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Mielko Z, Zhang Y, Sahay H, Liu Y, Schaich MA, Schnable B, Morrison AM, Burdinski D, Adar S, Pufall M, Van Houten B, Gordân R, Afek A. UV irradiation remodels the specificity landscape of transcription factors. Proc Natl Acad Sci U S A 2023; 120:e2217422120. [PMID: 36888663 PMCID: PMC10089200 DOI: 10.1073/pnas.2217422120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
Somatic mutations are highly enriched at transcription factor (TF) binding sites, with the strongest trend being observed for ultraviolet light (UV)-induced mutations in melanomas. One of the main mechanisms proposed for this hypermutation pattern is the inefficient repair of UV lesions within TF-binding sites, caused by competition between TFs bound to these lesions and the DNA repair proteins that must recognize the lesions to initiate repair. However, TF binding to UV-irradiated DNA is poorly characterized, and it is unclear whether TFs maintain specificity for their DNA sites after UV exposure. We developed UV-Bind, a high-throughput approach to investigate the impact of UV irradiation on protein-DNA binding specificity. We applied UV-Bind to ten TFs from eight structural families, and found that UV lesions significantly altered the DNA-binding preferences of all the TFs tested. The main effect was a decrease in binding specificity, but the precise effects and their magnitude differ across factors. Importantly, we found that despite the overall reduction in DNA-binding specificity in the presence of UV lesions, TFs can still compete with repair proteins for lesion recognition, in a manner consistent with their specificity for UV-irradiated DNA. In addition, for a subset of TFs, we identified a surprising but reproducible effect at certain nonconsensus DNA sequences, where UV irradiation leads to a high increase in the level of TF binding. These changes in DNA-binding specificity after UV irradiation, at both consensus and nonconsensus sites, have important implications for the regulatory and mutagenic roles of TFs in the cell.
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Affiliation(s)
- Zachery Mielko
- Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27708
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27708
- Department of Computer Science, Duke University, Durham, NC 27708
| | - Yuning Zhang
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27708
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
| | - Harshit Sahay
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27708
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham NC 27708
| | - Yiling Liu
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27708
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham NC 27708
| | - Matthew A Schaich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
- UPMC-Hillman Cancer Center, Pittsburgh, PA 15213
| | - Brittani Schnable
- UPMC-Hillman Cancer Center, Pittsburgh, PA 15213
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Abigail M Morrison
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Debbie Burdinski
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Miles Pufall
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242
| | - Bennett Van Houten
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham NC 27708
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
- UPMC-Hillman Cancer Center, Pittsburgh, PA 15213
- Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, PA 15213
| | - Raluca Gordân
- Department of Computer Science, Duke University, Durham, NC 27708
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708
| | - Ariel Afek
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R. DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature 2020; 587:291-296. [PMID: 33087930 PMCID: PMC7666076 DOI: 10.1038/s41586-020-2843-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 09/17/2020] [Indexed: 12/17/2022]
Abstract
Transcription factors recognize specific genomic sequences to regulate complex gene-expression programs. Although it is well-established that transcription factors bind to specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood1,2. Many DNA-binding proteins induce changes in the structure of the DNA outside the intrinsic B-DNA envelope. However, how the energetic cost that is associated with distorting the DNA contributes to recognition has proven difficult to study, because the distorted DNA exists in low abundance in the unbound ensemble3-9. Here we use a high-throughput assay that we term SaMBA (saturation mismatch-binding assay) to investigate the role of DNA conformational penalties in transcription factor-DNA recognition. In SaMBA, mismatched base pairs are introduced to pre-induce structural distortions in the DNA that are much larger than those induced by changes in the Watson-Crick sequence. Notably, approximately 10% of mismatches increased transcription factor binding, and for each of the 22 transcription factors that were examined, at least one mismatch was found that increased the binding affinity. Mismatches also converted non-specific sites into high-affinity sites, and high-affinity sites into 'super sites' that exhibit stronger affinity than any known canonical binding site. Determination of high-resolution X-ray structures, combined with nuclear magnetic resonance measurements and structural analyses, showed that many of the DNA mismatches that increase binding induce distortions that are similar to those induced by protein binding-thus prepaying some of the energetic cost incurred from deforming the DNA. Our work indicates that conformational penalties are a major determinant of protein-DNA recognition, and reveals mechanisms by which mismatches can recruit transcription factors and thus modulate replication and repair activities in the cell10,11.
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Affiliation(s)
- Ariel Afek
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Harshit Sahay
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Alon Senitzki
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Mimi Fang
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Raul Salinas
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Zachery Mielko
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
- Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Tali E Haran
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA.
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
- Department of Computer Science, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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Panea RI, Love CL, Shingleton JR, Reddy A, Bailey JA, Moormann AM, Otieno JA, Ong'echa JM, Oduor CI, Schroeder KMS, Masalu N, Chao NJ, Agajanian M, Major MB, Fedoriw Y, Richards KL, Rymkiewicz G, Miles RR, Alobeid B, Bhagat G, Flowers CR, Ondrejka SL, Hsi ED, Choi WWL, Au-Yeung RKH, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig MA, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus BC, Seshadri V, Kim SY, Gascoyne RD, Levy S, Mukhopadyay M, Dunson DB, Dave SS. The whole-genome landscape of Burkitt lymphoma subtypes. Blood 2019; 134:1598-1607. [PMID: 31558468 PMCID: PMC6871305 DOI: 10.1182/blood.2019001880] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/28/2019] [Indexed: 01/10/2023] Open
Abstract
Burkitt lymphoma (BL) is an aggressive, MYC-driven lymphoma comprising 3 distinct clinical subtypes: sporadic BLs that occur worldwide, endemic BLs that occur predominantly in sub-Saharan Africa, and immunodeficiency-associated BLs that occur primarily in the setting of HIV. In this study, we comprehensively delineated the genomic basis of BL through whole-genome sequencing (WGS) of 101 tumors representing all 3 subtypes of BL to identify 72 driver genes. These data were additionally informed by CRISPR screens in BL cell lines to functionally annotate the role of oncogenic drivers. Nearly every driver gene was found to have both coding and non-coding mutations, highlighting the importance of WGS for identifying driver events. Our data implicate coding and non-coding mutations in IGLL5, BACH2, SIN3A, and DNMT1. Epstein-Barr virus (EBV) infection was associated with higher mutation load, with type 1 EBV showing a higher mutational burden than type 2 EBV. Although sporadic and immunodeficiency-associated BLs had similar genetic profiles, endemic BLs manifested more frequent mutations in BCL7A and BCL6 and fewer genetic alterations in DNMT1, SNTB2, and CTCF. Silencing mutations in ID3 were a common feature of all 3 subtypes of BL. In vitro, mass spectrometry-based proteomics demonstrated that the ID3 protein binds primarily to TCF3 and TCF4. In vivo knockout of ID3 potentiated the effects of MYC, leading to rapid tumorigenesis and tumor phenotypes consistent with those observed in the human disease.
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Affiliation(s)
- Razvan I Panea
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Cassandra L Love
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Jennifer R Shingleton
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Anupama Reddy
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Ann M Moormann
- Department of Medicine, University of Massachusetts, Worcester, MA
| | - Juliana A Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Health, Kisumu, Kenya
| | | | - Cliff I Oduor
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Kristin M S Schroeder
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
- Bugando Medical Center, Mwanza, Tanzania
| | | | - Nelson J Chao
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Megan Agajanian
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO
| | - Michael B Major
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO
| | | | | | - Grzegorz Rymkiewicz
- Poland Flow Cytometry Laboratory, Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland
| | - Rodney R Miles
- Department of Pathology, University of Utah, Salt Lake City, UT
| | - Bachir Alobeid
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | | | - Sarah L Ondrejka
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH
| | - Eric D Hsi
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH
| | - William W L Choi
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Rex K H Au-Yeung
- The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Georg Lenz
- Medical Department A, Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Howard Meyerson
- Department of Pathology, Case Western Reserve University, Cleveland, OH
| | | | | | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC
| | - Alexander Waldrop
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Tushar Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Devang Thakkar
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Harshit Sahay
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Guojie Li
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Brooke C Palus
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Vidya Seshadri
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC
| | - So Young Kim
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC
| | - Randy D Gascoyne
- Department of Pathology and Experimental Therapeutics, BC Cancer Agency and BC Cancer Research Centre, Vancouver, BC, Canada
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL; and
| | | | - David B Dunson
- Department of Statistical Science, Duke University, Durham, NC
| | - Sandeep S Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
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