells and during cellular reprogramming. In unchallenged basal breast cancer cells, CHD4 modulates chromatin accessibility. Its depletion leads to redistribution of transcription factors to previously unoccupied sites. During cellular reprogramming induced by the pioneer factor GATA3, CHD4 activity is necessary to prevent inappropriate chromatin opening. Mechanistically, CHD4 promotes nucleosome positioning over GATA3 binding motifs to compete with transcription factor-DNA interaction. We propose that CHD4 acts as a chromatin proof-reading enzyme that prevents unnecessary gene expression by editing chromatin binding activities of transcription factors.
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Affiliation(s)
- Mika Saotome
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Deepak B Poduval
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Sara A Grimm
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Aerica Nagornyuk
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Sakuntha Gunarathna
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Takashi Shimbo
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Motoki Takaku
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
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10
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Dai S, Guo L, Dey R, Guo M, Zhang X, Bates D, Cayford J, Jiang L, Wei H, Chen Z, Zhang Y, Chen L, Chen Y. Structural insights into the HDAC4-MEF2A-DNA complex and its implication in long-range transcriptional regulation. Nucleic Acids Res 2024; 52:2711-2723. [PMID: 38281192 PMCID: PMC10954479 DOI: 10.1093/nar/gkae036] [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: 07/27/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
Class IIa Histone deacetylases (HDACs), including HDAC4, 5, 7 and 9, play key roles in multiple important developmental and differentiation processes. Recent studies have shown that class IIa HDACs exert their transcriptional repressive function by interacting with tissue-specific transcription factors, such as members of the myocyte enhancer factor 2 (MEF2) family of transcription factors. However, the molecular mechanism is not well understood. In this study, we determined the crystal structure of an HDAC4-MEF2A-DNA complex. This complex adopts a dumbbell-shaped overall architecture, with a 2:4:2 stoichiometry of HDAC4, MEF2A and DNA molecules. In the complex, two HDAC4 molecules form a dimer through the interaction of their glutamine-rich domain (GRD) to form the stem of the 'dumbbell'; while two MEF2A dimers and their cognate DNA molecules are bridged by the HDAC4 dimer. Our structural observations were then validated using biochemical and mutagenesis assays. Further cell-based luciferase reporter gene assays revealed that the dimerization of HDAC4 is crucial in its ability to repress the transcriptional activities of MEF2 proteins. Taken together, our findings not only provide the structural basis for the assembly of the HDAC4-MEF2A-DNA complex but also shed light on the molecular mechanism of HDAC4-mediated long-range gene regulation.
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Affiliation(s)
- Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410078, China
| | - Liang Guo
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
| | - Raja Dey
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiangqian Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Darren Bates
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
| | - Justin Cayford
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Longying Jiang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhuchu Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ye Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lin Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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11
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Zhang Q, Wang Q, Chen H, Chen L, Wang F, Gu Z, Shi G, Liu L, Ding Z. Lignin-degrading enzyme production was enhanced by the novel transcription factor Ptf6 in synergistic microbial co-culture. Microbiol Res 2024; 280:127575. [PMID: 38147744 DOI: 10.1016/j.micres.2023.127575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/28/2023]
Abstract
Synergistic microbial co-culture has been an efficient and energy-saving strategy to produce lignin-degrading enzymes (LDEs), including laccase, manganese peroxidase, and versatile peroxidase. However, the regulatory mechanism of microbial co-culture is still unclear. Herein, the extracellular LDE activities of four white-rot fungi were significantly increased by 88-544% over monoculture levels when co-cultured with Rhodotorula mucilaginosa. Ptf6 was demonstrated from the 9 million Y1H clone library to be a shared GATA transcription factor in the four fungi, and could directly bind to the laccase gene promoter. Ptf6 exists in two alternatively spliced isoforms under monoculture, namely Ptf6-α (1078 amino acids) containing Cys2/Cys2-type zinc finger and Ptf6-β (963 amino acids) lacking the complete domain. Ptf6 responded to co-culture by up-regulation of both its own transcripts and the proportion of Ptf6-α. Ptf6-α positively activated the production of most LDE isoenzymes and bound to four GATA motifs on the LDEs' promoter with different affinities. Moreover, Ptf6-regulation mechanism can be applicable to a variety of microbial co-culture systems. This study lays a theoretical foundation for further improving LDEs production and providing an efficient way to enhance the effects of biological and enzymatic pretreatment for lignocellulosic biomass conversion.
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Affiliation(s)
- Qi Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Qiong Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Haixiu Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Lei Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Feng Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zhenghua Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Guiyang Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhongyang Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China.
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12
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Qiang Z, Jubber I, Lloyd K, Cumberbatch M, Griffin J. Gene of the month: GATA3. J Clin Pathol 2023; 76:793-797. [PMID: 37726118 DOI: 10.1136/jcp-2023-209017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/21/2023]
Abstract
GATA binding protein 3 (GATA3) is a zinc-finger pioneer transcription factor involved in diverse processes. GATA3 regulates gene expression through binding nucleosomal DNA and facilitating chromatin remodelling. Post-translational modifications modulate its activity. During development, GATA3 plays a key role in cell differentiation. Mutations in GATA3 are linked to breast and bladder cancer. GATA3 expression is a feature of the luminal subtype of bladder cancer and has implications for immune status and therapeutic response. It also has clinical relevance in squamous cell carcinomas and soft tissue sarcomas. This paper reviews the structure and function of GATA3, its role in cancer and its use and pitfalls as an immunohistochemical marker.
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Affiliation(s)
- Zekai Qiang
- Academic Urology Unit, The University of Sheffield, Sheffield, UK
| | - Ibrahim Jubber
- Academic Urology Unit, The University of Sheffield, Sheffield, UK
| | - Kirsty Lloyd
- Department of Histopathology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | | | - Jon Griffin
- Academic Urology Unit, The University of Sheffield, Sheffield, UK
- Department of Histopathology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
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13
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Jung MM, Shen S, Botten GA, Olender T, Katsumura KR, Johnson KD, Soukup AA, Liu P, Zhang Q, Jensvold ZD, Lewis PW, Beagrie RA, Low JK, Yang L, Mackay JP, Godley LA, Brand M, Xu J, Keles S, Bresnick EH. Pathogenic human variant that dislocates GATA2 zinc fingers disrupts hematopoietic gene expression and signaling networks. J Clin Invest 2023; 133:e162685. [PMID: 36809258 PMCID: PMC10065080 DOI: 10.1172/jci162685] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Although certain human genetic variants are conspicuously loss of function, decoding the impact of many variants is challenging. Previously, we described a patient with leukemia predisposition syndrome (GATA2 deficiency) with a germline GATA2 variant that inserts 9 amino acids between the 2 zinc fingers (9aa-Ins). Here, we conducted mechanistic analyses using genomic technologies and a genetic rescue system with Gata2 enhancer-mutant hematopoietic progenitor cells to compare how GATA2 and 9aa-Ins function genome-wide. Despite nuclear localization, 9aa-Ins was severely defective in occupying and remodeling chromatin and regulating transcription. Variation of the inter-zinc finger spacer length revealed that insertions were more deleterious to activation than repression. GATA2 deficiency generated a lineage-diverting gene expression program and a hematopoiesis-disrupting signaling network in progenitors with reduced granulocyte-macrophage colony-stimulating factor (GM-CSF) and elevated IL-6 signaling. As insufficient GM-CSF signaling caused pulmonary alveolar proteinosis and excessive IL-6 signaling promoted bone marrow failure and GATA2 deficiency patient phenotypes, these results provide insight into mechanisms underlying GATA2-linked pathologies.
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Affiliation(s)
- Mabel Minji Jung
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Siqi Shen
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Giovanni A. Botten
- Children’s Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Thomas Olender
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute–General Hospital, Ottawa, Ontario, Canada
| | - Koichi R. Katsumura
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Kirby D. Johnson
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Alexandra A. Soukup
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Peng Liu
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Qingzhou Zhang
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute–General Hospital, Ottawa, Ontario, Canada
| | - Zena D. Jensvold
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Peter W. Lewis
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Robert A. Beagrie
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jason K.K. Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Lihua Yang
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Lucy A. Godley
- Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Marjorie Brand
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Jian Xu
- Children’s Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sunduz Keles
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
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14
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Saotome M, Poduval DB, Grimm SA, Nagornyuk A, Gunarathna S, Shimbo T, Wade PA, Takaku M. Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4. RESEARCH SQUARE 2023:rs.3.rs-2587918. [PMID: 36993416 PMCID: PMC10055546 DOI: 10.21203/rs.3.rs-2587918/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Biologically precise enhancer licensing by lineage-determining transcription factors enables activation of transcripts appropriate to biological demand and prevents deleterious gene activation. This essential process is challenged by the millions of matches to most transcription factor binding motifs present in many eukaryotic genomes, leading to questions about how transcription factors achieve the exquisite specificity required. The importance of chromatin remodeling factors to enhancer activation is highlighted by their frequent mutation in developmental disorders and in cancer. Here we determine the roles of CHD4 to enhancer licensing and maintenance in breast cancer cells and during cellular reprogramming. In unchallenged basal breast cancer cells, CHD4 modulates chromatin accessibility at transcription factor binding sites; its depletion leads to altered motif scanning and redistribution of transcription factors to sites not previously occupied. During GATA3-mediated cellular reprogramming, CHD4 activity is necessary to prevent inappropriate chromatin opening and enhancer licensing. Mechanistically, CHD4 competes with transcription factor-DNA interaction by promoting nucleosome positioning over binding motifs. We propose that CHD4 acts as a chromatin proof-reading enzyme that prevents inappropriate gene expression by editing binding site selection by transcription factors.
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Affiliation(s)
- Mika Saotome
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Deepak Balakrishnan Poduval
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Sara A. Grimm
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Aerica Nagornyuk
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Sakuntha Gunarathna
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Takashi Shimbo
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
- Current address: StemRIM Institute of Regeneration-Inducing Medicine, Osaka University, Suita, Osaka, 5650871, Japan
| | - Paul A. Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Motoki Takaku
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
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15
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Lee SH, Kim JH, Seong Y, Moon JS, Kim Y, Shin BY, Shin JS, Park J, Park CS, Lee SK. Intranasal administration of nucleus-deliverable GATA3-TMD alleviates the symptoms of allergic asthma. Biochem Biophys Res Commun 2023; 640:32-39. [PMID: 36502629 DOI: 10.1016/j.bbrc.2022.11.095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022]
Abstract
Although the T helper 2 (Th2) subset is a critical player in the humoral immune response to extracellular parasites and suppression of Th1-mediated inflammation, Th2 cells have been implicated in allergic inflammatory diseases such as asthma, allergic rhinitis, and atopic dermatitis. GATA binding protein 3 (GATA3) is a primary transcription factor that mediates Th2 differentiation and secretion of Th2 cytokines, including IL-4, IL-5, and IL-13. Here, a nucleus-deliverable form of GATA3-transcription modulation domain (TMD) (ndG3-TMD) was generated using Hph-1 human protein transduction domain (PTD) to modulate the transcriptional function of endogenous GATA3 without genetic manipulation. ndG3-TMD was shown to be efficiently delivered into the cell nucleus quickly without affecting cell viability or intracellular signaling events for T cell activation. ndG3-TMD exhibited a specific inhibitory function for the endogenous GATA3-mediated transcription, such as Th2 cell differentiation and Th2-type cytokine production. Intranasal administration of ndG3-TMD significantly alleviated airway hyperresponsiveness, infiltration of immune cells, and serum IgE level in an OVA-induced mouse model of asthma. Also, Th2 cytokine secretion by the splenocytes isolated from the ndG3-TMD-treated mice substantially decreased. Our results suggest that ndG3-TMD can be a new therapeutic reagent to suppress Th2-mediated allergic diseases through intranasal delivery.
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Affiliation(s)
- Su-Hyeon Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03772, Republic of Korea
| | - Jung-Ho Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03772, Republic of Korea; Good T Cells, Inc., Seoul, 03929, Republic of Korea
| | - Yekyung Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03772, Republic of Korea
| | - Jae-Seung Moon
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03772, Republic of Korea
| | - Yuna Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03772, Republic of Korea
| | - Bo-Young Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03772, Republic of Korea
| | - Jin-Su Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03772, Republic of Korea
| | - Jiyoon Park
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03772, Republic of Korea
| | - Choon-Sik Park
- Genome Research Center for Allergy and Respiratory Disease, Soonchunhyang University Hospital, Bucheon, 14584, Republic of Korea
| | - Sang-Kyou Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03772, Republic of Korea; Good T Cells, Inc., Seoul, 03929, Republic of Korea.
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16
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Geng X, Wang C, Gao X, Chowdhury P, Weiss J, Villegas JA, Saed B, Perera T, Hu Y, Reneau J, Sverdlov M, Wolfe A, Brown N, Harms P, Bailey NG, Inamdar K, Hristov AC, Tejasvi T, Montes J, Barrionuevo C, Taxa L, Casavilca S, de Pádua Covas Lage JLA, Culler HF, Pereira J, Runge JS, Qin T, Tsoi LC, Hong HS, Zhang L, Lyssiotis CA, Ohe R, Toubai T, Zevallos-Morales A, Murga-Zamalloa C, Wilcox RA. GATA-3 is a proto-oncogene in T-cell lymphoproliferative neoplasms. Blood Cancer J 2022; 12:149. [PMID: 36329027 PMCID: PMC9633835 DOI: 10.1038/s41408-022-00745-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Neoplasms originating from thymic T-cell progenitors and post-thymic mature T-cell subsets account for a minority of lymphoproliferative neoplasms. These T-cell derived neoplasms, while molecularly and genetically heterogeneous, exploit transcription factors and signaling pathways that are critically important in normal T-cell biology, including those implicated in antigen-, costimulatory-, and cytokine-receptor signaling. The transcription factor GATA-3 regulates the growth and proliferation of both immature and mature T cells and has recently been implicated in T-cell neoplasms, including the most common mature T-cell lymphoma observed in much of the Western world. Here we show that GATA-3 is a proto-oncogene across the spectrum of T-cell neoplasms, including those derived from T-cell progenitors and their mature progeny, and further define the transcriptional programs that are GATA-3 dependent, which include therapeutically targetable gene products. The discovery that p300-dependent acetylation regulates GATA-3 mediated transcription by attenuating DNA binding has novel therapeutic implications. As most patients afflicted with GATA-3 driven T-cell neoplasms will succumb to their disease within a few years of diagnosis, these findings suggest opportunities to improve outcomes for these patients.
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Affiliation(s)
- Xiangrong Geng
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Chenguang Wang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Xin Gao
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Pinki Chowdhury
- Department of Pediatrics, Dayton Children's Hospital, Wright State University Boonshoft School of Medicine, Dayton, OH, USA
| | - Jonathan Weiss
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - José A Villegas
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Badeia Saed
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Thilini Perera
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Ying Hu
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - John Reneau
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Maria Sverdlov
- Department of Pathology, University of Illinois Chicago, Chicago, IL, USA
| | - Ashley Wolfe
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Noah Brown
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Paul Harms
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Nathanael G Bailey
- Division of Hematopathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kedar Inamdar
- Department of Pathology, Henry Ford Hospital, Detroit, MI, USA
| | - Alexandra C Hristov
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Jaime Montes
- Department of Pathology, Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Peru
| | - Carlos Barrionuevo
- Department of Pathology, Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Peru
| | - Luis Taxa
- Department of Pathology, Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Peru
| | - Sandro Casavilca
- Department of Pathology, Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Peru
| | - J Luís Alberto de Pádua Covas Lage
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, Sao Paulo University, Laboratory of Medical Investigation 31 in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology, Sao Paulo, Brazil
| | - Hebert Fabrício Culler
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, Sao Paulo University, Laboratory of Medical Investigation 31 in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology, Sao Paulo, Brazil
| | - Juliana Pereira
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, Sao Paulo University, Non-Hodgkin's Lymphomas and Histiocytic Disorders, Sao Paulo, Brazil
| | - John S Runge
- Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Hanna S Hong
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Rintaro Ohe
- Department of Pathology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Tomomi Toubai
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University of Medicine, Yamagata, Japan
| | | | | | - Ryan A Wilcox
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA.
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17
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Ghoshdastidar D, Bansal M. Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif. Biophys J 2022; 121:3987-4000. [PMID: 35978548 PMCID: PMC9674967 DOI: 10.1016/j.bpj.2022.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/02/2022] Open
Abstract
Selective gene regulation is mediated by recognition of specific DNA sequences by transcription factors (TFs). The extremely challenging task of searching out specific cognate DNA binding sites among several million putative sites within the eukaryotic genome is achieved by complex molecular recognition mechanisms. Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. To unravel the extent to which DNA flexibility modulates TF binding, in this study, we employed experimentally guided molecular dynamics simulations of ternary complex of closely related Hox heterodimers Exd-Ubx and Exd-Scr with DNA. Results demonstrate that flexibility signatures embedded in the flanking sequences impact TF binding at the cognate binding site. A DNA sequence has intrinsic shape and flexibility features. While shape features are localized, our analyses reveal that flexibility features of the flanking sequences percolate several basepairs and allosterically modulate TF binding at the core. We also show that lack of flexibility in the motif context can render the cognate site resistant to protein-induced shape changes and subsequently lower TF binding affinity. Overall, this study suggests that flexibility-guided DNA shape, and not merely the static shape, is a key unexplored component of the complex DNA-TF recognition code.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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18
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Cuartero S, Stik G, Stadhouders R. Three-dimensional genome organization in immune cell fate and function. Nat Rev Immunol 2022; 23:206-221. [PMID: 36127477 DOI: 10.1038/s41577-022-00774-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Immune cell development and activation demand the precise and coordinated control of transcriptional programmes. Three-dimensional (3D) organization of the genome has emerged as an important regulator of chromatin state, transcriptional activity and cell identity by facilitating or impeding long-range genomic interactions among regulatory elements and genes. Chromatin folding thus enables cell type-specific and stimulus-specific transcriptional responses to extracellular signals, which are essential for the control of immune cell fate, for inflammatory responses and for generating a diverse repertoire of antigen receptor specificities. Here, we review recent findings connecting 3D genome organization to the control of immune cell differentiation and function, and discuss how alterations in genome folding may lead to immune dysfunction and malignancy.
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Affiliation(s)
- Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain. .,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - Grégoire Stik
- Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands. .,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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19
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Huang P, Peslak SA, Ren R, Khandros E, Qin K, Keller CA, Giardine B, Bell HW, Lan X, Sharma M, Horton JR, Abdulmalik O, Chou ST, Shi J, Crossley M, Hardison RC, Cheng X, Blobel GA. HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription. Nat Genet 2022; 54:1417-1426. [PMID: 35941187 PMCID: PMC9940634 DOI: 10.1038/s41588-022-01152-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 07/05/2022] [Indexed: 02/02/2023]
Abstract
The fetal-to-adult switch in hemoglobin production is a model of developmental gene control with relevance to the treatment of hemoglobinopathies. The expression of transcription factor BCL11A, which represses fetal β-type globin (HBG) genes in adult erythroid cells, is predominantly controlled at the transcriptional level but the underlying mechanism is unclear. We identify HIC2 as a repressor of BCL11A transcription. HIC2 and BCL11A are reciprocally expressed during development. Forced expression of HIC2 in adult erythroid cells inhibits BCL11A transcription and induces HBG expression. HIC2 binds to erythroid BCL11A enhancers to reduce chromatin accessibility and binding of transcription factor GATA1, diminishing enhancer activity and enhancer-promoter contacts. DNA-binding and crystallography studies reveal direct steric hindrance as one mechanism by which HIC2 inhibits GATA1 binding at a critical BCL11A enhancer. Conversely, loss of HIC2 in fetal erythroblasts increases enhancer accessibility, GATA1 binding and BCL11A transcription. HIC2 emerges as an evolutionarily conserved regulator of hemoglobin switching via developmental control of BCL11A.
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Affiliation(s)
- Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Scott A Peslak
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eugene Khandros
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kunhua Qin
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Genomics Research Incubator, Pennsylvania State University, University Park, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Henry W Bell
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Xianjiang Lan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malini Sharma
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stella T Chou
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Junwei Shi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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20
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DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers. Nat Genet 2022; 54:613-624. [PMID: 35551305 DOI: 10.1038/s41588-022-01048-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/08/2022] [Indexed: 02/06/2023]
Abstract
Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood, and de novo enhancer design has been challenging. Here, we built a deep-learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. The model learned relevant TF motifs and higher-order syntax rules, including functionally nonequivalent instances of the same TF motif that are determined by motif-flanking sequence and intermotif distances. We validated these rules experimentally and demonstrated that they can be generalized to humans by testing more than 40,000 wildtype and mutant Drosophila and human enhancers. Finally, we designed and functionally validated synthetic enhancers with desired activities de novo.
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21
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Transcriptome-wide subtyping of pediatric and adult T cell acute lymphoblastic leukemia in an international study of 707 cases. Proc Natl Acad Sci U S A 2022; 119:e2120787119. [PMID: 35385357 PMCID: PMC9169777 DOI: 10.1073/pnas.2120787119] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We provide transcriptomic insights into differences between pediatric and adult T cell acute lymphoblastic leukemia (T-ALL) patients through an international collaborative effort integrating RNA-sequencing data of 707 patients. Ten subtypes were identified, each characterized by distinct gene mutation profiles and dysregulated expression signatures of leukemogenic factors, and associated with T cell development stages. Adult T-ALL tends to have characteristics of early T cell precursor ALL, mostly corresponding to the mixed phenotype acute leukemia, whereas pediatric T-ALL shows a wide spectrum of aberrant molecular features, from early T cell precursor to mature T cell compartments. Our findings have important implications for disease mechanism of T-ALL that differs between pediatric and adult patients, facilitating further refined targeted therapy. T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy of T cell progenitors, known to be a heterogeneous disease in pediatric and adult patients. Here we attempted to better understand the disease at the molecular level based on the transcriptomic landscape of 707 T-ALL patients (510 pediatric, 190 adult patients, and 7 with unknown age; 599 from published cohorts and 108 newly investigated). Leveraging the information of gene expression enabled us to identify 10 subtypes (G1–G10), including the previously undescribed one characterized by GATA3 mutations, with GATA3R276Q capable of affecting lymphocyte development in zebrafish. Through associating with T cell differentiation stages, we found that high expression of LYL1/LMO2/SPI1/HOXA (G1–G6) might represent the early T cell progenitor, pro/precortical/cortical stage with a relatively high age of disease onset, and lymphoblasts with TLX3/TLX1 high expression (G7–G8) could be blocked at the cortical/postcortical stage, while those with high expression of NKX2-1/TAL1/LMO1 (G9–G10) might correspond to cortical/postcortical/mature stages of T cell development. Notably, adult patients harbored more cooperative mutations among epigenetic regulators, and genes involved in JAK-STAT and RAS signaling pathways, with 44% of patients aged 40 y or above in G1 bearing DNMT3A/IDH2 mutations usually seen in acute myeloid leukemia, suggesting the nature of mixed phenotype acute leukemia.
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22
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Liu J, Lin F, Wang X, Li C, Qi Q. GATA binding protein 5-mediated transcriptional activation of transmembrane protein 100 suppresses cell proliferation, migration and epithelial-to-mesenchymal transition in prostate cancer DU145 cells. Bioengineered 2022; 13:7972-7983. [PMID: 35358005 PMCID: PMC9162018 DOI: 10.1080/21655979.2021.2018979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It has been reported that transmembrane protein 100 (TMEM100) acts as a tumor regulator in several types of cancers. However, whether the expression of TMEM100 is associated with the development and prognosis of prostate cancer (PCa) remains elusive. Therefore, the present study aimed to uncover the role of GATA binding protein 5 (GATA5)-mediated activation of TMEM100 in the proliferation, migration and epithelial-to-mesenchymal transition (EMT) of PCa cells. The expressions of TMEM100 and GATA5 in PCa patients were analyzed by the GEPIA database. The binding site of GATA5 and TMEM100 promoter was predicted by the JASPAR database. Expressions of TMEM100 and GATA5 in PCa cells were detected by qRT-PCR and Western blot analysis. Cell Counting Kit 8 and colony formation assays were performed to measure cell proliferation. In addition, cell migration, invasion and the expression of EMT-associated proteins were evaluated using wound healing, transwell assay and Western blotting assays, respectively. The bioinformatics analysis revealed that TMEM100 was downregulated in PCa and was associated with overall survival of PCa. In addition, TMEM10 overexpression attenuated cell proliferation, migration, invasion and EMT in PCa cells. The interaction between TMEM100 and GATA5 was verified using dual luciferase reporter and chromatin immunoprecipitation assays. Furthermore, the results showed that GATA5 was downregulated and GATA5 silencing reversed the inhibitory effects of TMEM10 on PCa cells. Overall, the current study suggested that the GATA5-mediated transcriptional activation of TMEM100 could affect the behavior of PCa cells and was associated with poor prognosis in PCa.
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Affiliation(s)
- Jiaolin Liu
- Department of Urology, The Central Hospital of Linyi, Linyi, Shandong, China
| | - Fanlu Lin
- Department of Urology, The Central Hospital of Linyi, Linyi, Shandong, China
| | - Xin Wang
- Department of Urology, Linyi People's Hospital, Linyi, Shandong, China
| | - Chaopeng Li
- Department of Urology, The Central Hospital of Linyi, Linyi, Shandong, China
| | - Qiangyuan Qi
- Department of Urology, The Central Hospital of Linyi, Linyi, Shandong, China
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23
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Vanaja A, Yella VR. Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes. ACS OMEGA 2022; 7:5657-5669. [PMID: 35224327 PMCID: PMC8867553 DOI: 10.1021/acsomega.1c04603] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/27/2022] [Indexed: 05/02/2023]
Abstract
The eukaryotic transcription is orchestrated from a chunk of the DNA region stated as the core promoter. Multifarious and punctilious core promoter signals, viz., TATA-box, Inr, BREs, and Pause Button, are associated with a subset of genes and regulate their spatiotemporal expression. However, the core promoter architecture linked with these signals has not been investigated exhaustively for several species. In this study, we attempted to envisage the adaptive binding landscape of the transcription initiation machinery as a function of DNA structure. To this end, we deployed a set of k-mer based DNA structural estimates and regular expression models derived from experiments, molecular dynamic simulations, and theoretical frameworks, and high-throughout promoter data sets retrieved from the eukaryotic promoter database. We categorized protein-coding gene core promoters based on characteristic motifs at precise locations and analyzed the B-DNA structural properties and non-B-DNA structural motifs for 15 different eukaryotic genomes. We observed that Inr, BREd, and no-motif classes display common patterns of DNA sequence and structural environment. TATA-containing, BREu, and Pause Button classes show a deviant behavior with the TATA class displaying varied axial and twisting flexibility while BREu and Pause Button leaned toward G-quadruplex motif enrichment. Intriguingly, DNA meltability and shape signals are conserved irrespective of the presence or absence of distinct core promoter motifs in the majority of species. Altogether, here we delineated the conserved DNA structural signals associated with several promoter classes that may contribute to the chromatin configuration, orchestration of transcription machinery, and DNA duplex melting during the transcription process.
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Affiliation(s)
- Akkinepally Vanaja
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
- KL
College of Pharmacy, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
| | - Venkata Rajesh Yella
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
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24
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Singh P, Bhadada SK, Dahiya D, Saikia UN, Arya AK, Sachdeva N, Kaur J, Behera A, Brandi ML, Rao SD. GCM2 Silencing in Parathyroid Adenoma Is Associated With Promoter Hypermethylation and Gain of Methylation on Histone 3. J Clin Endocrinol Metab 2021; 106:e4084-e4096. [PMID: 34077544 PMCID: PMC8475237 DOI: 10.1210/clinem/dgab374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Indexed: 02/06/2023]
Abstract
CONTEXT Glial cells missing 2 (GCM2), a zinc finger-transcription factor, is essentially required for the development of the parathyroid glands. OBJECTIVE We sought to identify whether the epigenetic alterations in GCM2 transcription are involved in the pathogenesis of sporadic parathyroid adenoma. In addition, we examined the association between promoter methylation and histone modifications with disease indices. METHODS Messenger RNA (mRNA) and protein expression of GCM2 were analyzed by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry in 33 adenomatous and 10 control parathyroid tissues. DNA methylation and histone methylation/acetylation of the GCM2 promoter were measured by bisulfite sequencing and chromatin immunoprecipitation-qPCR. Additionally, we investigated the role of epigenetic modifications on GCM2 and DNA methyltransferase 1 (DNMT1) expression in parathyroid (PTH)-C1 cells by treating with 5-aza-2'-deoxycytidine (DAC) and BRD4770 and assessed for GCM2 mRNA and DNMT1 protein levels. RESULTS mRNA and protein expression of GCM2 were lower in sporadic adenomatous than in control parathyroid tissues. This reduction correlated with hypermethylation (P < .001) and higher H3K9me3 levels in the GCM2 promoter (P < .04) in adenomas. In PTH-C1 cells, DAC treatment resulted in increased GCM2 transcription and decreased DNMT1 protein expression, while cells treated with the BRD4770 showed reduced H3K9me3 levels but a nonsignificant change in GCM2 transcription. CONCLUSION These findings suggest the concurrent association of promoter hypermethylation and higher H3K9me3 with the repression of GCM2 expression in parathyroid adenomas. Treatment with DAC restored GCM2 expression in PTH-C1 cells. Our results showed a possible epigenetic landscape in the tumorigenesis of parathyroid adenoma and also that DAC may be a promising avenue of research for parathyroid adenoma therapeutics.
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Affiliation(s)
- Priyanka Singh
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Sanjay Kumar Bhadada
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Divya Dahiya
- Department of General Surgery, PGIMER, Chandigarh, 160012, India
| | | | - Ashutosh Kumar Arya
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Naresh Sachdeva
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Jyotdeep Kaur
- Department of Biochemistry, PGIMER, Chandigarh, 160012, India
| | - Arunanshu Behera
- Department of General Surgery, PGIMER, Chandigarh, 160012, India
| | - Maria Luisa Brandi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50121, Italy
| | - Sudhaker Dhanwada Rao
- Bone and Mineral Research Laboratory, Henry Ford Hospital, Detroit, Michigan 48202, USA
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25
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John E, Singh KB, Oliver RP, Tan K. Transcription factor control of virulence in phytopathogenic fungi. MOLECULAR PLANT PATHOLOGY 2021; 22:858-881. [PMID: 33973705 PMCID: PMC8232033 DOI: 10.1111/mpp.13056] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Karam B. Singh
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern AustraliaAustralia
| | - Richard P. Oliver
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kar‐Chun Tan
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
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26
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Kagawa W, Kurumizaka H. Structural basis for DNA sequence recognition by pioneer factors in nucleosomes. Curr Opin Struct Biol 2021; 71:59-64. [PMID: 34218163 DOI: 10.1016/j.sbi.2021.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/12/2021] [Indexed: 12/20/2022]
Abstract
Most of the genomic DNA in eukaryotes is bound to histone complexes, which hinders transcription factors from accessing their target DNA sequences. Here, we discuss recent structural insights into the mechanisms by which pioneer factors, an emerging class of transcription factors, can recognize DNA motifs located on the nucleosome surface.
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Affiliation(s)
- Wataru Kagawa
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo, 191-8506, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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27
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Srivastava M, Kaplan MH. Transcription Factors in the Development and Pro-Allergic Function of Mast Cells. FRONTIERS IN ALLERGY 2021; 2:679121. [PMID: 35387064 PMCID: PMC8974754 DOI: 10.3389/falgy.2021.679121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Mast cells (MCs) are innate immune cells of hematopoietic origin localized in the mucosal tissues of the body and are broadly implicated in the pathogenesis of allergic inflammation. Transcription factors have a pivotal role in the development and differentiation of mast cells in response to various microenvironmental signals encountered in the resident tissues. Understanding the regulation of mast cells by transcription factors is therefore vital for mechanistic insights into allergic diseases. In this review we summarize advances in defining the transcription factors that impact the development of mast cells throughout the body and in specific tissues, and factors that are involved in responding to the extracellular milieu. We will further describe the complex networks of transcription factors that impact mast cell physiology and expansion during allergic inflammation and functions from degranulation to cytokine secretion. As our understanding of the heterogeneity of mast cells becomes more detailed, the contribution of specific transcription factors in mast cell-dependent functions will potentially offer new pathways for therapeutic targeting.
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Affiliation(s)
- Mansi Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University, Indianapolis, IN, United States
| | - Mark H. Kaplan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Mark H. Kaplan
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28
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Panigrahi A, O'Malley BW. Mechanisms of enhancer action: the known and the unknown. Genome Biol 2021; 22:108. [PMID: 33858480 PMCID: PMC8051032 DOI: 10.1186/s13059-021-02322-1] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs are the enhancers, the gene-distal cis-regulatory sequences that govern spatiotemporal and quantitative expression dynamics of target genes. Enhancers are widely believed to physically contact the target promoters to effect transcriptional activation. However, our understanding of the full complement of regulatory proteins and the definitive mechanics of enhancer action is incomplete. Here, we review recent findings to present some emerging concepts on enhancer action and also outline a set of outstanding questions.
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Affiliation(s)
- Anil Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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29
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Li J, Dai S, Chen X, Liang X, Qu L, Jiang L, Guo M, Zhou Z, Wei H, Zhang H, Chen Z, Chen L, Chen Y. Mechanism of forkhead transcription factors binding to a novel palindromic DNA site. Nucleic Acids Res 2021; 49:3573-3583. [PMID: 33577686 PMCID: PMC8034652 DOI: 10.1093/nar/gkab086] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 12/15/2022] Open
Abstract
Forkhead transcription factors bind a canonical consensus DNA motif, RYAAAYA (R = A/G, Y = C/T), as a monomer. However, the molecular mechanisms by which forkhead transcription factors bind DNA as a dimer are not well understood. In this study, we show that FOXO1 recognizes a palindromic DNA element DIV2, and mediates transcriptional regulation. The crystal structure of FOXO1/DIV2 reveals that the FOXO1 DNA binding domain (DBD) binds the DIV2 site as a homodimer. The wing1 region of FOXO1 mediates the dimerization, which enhances FOXO1 DNA binding affinity and complex stability. Further biochemical assays show that FOXO3, FOXM1 and FOXI1 also bind the DIV2 site as homodimer, while FOXC2 can only bind this site as a monomer. Our structural, biochemical and bioinformatics analyses not only provide a novel mechanism by which FOXO1 binds DNA as a homodimer, but also shed light on the target selection of forkhead transcription factors.
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Affiliation(s)
- Jun Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaojuan Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xujun Liang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lingzhi Qu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Longying Jiang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhan Zhou
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Huajun Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhuchu Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lin Chen
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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30
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Biophysical characterization of the complex between the iron-responsive transcription factor Fep1 and DNA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:501-512. [PMID: 33398461 DOI: 10.1007/s00249-020-01489-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/28/2020] [Accepted: 12/05/2020] [Indexed: 12/16/2022]
Abstract
Fep1 is an iron-responsive GATA-type transcriptional repressor present in numerous fungi. The DNA-binding domain of this protein is characterized by the presence of two zinc fingers of the Cys2-Cys2 type and a Cys-X5-Cys-X8-Cys-X2-Cys motif located between the two zinc fingers, that is involved in binding of a [2Fe-2S] cluster. In this work, biophysical characterization of the DNA-binding domain of Pichia pastoris Fep1 and of the complex of the protein with cognate DNA has been undertaken. The results obtained by analytical ultracentrifugation sedimentation velocity, small-angle X-ray scattering and differential scanning calorimetry indicate that Fep1 is a natively unstructured protein that is able to bind DNA forming 1:1 and 2:1 complexes more compact than the individual partners. Complex formation takes place independently of the presence of a stoichiometric [2Fe-2S] cluster, suggesting that the cluster may play a role in recruiting other protein(s) required for regulation of transcription in response to changes in intracellular iron levels.
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31
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Dai S, Li J, Zhang H, Chen X, Guo M, Chen Z, Chen Y. Structural Basis for DNA Recognition by FOXG1 and the Characterization of Disease-causing FOXG1 Mutations. J Mol Biol 2020; 432:6146-6156. [PMID: 33058871 DOI: 10.1016/j.jmb.2020.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/22/2020] [Accepted: 10/07/2020] [Indexed: 12/22/2022]
Abstract
Forkhead box G1 (FOXG1) is a transcription factor mainly expressed in the brain that plays a critical role in the development and regionalization of the forebrain. Aberrant expression of FOXG1 has implications in FOXG1 syndrome, a serious neurodevelopmental disorder. Here, we report the crystal structure of the FOXG1 DNA-binding domain (DBD) in complex with the forkhead consensus DNA site DBE2 at the resolution of 1.6 Å. FOXG1-DBD adopts a typical winged helix fold. Compared to those of other FOX-DBD/DBE2 structures, the N terminus, H3 helix and wing2 region of FOXG1-DBD exhibit differences in DNA recognition. The FOXG1-DBD wing2 region adopts a unique architecture composed of two β-strands that differs from all other known FOX-DBD wing2 folds. Mutation assays revealed that the disease-causing mutations within the FOXG1-DBD affect DNA binding, protein thermal stability, or both. Our report provides initial insight into how FOXG1 binds DNA and sheds light on how disease-causing mutations in FOXG1-DBD affect its DNA-binding ability.
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Affiliation(s)
- Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Huajun Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaojuan Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhuchu Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
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32
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Cascant-Lopez E, Crosthwaite SK, Johnson LJ, Harrison RJ. No Evidence That Homologs of Key Circadian Clock Genes Direct Circadian Programs of Development or mRNA Abundance in Verticillium dahliae. Front Microbiol 2020; 11:1977. [PMID: 33013740 PMCID: PMC7493669 DOI: 10.3389/fmicb.2020.01977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 07/27/2020] [Indexed: 01/24/2023] Open
Abstract
Many organisms harbor circadian clocks that promote their adaptation to the rhythmic environment. While a broad knowledge of the molecular mechanism of circadian clocks has been gained through the fungal model Neurospora crassa, little is known about circadian clocks in other fungi. N. crassa belongs to the same class as many important plant pathogens including the vascular wilt fungus Verticillium dahliae. We identified homologs of N. crassa clock proteins in V. dahliae, which showed high conservation in key protein domains. However, no evidence for an endogenous, free-running and entrainable rhythm was observed in the daily formation of conidia and microsclerotia. In N. crassa the frequency (frq) gene encodes a central clock protein expressed rhythmically and in response to light. In contrast, expression of Vdfrq is not light-regulated. Temporal gene expression profiling over 48 h in constant darkness and temperature revealed no circadian expression of key clock genes. Furthermore, RNA-seq over a 24 h time-course revealed no robust oscillations of clock-associated transcripts in constant darkness. Comparison of gene expression between wild-type V. dahliae and a ΔVdfrq mutant showed that genes involved in metabolism, transport and redox processes are mis-regulated in the absence of Vdfrq. In addition, VdΔfrq mutants display growth defects and reduced pathogenicity in a strain dependent manner. Our data indicate that if a circadian clock exists in Verticillium, it is based on alternative mechanisms such as post-transcriptional interactions of VdFRQ and the WC proteins or the components of a FRQ-less oscillator. Alternatively, it could be that whilst the original functions of the clock proteins have been maintained, in this species the interactions that generate robust rhythmicity have been lost or are only triggered when specific environmental conditions are met. The presence of conserved clock genes in genomes should not be taken as definitive evidence of circadian function.
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Affiliation(s)
| | | | - Louise J Johnson
- The School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Richard J Harrison
- Genetics, Genomics and Breeding, NIAB EMR, East Malling, United Kingdom.,National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
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33
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Tanaka H, Takizawa Y, Takaku M, Kato D, Kumagawa Y, Grimm SA, Wade PA, Kurumizaka H. Interaction of the pioneer transcription factor GATA3 with nucleosomes. Nat Commun 2020; 11:4136. [PMID: 32811816 PMCID: PMC7434886 DOI: 10.1038/s41467-020-17959-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 07/22/2020] [Indexed: 01/23/2023] Open
Abstract
During cellular reprogramming, the pioneer transcription factor GATA3 binds chromatin, and in a context-dependent manner directs local chromatin remodeling and enhancer formation. Here, we use high-resolution nucleosome mapping in human cells to explore the impact of the position of GATA motifs on the surface of nucleosomes on productive enhancer formation, finding productivity correlates with binding sites located near the nucleosomal dyad axis. Biochemical experiments with model nucleosomes demonstrate sufficiently stable transcription factor-nucleosome interaction to empower cryo-electron microscopy structure determination of the complex at 3.15 Å resolution. The GATA3 zinc fingers efficiently bind their target 5′-GAT-3′ sequences in the nucleosome when they are located in solvent accessible, consecutive major grooves without significant changes in nucleosome structure. Analysis of genomic loci bound by GATA3 during reprogramming suggests a correlation of recognition motif sequence and spacing that may distinguish productivity of new enhancer formation. GATA 3 functions as a pioneer factor during cellular reprogramming. Here the authors delineate nucleosome positioning relative to GATA3 binding motifs and describe the structure of a GATA3–nucleosome complex; providing insight into how a pioneer factor interacts with nucleosomes and catalyze their local remodelling to produce an accessible enhancer.
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Affiliation(s)
- Hiroki Tanaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Motoki Takaku
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA.,Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA
| | - Daiki Kato
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Laboratory for Drug Discovery, Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 MifukuIzunokuni-shi, Shizuoka, 410-2321, Japan
| | - Yusuke Kumagawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Sara A Grimm
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA.
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan. .,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
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34
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Dietlein F, Weghorn D, Taylor-Weiner A, Richters A, Reardon B, Liu D, Lander ES, Van Allen EM, Sunyaev SR. Identification of cancer driver genes based on nucleotide context. Nat Genet 2020; 52:208-218. [PMID: 32015527 PMCID: PMC7031046 DOI: 10.1038/s41588-019-0572-y] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 12/16/2019] [Indexed: 12/26/2022]
Abstract
Cancer genomes contain large numbers of somatic mutations but few of these mutations drive tumor development. Current approaches either identify driver genes on the basis of mutational recurrence or approximate the functional consequences of nonsynonymous mutations by using bioinformatic scores. Passenger mutations are enriched in characteristic nucleotide contexts, whereas driver mutations occur in functional positions, which are not necessarily surrounded by a particular nucleotide context. We observed that mutations in contexts that deviate from the characteristic contexts around passenger mutations provide a signal in favor of driver genes. We therefore developed a method that combines this feature with the signals traditionally used for driver-gene identification. We applied our method to whole-exome sequencing data from 11,873 tumor-normal pairs and identified 460 driver genes that clustered into 21 cancer-related pathways. Our study provides a resource of driver genes across 28 tumor types with additional driver genes identified according to mutations in unusual nucleotide contexts.
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Affiliation(s)
- Felix Dietlein
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
| | - Donate Weghorn
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Centre for Genomic Regulation, Barcelona, Spain
| | - Amaro Taylor-Weiner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - André Richters
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brendan Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Eric S Lander
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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35
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Abstract
Various strategies have been applied to replace the loss of cardiomyocytes in order to restore reduced cardiac function and prevent the progression of heart disease. Intensive research efforts in the field of cellular reprogramming and cell transplantation may eventually lead to efficient in vivo applications for the treatment of cardiac injuries, representing a novel treatment strategy for regenerative medicine. Modulation of cardiac transcription factor (TF) networks by chemical entities represents another viable option for therapeutic interventions. Comprehensive screening projects have revealed a number of molecular entities acting on molecular pathways highly critical for cellular lineage commitment and differentiation, including compounds targeting Wnt- and transforming growth factor beta (TGFβ)-signaling. Furthermore, previous studies have demonstrated that GATA4 and NKX2-5 are essential TFs in gene regulation of cardiac development and hypertrophy. For example, both of these TFs are required to fully activate mechanical stretch-responsive genes such as atrial natriuretic peptide and brain natriuretic peptide (BNP). We have previously reported that the compound 3i-1000 efficiently inhibited the synergy of the GATA4-NKX2-5 interaction. Cellular effects of 3i-1000 have been further characterized in a number of confirmatory in vitro bioassays, including rat cardiac myocytes and animal models of ischemic injury and angiotensin II-induced pressure overload, suggesting the potential for small molecule-induced cardioprotection.
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Affiliation(s)
- Mika J. Välimäki
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of PharmacyUniversity of HelsinkiHelsinki, Finland
| | - Heikki J. Ruskoaho
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of PharmacyUniversity of HelsinkiHelsinki, Finland
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36
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Kumar R, Kumar R, Tanwar P, Deo SVS, Mathur S, Agarwal U, Hussain S. Structural and conformational changes induced by missense variants in the zinc finger domains of GATA3 involved in breast cancer. RSC Adv 2020; 10:39640-39653. [PMID: 35515377 PMCID: PMC9057444 DOI: 10.1039/d0ra07786k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the main cancer in women having multiple receptor based tumour subtypes. Large scale genome sequencing studies of BC have identified several genes among which GATA3 is reported as a highly mutated gene followed by TP53 and PIK3CA. GATA3 is a crucial transcription factor, and was initially identified as a DNA-binding protein involved in the regulation of immune cell functions. Different missense mutations in the region of the DNA-binding domain of GATA3 are associated with BC and other neoplastic disorders. In this study, computational based approaches have been exploited to reveal associations of various mutations on structure, stability, conformation and function of GATA3. Our findings have suggested that, all analysed missense mutations were deleterious and highly pathogenic in nature. A molecular dynamics simulation study showed that all mutations led to structural destabilisation by reducing protein globularity and flexibility, by altering secondary structural configuration and decreasing protein ligand stability. Essential dynamics analysis indicated that mutations in GATA3 decreased protein mobility and increased its conformational instability. Furthermore, residue network analysis showed that the mutations affected the signal transduction of important residues that potentially influenced GATA3-DNA binding. The present study highlights the importance of different variants of GATA3 which have potential impact on neoplastic progression in breast cancer and may facilitate development of precise and personalized therapeutics. Mutations in the N- and C-finger domains of GATA3 lead to breast cancer.![]()
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Affiliation(s)
- Rakesh Kumar
- Dr B. R. A.-Institute Rotary Cancer Hospital
- All India Institute of Medical Sciences
- New Delhi
- India-110029
| | - Rahul Kumar
- Dr B. R. A.-Institute Rotary Cancer Hospital
- All India Institute of Medical Sciences
- New Delhi
- India-110029
| | - Pranay Tanwar
- Dr B. R. A.-Institute Rotary Cancer Hospital
- All India Institute of Medical Sciences
- New Delhi
- India-110029
| | - S. V. S. Deo
- Dr B. R. A.-Institute Rotary Cancer Hospital
- All India Institute of Medical Sciences
- New Delhi
- India-110029
| | - Sandeep Mathur
- Department of Pathology
- All India Institute of Medical Sciences
- New Delhi
- India-110029
| | - Usha Agarwal
- National Institute of Pathology
- New Delhi
- India-110029
| | - Showket Hussain
- Division of Molecular Oncology
- National Institute of Cancer Prevention and Research
- Noida
- India-201301
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37
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Cheng X, Zhao Y, Jiang Q, Yang J, Zhao W, Taylor IA, Peng YL, Wang D, Liu J. Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain. Nucleic Acids Res 2019; 47:4308-4318. [PMID: 30783673 PMCID: PMC6486541 DOI: 10.1093/nar/gkz113] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/10/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022] Open
Abstract
In rice, the critical regulator of the salicylic acid signalling pathway is OsWRKY45, a transcription factor (TF) of the WRKY TF family that functions by binding to the W-box of gene promoters, but the structural basis of OsWRKY45/W-box DNA recognition is unknown. Here, we show the crystal structure of the DNA binding domain of OsWRKY45 (OsWRKY45–DBD, i.e. the WRKY and zinc finger domain) in complex with a W-box DNA. Surprisingly, two OsWRKY45–DBD molecules exchange β4-β5 strands to form a dimer. The domain swapping occurs at the hinge region between the β3 and β4 strands, and is bridged and stabilized by zinc ion via coordinating residues from different chains. The dimer contains two identical DNA binding domains that interact with the major groove of W-box DNA. In addition to hydrophobic and direct hydrogen bonds, water mediated hydrogen bonds are also involved in base-specific interaction between protein and DNA. Finally, we discussed the cause and consequence of domain swapping of OsWRKY45–DBD, and based on our work and that of previous studies present a detailed mechanism of W-box recognition by WRKY TFs. This work reveals a novel dimerization and DNA-binding mode of WRKY TFs, and an intricate picture of the WRKY/W-box DNA recognition.
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Affiliation(s)
- Xiankun Cheng
- MOA Key Laboratory of Plant Pathology, joint international Research Laboratory of Crop Molecular Breeding, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yanxiang Zhao
- College of Plant Health and Medicine, and Key Lab of Integrated Crop Disease and Pest Management of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Qingshan Jiang
- MOA Key Laboratory of Plant Pathology, joint international Research Laboratory of Crop Molecular Breeding, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jun Yang
- MOA Key Laboratory of Plant Pathology, joint international Research Laboratory of Crop Molecular Breeding, College of Plant Protection, China Agricultural University, Beijing 100193, China.,State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Wensheng Zhao
- MOA Key Laboratory of Plant Pathology, joint international Research Laboratory of Crop Molecular Breeding, College of Plant Protection, China Agricultural University, Beijing 100193, China.,State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - You-Liang Peng
- MOA Key Laboratory of Plant Pathology, joint international Research Laboratory of Crop Molecular Breeding, College of Plant Protection, China Agricultural University, Beijing 100193, China.,State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Dongli Wang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Junfeng Liu
- MOA Key Laboratory of Plant Pathology, joint international Research Laboratory of Crop Molecular Breeding, College of Plant Protection, China Agricultural University, Beijing 100193, China
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38
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Nomura S, Takahashi H, Suzuki J, Kuwahara M, Yamashita M, Sawasaki T. Pyrrothiogatain acts as an inhibitor of GATA family proteins and inhibits Th2 cell differentiation in vitro. Sci Rep 2019; 9:17335. [PMID: 31758034 PMCID: PMC6874683 DOI: 10.1038/s41598-019-53856-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 11/04/2019] [Indexed: 12/19/2022] Open
Abstract
The transcription factor GATA3 is a master regulator that modulates T helper 2 (Th2) cell differentiation and induces expression of Th2 cytokines, such as IL-4, IL-5, and IL-13. Th2 cytokines are involved in the protective immune response against foreign pathogens, such as parasites. However, excessive production of Th2 cytokines results in type-2 allergic inflammation. Therefore, the application of a GATA3 inhibitor provides a new therapeutic strategy to regulate Th2 cytokine production. Here, we established a novel high-throughput screening system for an inhibitor of a DNA-binding protein, such as a transcription factor, and identified pyrrothiogatain as a novel inhibitor of GATA3 DNA-binding activity. Pyrrothiogatain inhibited the DNA-binding activity of GATA3 and other members of the GATA family. Pyrrothiogatain also inhibited the interaction between GATA3 and SOX4, suggesting that it interacts with the DNA-binding region of GATA3. Furthermore, pyrrothiogatain significantly suppressed Th2 cell differentiation, without impairing Th1 cell differentiation, and inhibited the expression and production of Th2 cytokines. Our results suggest that pyrrothiogatain regulates the differentiation and function of Th2 cells via inhibition of GATA3 DNA binding activity, which demonstrates the efficiency of our drug screening system for the development of novel small compounds that inhibit the DNA-binding activity of transcription factors.
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Affiliation(s)
- Shunsuke Nomura
- Proteo-Science Center (PROS), Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Hirotaka Takahashi
- Proteo-Science Center (PROS), Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Junpei Suzuki
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, 791-0295, Ehime, Japan
| | - Makoto Kuwahara
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, 791-0295, Ehime, Japan
| | - Masakatsu Yamashita
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, 791-0295, Ehime, Japan
| | - Tatsuya Sawasaki
- Proteo-Science Center (PROS), Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
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39
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Sun B, Chang HH, Salinger A, Tomita B, Bawadekar M, Holmes CL, Shelef MA, Weerapana E, Thompson PR, Ho IC. Reciprocal regulation of Th2 and Th17 cells by PAD2-mediated citrullination. JCI Insight 2019; 4:129687. [PMID: 31723060 DOI: 10.1172/jci.insight.129687] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 10/16/2019] [Indexed: 12/26/2022] Open
Abstract
Dysregulated citrullination, a unique form of posttranslational modification catalyzed by the peptidylarginine deiminases (PADs), has been observed in several human diseases, including rheumatoid arthritis. However, the physiological roles of PADs in the immune system are still poorly understood. Here, we report that global inhibition of citrullination enhances the differentiation of type 2 helper T (Th2) cells but attenuates the differentiation of Th17 cells, thereby increasing the susceptibility to allergic airway inflammation. This effect on Th cells is due to inhibition of PAD2 but not PAD4. Mechanistically, PAD2 directly citrullinates GATA3 and RORγt, 2 key transcription factors determining the fate of differentiating Th cells. Citrullination of R330 of GATA3 weakens its DNA binding ability, whereas citrullination of 4 arginine residues of RORγt strengthens its DNA binding. Finally, PAD2-deficient mice also display altered Th2/Th17 immune response and heightened sensitivity to allergic airway inflammation. Thus, our data highlight the potential and caveat of PAD2 as a therapeutic target of Th cell-mediated diseases.
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Affiliation(s)
- Bo Sun
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Hui-Hsin Chang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Ari Salinger
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Beverly Tomita
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | | | - Caitlyn L Holmes
- Department of Medicine and.,Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Miriam A Shelef
- Department of Medicine and.,William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - I-Cheng Ho
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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40
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Fernandez Garcia M, Moore CD, Schulz KN, Alberto O, Donague G, Harrison MM, Zhu H, Zaret KS. Structural Features of Transcription Factors Associating with Nucleosome Binding. Mol Cell 2019; 75:921-932.e6. [PMID: 31303471 DOI: 10.1016/j.molcel.2019.06.009] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/01/2019] [Accepted: 06/07/2019] [Indexed: 10/26/2022]
Abstract
Fate-changing transcription factors (TFs) scan chromatin to initiate new genetic programs during cell differentiation and reprogramming. Yet the protein structure domains that allow TFs to target nucleosomal DNA remain unexplored. We screened diverse TFs for binding to nucleosomes containing motif-enriched sequences targeted by pioneer factors in vivo. FOXA1, OCT4, ASCL1/E12α, PU1, CEBPα, and ZELDA display a range of nucleosome binding affinities that correlate with their cell reprogramming potential. We further screened 593 full-length human TFs on protein microarrays against different nucleosome sequences, followed by confirmation in solution, to distinguish among factors that bound nucleosomes, such as the neuronal AP-2α/β/γ, versus factors that only bound free DNA. Structural comparisons of DNA binding domains revealed that efficient nucleosome binders use short anchoring α helices to bind DNA, whereas weak nucleosome binders use unstructured regions and/or β sheets. Thus, specific modes of DNA interaction allow nucleosome scanning that confers pioneer activity to transcription factors.
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Affiliation(s)
- Meilin Fernandez Garcia
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA
| | - Cedric D Moore
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Katharine N Schulz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Oscar Alberto
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA
| | - Greg Donague
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA.
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41
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Ding Y, Kathiresan V, Zhang X, Haworth IS, Qin PZ. Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes. J Phys Chem A 2019; 123:3592-3598. [PMID: 30978022 DOI: 10.1021/acs.jpca.9b01027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Measurement of distances between spectroscopic labels (e.g., spin labels, fluorophores) attached to specific sites of biomolecules is an important method for studying biomolecular complexes. ALLNOX (Addition of Labels and Linkers) has been developed as a program to model interlabel distances based on an input macromolecule structure. Here, we report validation of ALLNOX using measured distances between nitroxide spin labels attached to specific sites of a protein-DNA complex. The results demonstrate that ALLNOX predicts average interspin distances that matched with values measured with pairs of labels attached at the protein and/or DNA. This establishes a solid foundation for using spin labeling in conjunction with ALLNOX to investigate complexes without high-resolution structures. With its high degree of flexibility for the label or the target biomolecule, ALLNOX provides a useful tool for investigating the structure-function relationship in a large variety of biological molecules.
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Affiliation(s)
- Yuan Ding
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Venkatesan Kathiresan
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Xiaojun Zhang
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Ian S Haworth
- Department of Pharmacology and Pharmaceutical Sciences , University of Southern California , Los Angeles , California 90089 , United States
| | - Peter Z Qin
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States.,Department of Biological Sciences , University of Southern California , Los Angeles , California 90089 , United States
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42
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Chen X, Wei H, Li J, Liang X, Dai S, Jiang L, Guo M, Qu L, Chen Z, Chen L, Chen Y. Structural basis for DNA recognition by FOXC2. Nucleic Acids Res 2019; 47:3752-3764. [PMID: 30722065 PMCID: PMC6468292 DOI: 10.1093/nar/gkz077] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/26/2019] [Accepted: 01/30/2019] [Indexed: 12/15/2022] Open
Abstract
The FOXC family of transcription factors (FOXC1 and FOXC2) plays essential roles in the regulation of embryonic, ocular, and cardiac development. Mutations and abnormal expression of FOXC proteins are implicated in genetic diseases as well as cancer. In this study, we determined two crystal structures of the DNA-binding domain (DBD) of human FOXC2 protein, in complex with different DNA sites. The FOXC2-DBD adopts the winged-helix fold with helix H3 contributing to all the base specific contacts, while the N-terminus, wing 1, and the C-terminus of FOXC2-DBD all make additional contacts with the phosphate groups of DNA. Our structural, biochemical, and bioinformatics analyses allow us to revise the previously proposed DNA recognition mechanism and provide a model of DNA binding for the FOXC proteins. In addition, our structural analysis and accompanying biochemical assays provide a molecular basis for understanding disease-causing mutations in FOXC1 and FOXC2.
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Affiliation(s)
- Xiaojuan Chen
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Medical Genetics and College of Life Science, Central South University, Changsha, Hunan 410008, China
| | - Hudie Wei
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Li
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xujun Liang
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Shuyan Dai
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Longying Jiang
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ming Guo
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lingzhi Qu
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhuchu Chen
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lin Chen
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Yongheng Chen
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Medical Genetics and College of Life Science, Central South University, Changsha, Hunan 410008, China
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43
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Feng H, Zhu M, Zhang R, Wang Q, Li W, Dong X, Chen Y, Lu Y, Liu K, Lin B, Guo J, Li M. GATA5 inhibits hepatocellular carcinoma cells malignant behaviours by blocking expression of reprogramming genes. J Cell Mol Med 2019; 23:2536-2548. [PMID: 30672133 PMCID: PMC6433710 DOI: 10.1111/jcmm.14144] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/28/2022] Open
Abstract
Evidence indicated that GATA5 may suppress hepatocellular carcinoma (HCC) cell malignant transformation, but the mechanism of how GATA5 affects cancer cell reprogramming to inhibit HCC malignant behaviour is still unclear. In this study, we report that the expression of β-catenin and reprogramming genes p-Oct4, Nanog, Klf4, c-myc and EpCAM was significantly higher in HCC tissues compared to normal liver tissues. In contrast, the expression of GATA5 was significantly lower in HCC tissues compared to normal liver tissues. Transfection of CDH-GATA5 vectors into HCC cells (HLE, Bel 7402 and PLC/PRF/5 cells) increased the GATA5 expression and decreased the expression of β-catenin and reprogramming genes p-Oct4, Nanog, Klf4, c-myc and EpCAM. Increased GATA5 expression by transfection with its expression vectors was also able to inhibit the cell growth, colony formation and capability of migration, invasion, while promoting apoptosis in HCC cells. Results revealed that GATA5 co-localization with β-catenin in the cytoplasm, preventing β-catenin from entering the nucleus. Treatment with the specific Wnt/β-catenin pathway inhibitor salinomycin was able to reduce the expression of β-catenin and reprogramming genes. Salinomycin exerted a similar influence as GATA5, and siRNA-GATA5 restored β-catenin and reprogramming gene expression. This study demonstrates that an increase in the expression of GATA5 inhibits the expression of β-catenin and reprogramming genes and suppresses tumour growth, colony formation, metastasis and invasion, while promoting apoptosis in HCC cells. The mechanism of GATA5 inhibiting the malignant behaviours of HCC cells may involve in the disruption of the Wnt/β-catenin pathway and the reduction of reprogramming gene expression.
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MESH Headings
- Adult
- Aged
- Apoptosis/drug effects
- Apoptosis/genetics
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/surgery
- Case-Control Studies
- Cell Line, Tumor
- Cell Movement/drug effects
- Cell Proliferation/drug effects
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Epithelial Cell Adhesion Molecule/antagonists & inhibitors
- Epithelial Cell Adhesion Molecule/genetics
- Epithelial Cell Adhesion Molecule/metabolism
- Female
- GATA5 Transcription Factor/antagonists & inhibitors
- GATA5 Transcription Factor/genetics
- GATA5 Transcription Factor/metabolism
- Gene Expression Regulation, Neoplastic
- Hepatocytes/drug effects
- Hepatocytes/metabolism
- Hepatocytes/pathology
- Humans
- Kruppel-Like Factor 4
- Kruppel-Like Transcription Factors/antagonists & inhibitors
- Kruppel-Like Transcription Factors/genetics
- Kruppel-Like Transcription Factors/metabolism
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Liver Neoplasms/surgery
- Male
- Middle Aged
- Nanog Homeobox Protein/antagonists & inhibitors
- Nanog Homeobox Protein/genetics
- Nanog Homeobox Protein/metabolism
- Octamer Transcription Factor-3/antagonists & inhibitors
- Octamer Transcription Factor-3/genetics
- Octamer Transcription Factor-3/metabolism
- Proto-Oncogene Proteins c-myc/antagonists & inhibitors
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Pyrans/pharmacology
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Wnt Signaling Pathway
- beta Catenin/antagonists & inhibitors
- beta Catenin/genetics
- beta Catenin/metabolism
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Affiliation(s)
- Haipeng Feng
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Mingyue Zhu
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Ruizhu Zhang
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Qiaoyun Wang
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Wei Li
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Xu Dong
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Yi Chen
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Yan Lu
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Kun Liu
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Bo Lin
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Junli Guo
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
| | - Mengsen Li
- Hainan Provincial Key Laboratory of Carcinogenesis and InterventionHainan Medical CollegeHainan ProvinceHaikouPR. China
- Key Laboratory of Molecular BiologyHainan Medical CollegeHainan ProvinceHaikouPR. China
- Institution of TumorHainan Medical CollegeHainan ProvinceHaikouPR. China
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44
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Panigrahi AK, Foulds CE, Lanz RB, Hamilton RA, Yi P, Lonard DM, Tsai MJ, Tsai SY, O'Malley BW. SRC-3 Coactivator Governs Dynamic Estrogen-Induced Chromatin Looping Interactions during Transcription. Mol Cell 2019; 70:679-694.e7. [PMID: 29775582 DOI: 10.1016/j.molcel.2018.04.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/15/2018] [Accepted: 04/18/2018] [Indexed: 01/09/2023]
Abstract
Enhancers are thought to activate transcription by physically contacting promoters via looping. However, direct assays demonstrating these contacts are required to mechanistically verify such cellular determinants of enhancer function. Here, we present versatile cell-free assays to further determine the role of enhancer-promoter contacts (EPCs). We demonstrate that EPC is linked to mutually stimulatory transcription at the enhancer and promoter in vitro. SRC-3 was identified as a critical looping determinant for the estradiol-(E2)-regulated GREB1 locus. Surprisingly, the GREB1 enhancer and promoter contact two internal gene body SRC-3 binding sites, GBS1 and GBS2, which stimulate their transcription. Utilizing time-course 3C assays, we uncovered SRC-3-dependent dynamic chromatin interactions involving the enhancer, promoter, GBS1, and GBS2. Collectively, these data suggest that the enhancer and promoter remain "poised" for transcription via their contacts with GBS1 and GBS2. Upon E2 induction, GBS1 and GBS2 disengage from the enhancer, allowing direct EPC for active transcription.
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Affiliation(s)
- Anil K Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Center for Precision Environmental Health, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ross A Hamilton
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ping Yi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ming-Jer Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Sophia Y Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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45
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Yella VR, Bhimsaria D, Ghoshdastidar D, Rodríguez-Martínez J, Ansari AZ, Bansal M. Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif. Nucleic Acids Res 2018; 46:11883-11897. [PMID: 30395339 PMCID: PMC6294565 DOI: 10.1093/nar/gky1057] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/11/2018] [Accepted: 10/17/2018] [Indexed: 01/13/2023] Open
Abstract
Spatial and temporal expression of genes is essential for maintaining phenotype integrity. Transcription factors (TFs) modulate expression patterns by binding to specific DNA sequences in the genome. Along with the core binding motif, the flanking sequence context can play a role in DNA-TF recognition. Here, we employ high-throughput in vitro and in silico analyses to understand the influence of sequences flanking the cognate sites in binding of three most prevalent eukaryotic TF families (zinc finger, homeodomain and bZIP). In vitro binding preferences of each TF toward the entire DNA sequence space were correlated with a wide range of DNA structural parameters, including DNA flexibility. Results demonstrate that conformational plasticity of flanking regions modulates binding affinity of certain TF families. DNA duplex stability and minor groove width also play an important role in DNA-TF recognition but differ in how exactly they influence the binding in each specific case. Our analyses further reveal that the structural features of preferred flanking sequences are not universal, as similar DNA-binding folds can employ distinct DNA recognition modes.
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Affiliation(s)
- Venkata Rajesh Yella
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur, Andhra Pradesh 522502, India
| | - Devesh Bhimsaria
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - José A Rodríguez-Martínez
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan, PR 00925, USA
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- The Genome Center of Wisconsin, Madison, WI 53706, USA
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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46
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Mitra S, Biswas A, Narlikar L. DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP. PLoS Comput Biol 2018; 14:e1006090. [PMID: 29684008 PMCID: PMC5933800 DOI: 10.1371/journal.pcbi.1006090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 05/03/2018] [Accepted: 03/14/2018] [Indexed: 12/27/2022] Open
Abstract
Genome-wide in vivo protein-DNA interactions are routinely mapped using high-throughput chromatin immunoprecipitation (ChIP). ChIP-reported regions are typically investigated for enriched sequence-motifs, which are likely to model the DNA-binding specificity of the profiled protein and/or of co-occurring proteins. However, simple enrichment analyses can miss insights into the binding-activity of the protein. Note that ChIP reports regions making direct contact with the protein as well as those binding through intermediaries. For example, consider a ChIP experiment targeting protein X, which binds DNA at its cognate sites, but simultaneously interacts with four other proteins. Each of these proteins also binds to its own specific cognate sites along distant parts of the genome, a scenario consistent with the current view of transcriptional hubs and chromatin loops. Since ChIP will pull down all X-associated regions, the final reported data will be a union of five distinct sets of regions, each containing binding sites of one of the five proteins, respectively. Characterizing all five different motifs and the corresponding sets is important to interpret the ChIP experiment and ultimately, the role of X in regulation. We present diversity which attempts exactly this: it partitions the data so that each partition can be characterized with its own de novo motif. Diversity uses a Bayesian approach to identify the optimal number of motifs and the associated partitions, which together explain the entire dataset. This is in contrast to standard motif finders, which report motifs individually enriched in the data, but do not necessarily explain all reported regions. We show that the different motifs and associated regions identified by diversity give insights into the various complexes that may be forming along the chromatin, something that has so far not been attempted from ChIP data. Webserver at http://diversity.ncl.res.in/; standalone (Mac OS X/Linux) from https://github.com/NarlikarLab/DIVERSITY/releases/tag/v1.0.0. A high-throughput chromatin immunoprecipitation (ChIP) experiment identifies genomic regions bound by a protein in vivo. Current motif-discovery approaches seek an enriched motif signature in the reported regions, which they can attribute to the protein’s binding preferences. However, Diversity models the fact that since a ChIP experiment pulls down regions participating in all complexes involving the profiled protein, the reported regions are in all likelihood, a collection of different types of protein-DNA contacts. Diversity asks a different question: what sequence component caused a specific region to be reported in a ChIP experiment? The answer, in combination with additional data such as sequence conservation, SNPs, chromatin structure, downstream gene-expression, etc. can yield insights into the diverse regulatory mechanisms at play. The added benefits of a webserver and a standalone parallel version make diversity a practical tool for discovering new biology from ChIP experiments.
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Affiliation(s)
- Sneha Mitra
- Department of Chemical Engineering, CSIR-National Chemical Laboratory, Pune, India
| | - Anushua Biswas
- Department of Chemical Engineering, CSIR-National Chemical Laboratory, Pune, India
| | - Leelavati Narlikar
- Department of Chemical Engineering, CSIR-National Chemical Laboratory, Pune, India
- * E-mail:
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47
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Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S. Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes (Basel) 2017; 8:genes8080192. [PMID: 28763006 PMCID: PMC5575656 DOI: 10.3390/genes8080192] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Muhammad Ayaz Anwar
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Suresh Panneerselvam
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
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48
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Li J, Dantas Machado AC, Guo M, Sagendorf JM, Zhou Z, Jiang L, Chen X, Wu D, Qu L, Chen Z, Chen L, Rohs R, Chen Y. Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site. Biochemistry 2017. [PMID: 28644006 DOI: 10.1021/acs.biochem.7b00211] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
FOXA2, a member of the forkhead family of transcription factors, plays essential roles in liver development and bile acid homeostasis. In this study, we report a 2.8 Å co-crystal structure of the FOXA2 DNA-binding domain (FOXA2-DBD) bound to a DNA duplex containing a forkhead consensus binding site (GTAAACA). The FOXA2-DBD adopts the canonical winged-helix fold, with helix H3 and wing 1 regions mainly mediating the DNA recognition. Although the wing 2 region was not defined in the structure, isothermal titration calorimetry assays suggested that this region was required for optimal DNA binding. Structure comparison with the FOXA3-DBD bound to DNA revealed more major groove contacts and fewer minor groove contacts in the FOXA2 structure than in the FOXA3 structure. Structure comparison with the FOXO1-DBD bound to DNA showed that different forkhead proteins could induce different DNA conformations upon binding to identical DNA sequences. Our findings provide the structural basis for FOXA2 protein binding to a consensus forkhead site and elucidate how members of the forkhead protein family bind different DNA sites.
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Affiliation(s)
- Jun Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China
| | - Ana Carolina Dantas Machado
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States
| | - Ming Guo
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Jared M Sagendorf
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States
| | - Zhan Zhou
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Longying Jiang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Xiaojuan Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China
| | - Daichao Wu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Lingzhi Qu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Zhuchu Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Lin Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Remo Rohs
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States
| | - Yongheng Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China.,Collaborative Innovation Center for Cancer Medicine , Guangzhou, Guangdong 510060, China
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49
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Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns. Sci Rep 2017; 7:3626. [PMID: 28620196 PMCID: PMC5472622 DOI: 10.1038/s41598-017-03837-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/08/2017] [Indexed: 12/29/2022] Open
Abstract
Despite numerous studies done on understanding the role of DNA methylation, limited work has focused on systems integration of cell type-specific interplay between DNA methylation and gene transcription. Through a genome-wide analysis of DNA methylation across 19 cell types with T-47D as reference, we identified 106,252 cell type-specific differentially-methylated CpGs categorized into 7,537 differentially (46.6% hyper- and 53.4% hypo-) methylated regions. We found 44% promoter regions and 75% CpG islands were T-47D cell type-specific methylated. Pyrosequencing experiments validated the cell type-specific methylation across three benchmark cell lines. Interestingly, these DMRs overlapped with 1,145 known tumor suppressor genes. We then developed a Bayesian Gaussian Regression model to measure the relationship among DNA methylation, genomic segment distribution, differential gene expression and tumor suppressor gene status. The model uncovered that 3′UTR methylation has much less impact on transcriptional activity than other regions. Integration of DNA methylation and 82 transcription factor binding information across the 19 cell types suggested diverse interplay patterns between the two regulators. Our integrative analysis reveals cell type-specific and genomic region-dependent regulatory patterns and provides a perspective for integrating hundreds of various omics-seq data together.
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Chillemi G, Kehrloesser S, Bernassola F, Desideri A, Dötsch V, Levine AJ, Melino G. Structural Evolution and Dynamics of the p53 Proteins. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a028308. [PMID: 27091942 DOI: 10.1101/cshperspect.a028308] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The family of the p53 tumor suppressive transcription factors includes p73 and p63 in addition to p53 itself. Given the high degree of amino-acid-sequence homology and structural organization shared by the p53 family members, they display some common features (i.e., induction of cell death, cell-cycle arrest, senescence, and metabolic regulation in response to cellular stress) as well as several distinct properties. Here, we describe the structural evolution of the family members with recent advances on the molecular dynamic studies of p53 itself. A crucial role of the carboxy-terminal domain in regulating the properties of the DNA-binding domain (DBD) supports an induced-fit mechanism, in which the binding of p53 on individual promoters is preferentially regulated by the KOFF over KON.
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Affiliation(s)
- Giovanni Chillemi
- CINECA, SCAI-SuperComputing Applications and Innovation Department, Rome 00185, Italy
| | - Sebastian Kehrloesser
- Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Francesca Bernassola
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata," 00133 Rome, Italy
| | | | - Volker Dötsch
- Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Arnold J Levine
- Institute for Advanced Study, Princeton, New Jersey 08540.,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903
| | - Gerry Melino
- Medical Research Council, Toxicology Unit, Leicester University, Leicester LE1 9HN, United Kingdom
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