1
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German RJ, Vuocolo B, Vossaert L, Saba L, Fletcher R, Tedder ML, Sadikovic B, Kerkhof J, Wangler M, Bacino CA. Recurrent carotid paragangliomas in a syndromic patient with a heterozygous missense variant in DNA Methyltransferase 3 Alpha. Am J Med Genet A 2024:e63849. [PMID: 39166703 DOI: 10.1002/ajmg.a.63849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/23/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
We report a 40-year-old African American female with a novel variant in exon 8 of DNA methyltransferase 3 alpha (DNMT3A), (NM_022552.4: c.905G>C, p.G302A) who presented with a history of recurrent carotid paragangliomas, mediastinal mass, intellectual disability, dysarthria, cholelithiasis, diabetes mellitus, hypertension, and dysmorphic features. We interpret this novel variant as likely pathogenic and causative for the patient's syndromic features of Heyn-Sproul-Jackson syndrome. Heyn-Sproul-Jackson syndrome is a condition caused by gain-of-function genetic changes in DNMT3A. Paragangliomas have also been observed in non-syndromic patients with genetic alterations in DNMT3A. We describe a patient with clinical features of Heyn-Sproul-Jackson syndrome such as intellectual disability, dysarthria, brachydactyly, and lack of brain MRI findings to add evidence to associate paragangliomas with DNMT3A and draw particular attention to the potential involvement of the proline-tryptophan-tryptophan-proline domain of DNMT3A.
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Affiliation(s)
- Ryan J German
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Blake Vuocolo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Lisa Saba
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Robin Fletcher
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Michael Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- Department of Genetics, Texas Children's Hospital, Houston, Texas, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Genetics, Texas Children's Hospital, Houston, Texas, USA
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2
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Koutná E, Lux V, Kouba T, Škerlová J, Nováček J, Srb P, Hexnerová R, Šváchová H, Kukačka Z, Novák P, Fábry M, Poepsel S, Veverka V. Multivalency of nucleosome recognition by LEDGF. Nucleic Acids Res 2023; 51:10011-10025. [PMID: 37615563 PMCID: PMC10570030 DOI: 10.1093/nar/gkad674] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/01/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Eukaryotic transcription is dependent on specific histone modifications. Their recognition by chromatin readers triggers complex processes relying on the coordinated association of transcription regulatory factors. Although various modification states of a particular histone residue often lead to differential outcomes, it is not entirely clear how they are discriminated. Moreover, the contribution of intrinsically disordered regions outside of the specialized reader domains to nucleosome binding remains unexplored. Here, we report the structures of a PWWP domain from transcriptional coactivator LEDGF in complex with the H3K36 di- and trimethylated nucleosome, indicating that both methylation marks are recognized by PWWP in a highly conserved manner. We identify a unique secondary interaction site for the PWWP domain at the interface between the acidic patch and nucleosomal DNA that might contribute to an H3K36-methylation independent role of LEDGF. We reveal DNA interacting motifs in the intrinsically disordered region of LEDGF that discriminate between the intra- or extranucleosomal DNA but remain dynamic in the context of dinucleosomes. The interplay between the LEDGF H3K36-methylation reader and protein binding module mediated by multivalent interactions of the intrinsically disordered linker with chromatin might help direct the elongation machinery to the vicinity of RNA polymerase II, thereby facilitating productive elongation.
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Affiliation(s)
- Eliška Koutná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Vanda Lux
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Tomáš Kouba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | | | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Rozálie Hexnerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Hana Šváchová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Milan Fábry
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Simon Poepsel
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, Cologne 509 31, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne 509 31, Germany
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
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3
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Sehrawat P, Shobhawat R, Kumar A. Catching Nucleosome by Its Decorated Tails Determines Its Functional States. Front Genet 2022; 13:903923. [PMID: 35910215 PMCID: PMC9329655 DOI: 10.3389/fgene.2022.903923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The fundamental packaging unit of chromatin, i.e., nucleosome, consists of ∼147 bp of DNA wrapped around a histone octamer composed of the core histones, H2A, H2B, H3, and H4, in two copies each. DNA packaged in nucleosomes must be accessible to various machineries, including replication, transcription, and DNA damage repair, implicating the dynamic nature of chromatin even in its compact state. As the tails protrude out of the nucleosome, they are easily accessible to various chromatin-modifying machineries and undergo post-translational modifications (PTMs), thus playing a critical role in epigenetic regulation. PTMs can regulate chromatin states via charge modulation on histones, affecting interaction with various chromatin-associated proteins (CAPs) and DNA. With technological advancement, the list of PTMs is ever-growing along with their writers, readers, and erasers, expanding the complexity of an already intricate epigenetic field. In this review, we discuss how some of the specific PTMs on flexible histone tails affect the nucleosomal structure and regulate the accessibility of chromatin from a mechanistic standpoint and provide structural insights into some newly identified PTM–reader interaction.
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4
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Ju MK, Lee JR, Choi Y, Park SY, Sul HJ, Chung HJ, An S, Lee S, Jung E, Kim B, Choi BY, Kim BJ, Kim HS, Lim H, Kang HS, Soh JS, Myung K, Kim KC, Cho JW, Seo J, Kim TM, Lee JY, Kim Y, Kim H, Zang DY. PWWP2B promotes DNA end resection and homologous recombination. EMBO Rep 2022; 23:e53492. [PMID: 35582821 PMCID: PMC9253748 DOI: 10.15252/embr.202153492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 04/18/2022] [Accepted: 05/02/2022] [Indexed: 11/15/2023] Open
Abstract
Genome instability is one of the leading causes of gastric cancers. However, the mutational landscape of driver genes in gastric cancer is poorly understood. Here, we investigate somatic mutations in 25 Korean gastric adenocarcinoma patients using whole-exome sequencing and show that PWWP2B is one of the most frequently mutated genes. PWWP2B mutation correlates with lower cancer patient survival. We find that PWWP2B has a role in DNA double-strand break repair. As a nuclear protein, PWWP2B moves to sites of DNA damage through its interaction with UHRF1. Depletion of PWWP2B enhances cellular sensitivity to ionizing radiation (IR) and impairs IR-induced foci formation of RAD51. PWWP2B interacts with MRE11 and participates in homologous recombination via promoting DNA end-resection. Taken together, our data show that PWWP2B facilitates the recruitment of DNA repair machinery to sites of DNA damage and promotes HR-mediated DNA double-strand break repair. Impaired PWWP2B function might thus cause genome instability and promote gastric cancer development.
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Affiliation(s)
- Min Kyung Ju
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Joo Rak Lee
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Yeonsong Choi
- Department of Biomedical EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
| | - Seon Young Park
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Hee Jung Sul
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Hee Jin Chung
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Soyeong An
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Semin Lee
- Department of Biomedical EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
| | - Eunyoung Jung
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Bohyun Kim
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Bo Youn Choi
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Bum Jun Kim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Hyeong Su Kim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Hyun Lim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Ho Suk Kang
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Jae Seung Soh
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Kyungjae Myung
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Kab Choong Kim
- Department of SurgeryHallym University Medical CenterHallym University College of MedicineAnyang‐siKorea
| | - Ji Woong Cho
- Department of SurgeryHallym University Medical CenterHallym University College of MedicineAnyang‐siKorea
| | - Jinwon Seo
- Department of PathologyHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Tae Moon Kim
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Ja Yil Lee
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Yonghwan Kim
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Hongtae Kim
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Dae Young Zang
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
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5
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Li J, Bergmann L, Rafael de Almeida A, Webb KM, Gogol M, Voigt P, Liu Y, Liang H, Smolle M. H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function. Nucleic Acids Res 2022; 50:2549-2565. [PMID: 35188579 PMCID: PMC8934638 DOI: 10.1093/nar/gkac077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 01/20/2022] [Accepted: 02/15/2022] [Indexed: 11/23/2022] Open
Abstract
The Isw1b chromatin-remodeling complex is specifically recruited to gene bodies to help retain pre-existing histones during transcription by RNA polymerase II. Recruitment is dependent on H3K36 methylation and the Isw1b subunit Ioc4, which contains an N-terminal PWWP domain. Here, we present the crystal structure of the Ioc4-PWWP domain, including a detailed functional characterization of the domain on its own as well as in the context of full-length Ioc4 and the Isw1b remodeler. The Ioc4-PWWP domain preferentially binds H3K36me3-containing nucleosomes. Its ability to bind DNA is required for nucleosome binding. It is also furthered by the unique insertion motif present in Ioc4-PWWP. The ability to bind H3K36me3 and DNA promotes the interaction of full-length Ioc4 with nucleosomes in vitro and they are necessary for its recruitment to gene bodies in vivo. Furthermore, a fully functional Ioc4-PWWP domain promotes efficient remodeling by Isw1b and the maintenance of ordered chromatin in vivo, thereby preventing the production of non-coding RNAs.
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Affiliation(s)
- Jian Li
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Lena Bergmann
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Andreia Rafael de Almeida
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Kimberly M Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Madelaine M Gogol
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Yingfang Liu
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- School of Medicine, Sun Yat-Sen University, Guangzhou 510275, China
| | - Huanhuan Liang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Michaela M Smolle
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
- BioPhysics Core Facility, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
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6
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Mechanistic similarities in recognition of histone tails and DNA by epigenetic readers. Curr Opin Struct Biol 2021; 71:1-6. [PMID: 33993059 DOI: 10.1016/j.sbi.2021.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/03/2021] [Accepted: 04/08/2021] [Indexed: 11/21/2022]
Abstract
The past two decades have witnessed rapid advances in the identification and characterization of epigenetic readers, capable of recognizing or reading post-translational modifications in histones. More recently, a new set of readers with the ability to interact with the nucleosome through concomitant binding to histones and DNA has emerged. In this review, we discuss mechanistic insights underlying bivalent histone and DNA recognition by newly characterized readers and highlight the importance of binding to DNA for their association with chromatin.
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7
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Structures of chromatin modulators in complex with nucleosome. Curr Opin Chem Biol 2021; 63:105-114. [PMID: 33823458 DOI: 10.1016/j.cbpa.2021.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/11/2021] [Accepted: 02/25/2021] [Indexed: 12/17/2022]
Abstract
The chromatin structure is dynamically regulated by many different modulators that post-translationally modify histones, replace canonical histones with histone variants, and unwind nucleosomal DNA, thereby modulating the accessibility of nucleosomal DNA and facilitating downstream DNA-templated nuclear processes. To understand how these modulators change the chromatin structure, it is essential to determine the 3D structures of chromatin modulators in complex with nucleosome. Here, we review the very recent progress in structural studies of some selected chromatin modulators in complex with nucleosome, including those of histone demethylases LSD1/2, some pioneer transcription factors, and the PWWP domain-containing protein LEDGF.
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8
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Zhang M, Lei M, Qin S, Dong A, Yang A, Li Y, Loppnau P, Hughes TR, Min J, Liu Y. Crystal structure of the BRPF2 PWWP domain in complex with DNA reveals a different binding mode than the HDGF family of PWWP domains. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194688. [PMID: 33556623 DOI: 10.1016/j.bbagrm.2021.194688] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 01/22/2023]
Abstract
The PWWP domain was first identified in the HDGF protein family and named after the conserved Proline-Tryptophan-Tryptophan-Proline motif in WHSC1. The PWWP domain-containing proteins play important roles in different biological processes, such as DNA replication, transcription, DNA repair, pre-mRNA processing by recognizing methylated histone and dsDNA simultaneously. Recently, how the HDGF family of PWWP domains recognize histone H3K36me3-modified nucleosome has been reported. In order to better understand the interactions between the PWWP domain and dsDNA, we carried out family-wide characterization of dsDNA binding abilities of human PWWP domains. Our binding assays confirmed that PWWP domains bind to dsDNA without sequence selectivity. Our crystal structure of the BRPF2 PWWP domain in complex with a 12-mer dsDNA reveals that the PWWP domain interacts with dsDNA by binding to its major groove, instead of the minor groove observed in the HDGF family of PWWP domains. Our study indicates that PWWP domains could bind to dsDNA in different modes.
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Affiliation(s)
- Mengmeng Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Ming Lei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Su Qin
- Life Science Research Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Ally Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Physiology, University of Toronto, Toronto, Ontario, Canada.
| | - Yanli Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China.
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9
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Small Molecules Targeting the Specific Domains of Histone-Mark Readers in Cancer Therapy. Molecules 2020; 25:molecules25030578. [PMID: 32013155 PMCID: PMC7037402 DOI: 10.3390/molecules25030578] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
Epigenetic modifications (or epigenetic tags) on DNA and histones not only alter the chromatin structure, but also provide a recognition platform for subsequent protein recruitment and enable them to acquire executive instructions to carry out specific intracellular biological processes. In cells, different epigenetic-tags on DNA and histones are often recognized by the specific domains in proteins (readers), such as bromodomain (BRD), chromodomain (CHD), plant homeodomain (PHD), Tudor domain, Pro-Trp-Trp-Pro (PWWP) domain and malignant brain tumor (MBT) domain. Recent accumulating data reveal that abnormal intracellular histone modifications (histone marks) caused by tumors can be modulated by small molecule-mediated changes in the activity of the above domains, suggesting that small molecules targeting histone-mark reader domains may be the trend of new anticancer drug development. Here, we summarize the protein domains involved in histone-mark recognition, and introduce recent research findings about small molecules targeting histone-mark readers in cancer therapy.
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10
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Structure of H3K36-methylated nucleosome-PWWP complex reveals multivalent cross-gyre binding. Nat Struct Mol Biol 2019; 27:8-13. [PMID: 31819277 PMCID: PMC6955156 DOI: 10.1038/s41594-019-0345-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/30/2019] [Indexed: 01/05/2023]
Abstract
Recognition of histone-modified nucleosomes by specific reader domains underlies the regulation of chromatin-associated processes. Whereas structural studies revealed how reader domains bind modified histone peptides, it is unclear how reader domains interact with modified nucleosomes. Here we report the cryo-electron microscopy (cryo-EM) structure of the PWWP reader domain of human transcriptional coactivator LEDGF in complex with a H3K36-methylated nucleosome at 3.2 Å resolution. The structure reveals multivalent binding of the reader domain to the methylated histone tail and to both gyres of nucleosomal DNA, explaining the known cooperative interactions. The observed cross-gyre binding may contribute to nucleosome integrity during transcription. The structure also explains how human PWWP domain-containing proteins are recruited to H3K36-methylated regions of the genome for transcription, histone acetylation and methylation, and for DNA methylation and repair.
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11
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Connelly KE, Weaver TM, Alpsoy A, Gu BX, Musselman CA, Dykhuizen EC. Engagement of DNA and H3K27me3 by the CBX8 chromodomain drives chromatin association. Nucleic Acids Res 2019; 47:2289-2305. [PMID: 30597065 PMCID: PMC6411926 DOI: 10.1093/nar/gky1290] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 01/17/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) is critical for mediating gene repression during development and adult stem cell maintenance. Five CBX proteins, CBX2,4,6,7,8, form mutually exclusive PRC1 complexes and are thought to play a role in the association of PRC1 with chromatin. Specifically, the N-terminal chromodomain (CD) in the CBX proteins is thought to mediate specific targeting to methylated histones. For CBX8, however, the chromodomain has demonstrated weak affinity and specificity for methylated histones in vitro, leaving doubt as to its role in CBX8 chromatin association. Here, we investigate the function of the CBX8 CD in vitro and in vivo. We find that the CD is in fact a major driver of CBX8 chromatin association and determine that this is driven by both histone and previously unrecognized DNA binding activity. We characterize the structural basis of histone and DNA binding and determine how they integrate on multiple levels. Notably, we find that the chromatin environment is critical in determining the ultimate function of the CD in CBX8 association.
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Affiliation(s)
- Katelyn E Connelly
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Tyler M Weaver
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Brian X Gu
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | | | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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12
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Tian W, Yan P, Xu N, Chakravorty A, Liefke R, Xi Q, Wang Z. The HRP3 PWWP domain recognizes the minor groove of double-stranded DNA and recruits HRP3 to chromatin. Nucleic Acids Res 2019; 47:5436-5448. [PMID: 31162607 PMCID: PMC6547440 DOI: 10.1093/nar/gkz294] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/12/2022] Open
Abstract
HDGF-related protein 3 (HRP3, also known as HDGFL3) belongs to the family of HDGF-related proteins (HRPs) and plays an essential role in hepatocellular carcinoma pathogenesis. All HRPs have a PWWP domain at the N-terminus that binds both histone and DNA substrates. Despite previous advances in PWWP domains, the molecular basis by which HRP3 interacts with chromatin is unclear. In this study, we solved the crystal structures of the HRP3 PWWP domain in complex with various double-stranded DNAs with/without bound histone peptides. We found that HRP3 PWWP bound to the phosphate backbone of the DNA minor groove and showed a preference for DNA molecules bearing a narrow minor groove width. In addition, HRP3 PWWP preferentially bound to histone peptides bearing the H3K36me3/2 modification. HRP3 PWWP uses two adjacent surfaces to bind both DNA and histone substrates simultaneously, enabling us to generate a model illustrating the recruitment of PWWP to H3K36me3-containing nucleosomes. Cell-based analysis indicated that both DNA and histone binding by the HRP3 PWWP domain is important for HRP3 recruitment to chromatin in vivo. Our work establishes that HRP3 PWWP is a new family of minor groove-specific DNA-binding proteins, which improves our understanding of HRP3 and other PWWP domain-containing proteins.
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Affiliation(s)
- Wei Tian
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Peiqiang Yan
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ning Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Arghya Chakravorty
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
- Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg, 35043 Marburg, Germany
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhanxin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
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13
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Solution structure of TbTFIIS2-2 PWWP domain from Trypanosoma brucei and its binding to H4K17me3 and H3K32me3. Biochem J 2019; 476:421-431. [PMID: 30626613 DOI: 10.1042/bcj20180870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/01/2019] [Accepted: 01/08/2019] [Indexed: 11/17/2022]
Abstract
Posttranslational modifications (PTMs) of core histones, such as histone methylation, play critical roles in a variety of biological processes including transcription regulation, chromatin condensation and DNA repair. In T. brucei, no domain recognizing methylated histone has been identified so far. TbTFIIS2-2, as a potential transcription elongation factors in T. brucei, contains a PWWP domain in the N-terminus which shares low sequence similarity compared with other PWWP domains and is absent from other TFIIS factors. In the present study, the solution structure of TbTFIIS2-2 PWWP domain was determined by NMR spectroscopy. TbTFIIS2-2 PWWP domain adopts a global fold containing a five-strand β-barrel and two C-terminal α-helices similar to other PWWP domains. Moreover, through systematic screening, we revealed that TbTFIIS2-2 PWWP domain is able to bind H4K17me3 and H3K32me3. Meanwhile, we identified the critical residues responsible for the binding ability of TbTFIIS2-2 PWWP domain. The conserved cage formed by the aromatic amino acids in TbTFIIS2-2 PWWP domain is essential for its binding to methylated histones.
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14
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Weaver TM, Morrison EA, Musselman CA. Reading More than Histones: The Prevalence of Nucleic Acid Binding among Reader Domains. Molecules 2018; 23:molecules23102614. [PMID: 30322003 PMCID: PMC6222470 DOI: 10.3390/molecules23102614] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/02/2018] [Accepted: 10/07/2018] [Indexed: 01/09/2023] Open
Abstract
The eukaryotic genome is packaged into the cell nucleus in the form of chromatin, a complex of genomic DNA and histone proteins. Chromatin structure regulation is critical for all DNA templated processes and involves, among many things, extensive post-translational modification of the histone proteins. These modifications can be “read out” by histone binding subdomains known as histone reader domains. A large number of reader domains have been identified and found to selectively recognize an array of histone post-translational modifications in order to target, retain, or regulate chromatin-modifying and remodeling complexes at their substrates. Interestingly, an increasing number of these histone reader domains are being identified as also harboring nucleic acid binding activity. In this review, we present a summary of the histone reader domains currently known to bind nucleic acids, with a focus on the molecular mechanisms of binding and the interplay between DNA and histone recognition. Additionally, we highlight the functional implications of nucleic acid binding in chromatin association and regulation. We propose that nucleic acid binding is as functionally important as histone binding, and that a significant portion of the as yet untested reader domains will emerge to have nucleic acid binding capabilities.
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Affiliation(s)
- Tyler M Weaver
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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15
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Li Z, Kono H. Investigating the Influence of Arginine Dimethylation on Nucleosome Dynamics Using All-Atom Simulations and Kinetic Analysis. J Phys Chem B 2018; 122:9625-9634. [DOI: 10.1021/acs.jpcb.8b05067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Zhenhai Li
- Molecular Modeling and Simulation (MMS) Group, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7, Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation (MMS) Group, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7, Umemidai, Kizugawa, Kyoto 619-0215, Japan
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16
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Gain-of-function mutations in DNMT3A in patients with paraganglioma. Genet Med 2018; 20:1644-1651. [PMID: 29740169 DOI: 10.1038/s41436-018-0003-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 03/20/2018] [Indexed: 11/08/2022] Open
Abstract
PURPOSE The high percentage of patients carrying germline mutations makes pheochromocytomas/paragangliomas the most heritable of all tumors. However, there are still cases unexplained by mutations in the known genes. We aimed to identify the genetic cause of disease in patients strongly suspected of having hereditary tumors. METHODS Whole-exome sequencing was applied to the germlines of a parent-proband trio. Genome-wide methylome analysis, RNA-seq, CRISPR/Cas9 gene editing, and targeted sequencing were also performed. RESULTS We identified a novel de novo germline mutation in DNMT3A, affecting a highly conserved residue located close to the aromatic cage that binds to trimethylated histone H3. DNMT3A-mutated tumors exhibited significant hypermethylation of homeobox-containing genes, suggesting an activating role of the mutation. CRISPR/Cas9-mediated knock-in in HeLa cells led to global changes in methylation, providing evidence of the DNMT3A-altered function. Targeted sequencing revealed subclonal somatic mutations in six additional paragangliomas. Finally, a second germline DNMT3A mutation, also causing global tumor DNA hypermethylation, was found in a patient with a family history of pheochromocytoma. CONCLUSION Our findings suggest that DNMT3A may be a susceptibility gene for paragangliomas and, if confirmed in future studies, would represent the first example of gain-of-function mutations affecting a DNA methyltransferase gene involved in cancer predisposition.
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17
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Morrison EA, Bowerman S, Sylvers KL, Wereszczynski J, Musselman CA. The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome. eLife 2018; 7:31481. [PMID: 29648537 PMCID: PMC5953545 DOI: 10.7554/elife.31481] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/11/2018] [Indexed: 01/08/2023] Open
Abstract
Histone tails harbor a plethora of post-translational modifications that direct the function of chromatin regulators, which recognize them through effector domains. Effector domain/histone interactions have been broadly studied, but largely using peptide fragments of histone tails. Here, we extend these studies into the nucleosome context and find that the conformation adopted by the histone H3 tails is inhibitory to BPTF PHD finger binding. Using NMR spectroscopy and MD simulations, we show that the H3 tails interact robustly but dynamically with nucleosomal DNA, substantially reducing PHD finger association. Altering the electrostatics of the H3 tail via modification or mutation increases accessibility to the PHD finger, indicating that PTM crosstalk can regulate effector domain binding by altering nucleosome conformation. Together, our results demonstrate that the nucleosome context has a dramatic impact on signaling events at the histone tails, and highlights the importance of studying histone binding in the context of the nucleosome.
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Affiliation(s)
- Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Samuel Bowerman
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois.,Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Kelli L Sylvers
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Jeff Wereszczynski
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois.,Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
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18
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Affiliation(s)
- Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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19
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Bacot-Davis VR, Bassenden AV, Sprules T, Berghuis AM. Effect of solvent and protein dynamics in ligand recognition and inhibition of aminoglycoside adenyltransferase 2″-Ia. Protein Sci 2017; 26:1852-1863. [PMID: 28734024 DOI: 10.1002/pro.3224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/24/2017] [Accepted: 07/03/2017] [Indexed: 01/15/2023]
Abstract
The aminoglycoside modifying enzyme (AME) ANT(2″)-Ia is a significant target for next generation antibiotic development. Structural studies of a related aminoglycoside-modifying enzyme, ANT(3″)(9), revealed this enzyme contains dynamic, disordered, and well-defined segments that modulate thermodynamically before and after antibiotic binding. Characterizing these structural dynamics is critical for in situ screening, design, and development of contemporary antibiotics that can be implemented in a clinical setting to treat potentially lethal, antibiotic resistant, human infections. Here, the first NMR structural ensembles of ANT(2″)-Ia are presented, and suggest that ATP-aminoglycoside binding repositions the nucleotidyltransferase (NT) and C-terminal domains for catalysis to efficiently occur. Residues involved in ligand recognition were assessed by site-directed mutagenesis. In vitro activity assays indicate a critical role for I129 toward aminoglycoside modification in addition to known catalytic D44, D46, and D48 residues. These observations support previous claims that ANT aminoglycoside sub-class promiscuity is not solely due to binding cleft size, or inherent partial disorder, but can be controlled by ligand modulation on distinct dynamic and thermodynamic properties of ANTs under cellular conditions. Hydrophobic interactions in the substrate binding cleft, as well as solution dynamics in the C-terminal tail of ANT(2″)-Ia, advocate toward design of kanamycin-derived cationic lipid aminoglycoside analogs, some of which have already shown antimicrobial activity in vivo against kanamycin and gentamicin-resistant P. aeruginosa. This data will drive additional in silico, next generation antibiotic development for future human use to combat increasingly prevalent antimicrobial resistance.
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Affiliation(s)
- Valjean R Bacot-Davis
- McGill University, Biochemistry, 3649 Promenade Sir William Osler Room 470, Montreal, QC H3A 0G4, Canada
| | - Angelia V Bassenden
- McGill University, Biochemistry, 3649 Promenade Sir William Osler Room 470, Montreal, QC H3A 0G4, Canada
| | - Tara Sprules
- McGill University, Biochemistry, 3649 Promenade Sir William Osler Room 470, Montreal, QC H3A 0G4, Canada.,Quebec/Eastern Canada NMR Centre, Pulp & Paper Research Centre, 3420 University St. Room 023, Montreal, QC H3A 2A7, Canada
| | - Albert M Berghuis
- McGill University, Biochemistry, 3649 Promenade Sir William Osler Room 470, Montreal, QC H3A 0G4, Canada
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20
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Morrison EA, Sanchez JC, Ronan JL, Farrell DP, Varzavand K, Johnson JK, Gu BX, Crabtree GR, Musselman CA. DNA binding drives the association of BRG1/hBRM bromodomains with nucleosomes. Nat Commun 2017; 8:16080. [PMID: 28706277 PMCID: PMC5519978 DOI: 10.1038/ncomms16080] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 05/26/2017] [Indexed: 01/04/2023] Open
Abstract
BRG1 and BRM, central components of the BAF (mSWI/SNF) chromatin remodelling complex, are critical in chromatin structure regulation. Here, we show that the human BRM (hBRM) bromodomain (BRD) has moderate specificity for H3K14ac. Surprisingly, we also find that both BRG1 and hBRM BRDs have DNA-binding activity. We demonstrate that the BRDs associate with DNA through a surface basic patch and that the BRD and an adjacent AT-hook make multivalent contacts with DNA, leading to robust affinity and moderate specificity for AT-rich elements. Although we show that the BRDs can bind to both DNA and H3K14ac simultaneously, the histone-binding activity does not contribute substantially to nucleosome targeting in vitro. In addition, we find that neither BRD histone nor DNA binding contribute to the global chromatin affinity of BRG1 in mouse embryonic stem cells. Together, our results suggest that association of the BRG1/hBRM BRD with nucleosomes plays a regulatory rather than targeting role in BAF activity.
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Affiliation(s)
- Emma A. Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Julio C. Sanchez
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jehnna L. Ronan
- Program in Cancer Biology, and Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Daniel P. Farrell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Katayoun Varzavand
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jenna K. Johnson
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Brian X. Gu
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Gerald R. Crabtree
- Program in Cancer Biology, and Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Catherine A. Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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21
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Rondelet G, Dal Maso T, Willems L, Wouters J. Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B. J Struct Biol 2016; 194:357-67. [PMID: 26993463 DOI: 10.1016/j.jsb.2016.03.013] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 01/01/2023]
Abstract
DNA methylation is an important epigenetic modification involved in chromatin organization and gene expression. The function of DNA methylation depends on cell context and is correlated with histone modification patterns. In particular, trimethylation of Lys36 on histone H3 tail (H3K36me3) is associated with DNA methylation and elongation phase of transcription. PWWP domains of the de novo DNA methyltransferases DNMT3A and DNMT3B read this epigenetic mark to guide DNA methylation. Here we report the first crystal structure of the DNMT3B PWWP domain-H3K36me3 complex. Based on this structure, we propose a model of the DNMT3A PWWP domain-H3K36me3 complex and build a model of DNMT3A (PWWP-ADD-CD) in a nucleosomal context. The trimethylated side chain of Lys36 (H3K36me3) is inserted into an aromatic cage similar to the "Royal" superfamily domains known to bind methylated histones. A key interaction between trimethylated Lys36 and a conserved water molecule stabilized by Ser270 explains the lack of affinity of mutated DNMT3B (S270P) for the H3K36me3 epigenetic mark in the ICF (Immunodeficiency, Centromeric instability and Facial abnormalities) syndrome. The model of the DNMT3A-DNMT3L heterotetramer in complex with a dinucleosome highlights the mechanism for recognition of nucleosome by DNMT3s and explains the periodicity of de novo DNA methylation.
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Affiliation(s)
- Grégoire Rondelet
- Department of Chemistry, University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium.
| | - Thomas Dal Maso
- Department of Chemistry, University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Luc Willems
- Molecular and Cellular Epigenetics (GIGA) and Molecular Biology (Gembloux Agro-Bio Tech), University of Liège (ULg), 4000 Liège, Belgium
| | - Johan Wouters
- Department of Chemistry, University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium
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22
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Lopez AP, Kugelman JR, Garcia-Rivera J, Urias E, Salinas SA, Fernandez-Zapico ME, Llano M. The Structure-Specific Recognition Protein 1 Associates with Lens Epithelium-Derived Growth Factor Proteins and Modulates HIV-1 Replication. J Mol Biol 2016; 428:2814-31. [PMID: 27216501 DOI: 10.1016/j.jmb.2016.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 04/21/2016] [Accepted: 05/16/2016] [Indexed: 10/21/2022]
Abstract
The lens epithelium-derived growth factor p75 (LEDGF/p75) is a chromatin-bound protein essential for efficient lentiviral integration. Genome-wide studies have located LEDGF/p75 inside actively transcribed genes where it mediates lentiviral integration. Although its role in HIV-1 integration is clearly established, the role of LEDGF/p75-associated proteins in HIV-1 infection remains unexplored. Using protein-protein interaction assays, we demonstrated that LEDGF/p75 complexes with a chromatin-remodeling complex facilitates chromatin transcription (FACT), a heterodimer of the structure-specific recognition protein 1 (SSRP1) and the human homolog of suppressor of Ty 16 (hSpt16). Detailed analysis of the interaction of LEDGF/p75 with the FACT complex indicates that LEDGF/p75 interacts with SSRP1 in an hSpt16-independent manner that requires the PWWP domain of LEDGF proteins and the HMG domain of SSRP1. Functional characterizations demonstrate a LEDGF/p75-independent role of SSRP1 in the regulation of HIV-1 replication. shRNA-mediated partial knockdown of SSRP1 reduces HIV-1 infection, but not Murine Leukemia Virus, in human CD4(+) T cells. Similarly, SSRP1 knockdown affects infection by HIV-1-derived viruses that express genes from the viral LTR but not from an internal immediate-early CMV promoter, suggesting a role of SSRP1 in LTR-driven gene expression but not in viral DNA integration. Together, our data demonstrate for the first time the association of LEDGF proteins with the FACT complex and give further support to a role of SSRP1 in HIV-1 infection.
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Affiliation(s)
- Angelica P Lopez
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Jeffrey R Kugelman
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Jose Garcia-Rivera
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Eduardo Urias
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Sandra A Salinas
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | | | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA.
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23
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Wang R, Zhang J, Liao S, Tu X. Solution structure of TbTFIIS2-1 PWWP domain from Trypanosoma brucei. Proteins 2016; 84:912-9. [PMID: 27005948 DOI: 10.1002/prot.25035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/02/2016] [Accepted: 03/12/2016] [Indexed: 12/28/2022]
Abstract
TbTFIIS2-1, one of the two TFIIS homologues of Trypanosome brucei (T. brucei), cooperates with TbTFIIS1 in regulating transcription in T. brcuei. Structurally divergent from other TFIIS homologues from higher organisms, TbTFIIS2-1 contains an additional N-terminal PWWP domain besides other three conserved domains, which may imply potential role of TbTFIIS2-1 in transcription regulation. Here, we determined the solution structure of PWWP domain of TbTFIIS2-1 by NMR spectroscopy, which was the first solution structure of PWWP domain solved in trypanosomatid. In spite of poor sequence similarity between PWWP domains, this domain of TbTFIIS2-1 adopts a conserved 3D-structure, which contains a five-stranded β-barrel and a C-terminal α-helix. Furthermore, we found that TbTFIIS2-1 PWWP domain may be a protein-protein interaction module without the ability of DNA recognition and methyl-group interaction. Proteins 2016; 84:912-919. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rui Wang
- Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
| | - Shanhui Liao
- Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
| | - Xiaoming Tu
- Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
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24
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Rona GB, Eleutherio ECA, Pinheiro AS. PWWP domains and their modes of sensing DNA and histone methylated lysines. Biophys Rev 2016; 8:63-74. [PMID: 28510146 DOI: 10.1007/s12551-015-0190-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/14/2015] [Indexed: 12/21/2022] Open
Abstract
Chromatin plays an important role in gene transcription control, cell cycle progression, recombination, DNA replication and repair. The fundamental unit of chromatin, the nucleosome, is formed by a DNA duplex wrapped around an octamer of histones. Histones are susceptible to various post-translational modifications, covalent alterations that change the chromatin status. Lysine methylation is one of the major post-translational modifications involved in the regulation of chromatin function. The PWWP domain is a member of the Royal superfamily that functions as a chromatin methylation reader by recognizing both DNA and histone methylated lysines. The PWWP domain three-dimensional structure is based on an N-terminal hydrophobic β-barrel responsible for histone methyl-lysine binding, and a C-terminal α-helical domain. In this review, we set out to discuss the most recent literature on PWWP domains, focusing on their structural features and the mechanisms by which they specifically recognize DNA and histone methylated lysines at the level of the nucleosome.
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Affiliation(s)
- Germana B Rona
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Elis C A Eleutherio
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil.
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25
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van Nuland R, Gozani O. Histone H4 Lysine 20 (H4K20) Methylation, Expanding the Signaling Potential of the Proteome One Methyl Moiety at a Time. Mol Cell Proteomics 2015; 15:755-64. [PMID: 26598646 DOI: 10.1074/mcp.r115.054742] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Indexed: 12/13/2022] Open
Abstract
Covalent post-translational modifications (PTMs) of proteins can regulate the structural and functional state of a protein in the absence of primary changes in the underlying sequence. Common PTMs include phosphorylation, acetylation, and methylation. Histone proteins are critical regulators of the genome and are subject to a highly abundant and diverse array of PTMs. To highlight the functional complexity added to the proteome by lysine methylation signaling, here we will focus on lysine methylation of histone proteins, an important modification in the regulation of chromatin and epigenetic processes. We review the signaling pathways and functions associated with a single residue, H4K20, as a model chromatin and clinically important mark that regulates biological processes ranging from the DNA damage response and DNA replication to gene expression and silencing.
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Affiliation(s)
- Rick van Nuland
- From the Department of Biology, Stanford University, Stanford, California 94305
| | - Or Gozani
- From the Department of Biology, Stanford University, Stanford, California 94305
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26
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Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The First Residue of the PWWP Motif Modulates HATH Domain Binding, Stability, and Protein-Protein Interaction. Biochemistry 2015; 54:4063-74. [PMID: 26067205 DOI: 10.1021/acs.biochem.5b00454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hepatoma-derived growth factor (hHDGF) and HDGF-related proteins (HRPs) contain conserved N-terminal HATH domains with a characteristic structural motif, namely the PWWP motif. The HATH domain has attracted attention because of its ability to bind with heparin/heparan sulfate, DNA, and methylated histone peptide. Depending on the sequence of the PWWP motif, HRP HATHs are classified into P-type (Pro-His-Trp-Pro) and A-type (Ala-His-Trp-Pro) forms. A-type HATH is highly unstable and tends to precipitate in solution. We replaced the Pro residue in P-type HATHHDGF with Ala and evaluated the influence on structure, dynamics, and ligand binding. Nuclear magnetic resonance (NMR) hydrogen/deuterium exchange and circular dichroism (CD) measurements revealed reduced stability. Analysis of NMR backbone (15)N relaxations (R1, R2, and nuclear Overhauser effect) revealed additional backbone dynamics in the interface between the β-barrel and the C-terminal helix bundle. The β1-β2 loop, where the AHWP sequence is located, has great structural flexibility, which aids HATH-HATH interaction through the loop. A-type HATH, therefore, shows a stronger tendency to aggregate when binding with heparin and DNA oligomers. This study defines the role of the first residue of the PWWP motif in modulating HATH domain stability and oligomer formation in binding.
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Affiliation(s)
| | | | | | | | - Wei-Cheng Lo
- §Institute of Bioinformatics and Structural Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yi-Jan Lin
- ∥Graduate Institute of Natural Products and Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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27
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Kenzior A, Folk WR. Arabidopsis thaliana MSI4/FVE associates with members of a novel family of plant specific PWWP/RRM domain proteins. PLANT MOLECULAR BIOLOGY 2015; 87:329-339. [PMID: 25600937 DOI: 10.1007/s11103-014-0280-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
AtMSI4/FVE/ACG1, one of five Arabidopsis thaliana genes encoding MSI1-like proteins, helps determine plant growth and development (including control of flowering), as well as responses to certain biotic and abiotic stresses. We reasoned that the product of this gene, AtMSI4, acts through protein partners, which we have co-immunopurified with AtMSI4 from A. thaliana suspension culture cells and identified by liquid chromatography-mass spectrometry (LC-MS). Many of the proteins associated with AtMSI4 have distinct RNA recognition motif (RRM) domains, which we determined to be responsible for association with AtMSI4; and most of the associated RRM domain proteins also contain PWWP domains that are specific to plants. We propose these novel ATMSI4-associated proteins help form nucleoprotein complexes that determine pleiotropic functional properties of AtMSI4/FVE/ACG1 involving plant development and responses to stress.
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Affiliation(s)
- Alexander Kenzior
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA,
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Qin S, Min J. Structure and function of the nucleosome-binding PWWP domain. Trends Biochem Sci 2014; 39:536-47. [PMID: 25277115 DOI: 10.1016/j.tibs.2014.09.001] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/26/2014] [Accepted: 09/08/2014] [Indexed: 12/11/2022]
Abstract
PWWP domain-containing proteins are often involved in chromatin-associated biological processes, such as transcriptional regulation and DNA repair, and recent studies have shown that the PWWP domain specifies chromatin localization. Mutations in the PWWP domain, a 100-150 amino acid motif, have been linked to various human diseases, emphasizing its importance. Structural studies reveal that PWWP domains possess a conserved aromatic cage for histone methyl-lysine recognition, and synergistically bind both histone and DNA, which contributes to their nucleosome-binding ability and chromatin localization. Furthermore, the PWWP domain often cooperates with other histone and DNA 'reader' or 'modifier' domains to evoke crosstalk between various epigenetic marks. Here, we discuss these recent advances in understanding the structure and function of the PWWP domain.
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Affiliation(s)
- Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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Gilbert TM, McDaniel SL, Byrum SD, Cades JA, Dancy BCR, Wade H, Tackett AJ, Strahl BD, Taverna SD. A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions. Mol Cell Proteomics 2014; 13:2883-95. [PMID: 25104842 DOI: 10.1074/mcp.m114.038224] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Post-translational modifications of histones, such as acetylation and methylation, are differentially positioned in chromatin with respect to gene organization. For example, although histone H3 is often trimethylated on lysine 4 (H3K4me3) and acetylated on lysine 14 (H3K14ac) at active promoter regions, histone H3 lysine 36 trimethylation (H3K36me3) occurs throughout the open reading frames of transcriptionally active genes. The conserved yeast histone acetyltransferase complex, NuA3, specifically binds H3K4me3 through a plant homeodomain (PHD) finger in the Yng1 subunit, and subsequently catalyzes the acetylation of H3K14 through the histone acetyltransferase domain of Sas3, leading to transcription initiation at a subset of genes. We previously found that Ylr455w (Pdp3), an uncharacterized proline-tryptophan-tryptophan-proline (PWWP) domain-containing protein, copurifies with stable members of NuA3. Here, we employ mass-spectrometric analysis of affinity purified Pdp3, biophysical binding assays, and genetic analyses to classify NuA3 into two functionally distinct forms: NuA3a and NuA3b. Although NuA3a uses the PHD finger of Yng1 to interact with H3K4me3 at the 5'-end of open reading frames, NuA3b contains the unique member, Pdp3, which regulates an interaction between NuA3b and H3K36me3 at the transcribed regions of genes through its PWWP domain. We find that deletion of PDP3 decreases NuA3-directed transcription and results in growth defects when combined with transcription elongation mutants, suggesting NuA3b acts as a positive elongation factor. Finally, we determine that NuA3a, but not NuA3b, is synthetically lethal in combination with a deletion of the histone acetyltransferase GCN5, indicating NuA3b has a specialized role at coding regions that is independent of Gcn5 activity. Collectively, these studies define a new form of the NuA3 complex that associates with H3K36me3 to effect transcriptional elongation. MS data are available via ProteomeXchange with identifier PXD001156.
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Affiliation(s)
- Tonya M Gilbert
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Stephen L McDaniel
- ¶Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Stephanie D Byrum
- ‖Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205
| | - Jessica A Cades
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Blair C R Dancy
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Herschel Wade
- **Department of Biophysics and Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Alan J Tackett
- ‖Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205
| | - Brian D Strahl
- ¶Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599; ‡‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Sean D Taverna
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205;
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Musselman CA, Khorasanizadeh S, Kutateladze TG. Towards understanding methyllysine readout. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:686-93. [PMID: 24727128 DOI: 10.1016/j.bbagrm.2014.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 03/19/2014] [Accepted: 04/02/2014] [Indexed: 02/09/2023]
Abstract
BACKGROUND Lysine methylation is the most versatile covalent posttranslational modification (PTM) found in histones and non-histone proteins. Over the past decade a number of methyllysine-specific readers have been discovered and their interactions with histone tails have been structurally and biochemically characterized. More recently innovative experimental approaches have emerged that allow for studying reader interactions in the context of the full nucleosome and nucleosomal arrays. SCOPE OF REVIEW In this review we give a brief overview of the known mechanisms of histone lysine methylation readout, summarize progress recently made in exploring interactions with methylated nucleosomes, and discuss the latest advances in the development of small molecule inhibitors of the methyllysine-specific readers. MAJOR CONCLUSIONS New studies reveal various reader-nucleosome contacts outside the methylated histone tail, thus offering a better model for association of histone readers to chromatin and broadening our understanding of the functional implications of these interactions. In addition, some progress has been made in the design of antagonists of these interactions. GENERAL SIGNIFICANCE Specific lysine methylation patterns are commonly associated with certain chromatin states and genomic elements, and are linked to distinct biological outcomes such as transcription activation or repression. Disruption of patterns of histone modifications is associated with a number of diseases, and there is tremendous therapeutic potential in targeting histone modification pathways. Thus, investigating binding of readers of these modifications is not only important for elucidating fundamental mechanisms of chromatin regulation, but also necessary for the design of targeted therapeutics. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
| | - Sepideh Khorasanizadeh
- Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Liu Y, Liu K, Qin S, Xu C, Min J. Epigenetic targets and drug discovery: part 1: histone methylation. Pharmacol Ther 2014; 143:275-94. [PMID: 24704322 DOI: 10.1016/j.pharmthera.2014.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/24/2014] [Indexed: 01/10/2023]
Abstract
Dynamic chromatin structure is modulated by post-translational modifications on histones, such as acetylation, phosphorylation and methylation. Research on histone methylation has become the most flourishing area of epigenetics in the past fourteen years, and a large amount of data has been accumulated regarding its biology and disease implications. Correspondingly, a lot of efforts have been made to develop small molecule compounds that can specifically modulate histone methyltransferases and methylation reader proteins, aiming for potential therapeutic drugs. Here, we summarize recent progress in chemical probe and drug discovery of histone methyltransferases and methylation reader proteins. For each target, we will review their biological/biochemical functions first, and then focus on their disease implications and drug discovery. We can also see that structure-based compound design and optimization plays a critical role in facilitating the development of highly potent and selective chemical probes and inhibitors for these targets.
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Affiliation(s)
- Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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Wagner T, Robaa D, Sippl W, Jung M. Mind the Methyl: Methyllysine Binding Proteins in Epigenetic Regulation. ChemMedChem 2014; 9:466-83. [DOI: 10.1002/cmdc.201300422] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 11/07/2022]
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Collado-Romero M, Alós E, Prieto P. Unravelling the proteomic profile of rice meiocytes during early meiosis. FRONTIERS IN PLANT SCIENCE 2014; 5:356. [PMID: 25104955 PMCID: PMC4109522 DOI: 10.3389/fpls.2014.00356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/03/2014] [Indexed: 05/06/2023]
Abstract
Transfer of genetic traits from wild or related species into cultivated rice is nowadays an important aim in rice breeding. Breeders use genetic crosses to introduce desirable genes from exotic germplasms into cultivated rice varieties. However, in many hybrids there is only a low level of pairing (if existing) and recombination at early meiosis between cultivated rice and wild relative chromosomes. With the objective of getting deeper into the knowledge of the proteins involved in early meiosis, when chromosomes associate correctly in pairs and recombine, the proteome of isolated rice meiocytes has been characterized by nLC-MS/MS at every stage of early meiosis (prophase I). Up to 1316 different proteins have been identified in rice isolated meiocytes in early meiosis, being 422 exclusively identified in early prophase I (leptotene, zygotene, or pachytene). The classification of proteins in functional groups showed that 167 were related to chromatin structure and remodeling, nucleic acid binding, cell-cycle regulation, and cytoskeleton. Moreover, the putative roles of 16 proteins which have not been previously associated to meiosis or were not identified in rice before, are also discussed namely: seven proteins involved in chromosome structure and remodeling, five regulatory proteins [such as SKP1 (OSK), a putative CDK2 like effector], a protein with RNA recognition motifs, a neddylation-related protein, and two microtubule-related proteins. Revealing the proteins involved in early meiotic processes could provide a valuable tool kit to manipulate chromosome associations during meiosis in rice breeding programs. The data have been deposited to the ProteomeXchange with the PXD001058 identifier.
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Affiliation(s)
| | | | - Pilar Prieto
- *Correspondence: Pilar Prieto, Plant Breeding Department, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas, Av. Menéndez Pidal s/n, Campus Alameda del Obispo, Apartado 4084, Córdoba 14080, Spain e-mail:
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Morchikh M, Naughtin M, Di Nunzio F, Xavier J, Charneau P, Jacob Y, Lavigne M. TOX4 and NOVA1 proteins are partners of the LEDGF PWWP domain and affect HIV-1 replication. PLoS One 2013; 8:e81217. [PMID: 24312278 PMCID: PMC3842248 DOI: 10.1371/journal.pone.0081217] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 10/10/2013] [Indexed: 12/31/2022] Open
Abstract
PWWP domains are involved in the chromatin attachment of several proteins. They bind to both DNA and proteins and their interaction with specific histone methylation marks define them as a new class of histone code readers. The lens epithelium derived growth factor (LEDGF/p75) contains an N-terminal PWWP domain necessary for its interaction with chromatin but also a C-terminal domain which interacts with several proteins, such as lentiviral integrases. These two domains confer a chromatin-tethering function to LEDGF/p75 and in the case of lentiviral integrases, this tethering participates in the efficiency and site selectivity of integration. Although proteins interacting with LEDGF/p75 C-terminal domain have been extensively studied, no data exist about partners of its PWWP domain regulating its interaction with chromatin. In this study, we report the identification by yeast-two-hybrid of thirteen potential partners of the LEDGF PWWP domain. Five of these interactions were confirmed in mammalian cells, using both a protein complementation assay and co-immunoprecipitation approaches. Three of these partners interact with full length LEDGF/p75, they are specific for PWWP domains of the HDGF family and they require PWWP amino acids essential for the interaction with chromatin. Among them, the transcription activator TOX4 and the splicing cofactor NOVA1 were selected for a more extensive study. These two proteins or their PWWP interacting regions (PIR) colocalize with LEDGF/p75 in Hela cells and interact in vitro in the presence of DNA. Finally, single round VSV-G pseudotyped HIV-1 but not MLV infection is inhibited in cells overexpressing these two PIRs. The observed inhibition of infection can be attributed to a defect in the integration step. Our data suggest that a regulation of LEDGF interaction with chromatin by cellular partners of its PWWP domain could be involved in several processes linked to LEDGF tethering properties, such as lentiviral integration, DNA repair or transcriptional regulation.
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Affiliation(s)
- Mehdi Morchikh
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
- Institut Pasteur, Unité de Virologie Structurale, Centre National de la Recherche Scientifique, Unité de recherche associée, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Monica Naughtin
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
| | - Francesca Di Nunzio
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, Centre National de la Recherche Scientifique, Paris, France
| | - Johan Xavier
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
| | - Pierre Charneau
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, Centre National de la Recherche Scientifique, Paris, France
| | - Yves Jacob
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Centre National de la Recherche Scientifique, Paris, France
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Marc Lavigne
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
- Institut Pasteur, Unité de Virologie Structurale, Centre National de la Recherche Scientifique, Unité de recherche associée, Paris, France
- * E-mail:
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Zhang J, Dai K, Liao S, Tu X. ¹H, ¹³C and ¹³N resonance assignments of TbTFIIS2-2 PWWP domain from Trypanosoma brucei. BIOMOLECULAR NMR ASSIGNMENTS 2013; 7:207-209. [PMID: 22836947 DOI: 10.1007/s12104-012-9411-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 07/16/2012] [Indexed: 06/01/2023]
Abstract
PWWP domains are found in eukaryotic proteins from yeast to mammals and are involved in DNA methylation, DNA repair and regulation of transcription. Here we report the resonance assignments of TbTFIIS2-2 PWWP domain from Trypanosoma brucei for further understanding of the relationship between its structure and function.
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Affiliation(s)
- Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, People's Republic of China
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Abstract
Methylation of histone lysine and arginine residues constitutes a highly complex control system directing diverse functions of the genome. Owing to their immense signaling potential with distinct sites of methylation and defined methylation states of mono-, di- or trimethylation as well as their higher biochemical stability compared with other histone modifications, these marks are thought to be part of epigenetic regulatory networks. Biological principles of how histone methylation is read and translated have emerged over the last few years. Only very few methyl marks directly impact chromatin. Conversely, a large number of histone methylation binding proteins has been identified. These contain specialized modules that are recruited to chromatin in a methylation site- and state-specific manner. Besides the molecular mechanisms of interaction, patterns of regulation of the binding proteins are becoming evident.
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Affiliation(s)
- Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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Hu J, Wang Y. p53 and the PWWP domain containing effector proteins in chromatin damage repair. CELL & DEVELOPMENTAL BIOLOGY 2013; 2:112. [PMID: 25264544 PMCID: PMC4175562 DOI: 10.4172/2168-9296.1000112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In eukaryotic cells, DNA damage repair occurs on a template DNA that is organized with histones to form nucleosomes and chromatin structures. As such, chromatin plays an important role in DNA damage repair. In this review, we will use "chromatin damage repair" as a framework and highlight recent progress in understanding the role of chromatin, chromatin modifiers, chromatin binding effectors (e.g., the PWWP domain proteins), and the p53 tumor suppressor. We view chromatin as an active participant during DNA damage repair.
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Affiliation(s)
- Jing Hu
- Graduate Program in Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802 USA
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802 USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802 USA
| | - Yanming Wang
- Graduate Program in Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802 USA
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802 USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802 USA
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van Nuland R, van Schaik FM, Simonis M, van Heesch S, Cuppen E, Boelens R, Timmers HM, van Ingen H. Nucleosomal DNA binding drives the recognition of H3K36-methylated nucleosomes by the PSIP1-PWWP domain. Epigenetics Chromatin 2013; 6:12. [PMID: 23656834 PMCID: PMC3663649 DOI: 10.1186/1756-8935-6-12] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 04/16/2013] [Indexed: 12/31/2022] Open
Abstract
Background Recognition of histone modifications by specialized protein domains is a key step in the regulation of DNA-mediated processes like gene transcription. The structural basis of these interactions is usually studied using histone peptide models, neglecting the nucleosomal context. Here, we provide the structural and thermodynamic basis for the recognition of H3K36-methylated (H3K36me) nucleosomes by the PSIP1-PWWP domain, based on extensive mutational analysis, advanced nuclear magnetic resonance (NMR), and computational approaches. Results The PSIP1-PWWP domain binds H3K36me3 peptide and DNA with low affinity, through distinct, adjacent binding surfaces. PWWP binding to H3K36me nucleosomes is enhanced approximately 10,000-fold compared to a methylated peptide. Based on mutational analyses and NMR data, we derive a structure of the complex showing that the PWWP domain is bound to H3K36me nucleosomes through simultaneous interactions with both methylated histone tail and nucleosomal DNA. Conclusion Concerted binding to the methylated histone tail and nucleosomal DNA underlies the high- affinity, specific recognition of H3K36me nucleosomes by the PSIP1-PWWP domain. We propose that this bipartite binding mechanism is a distinctive and general property in the recognition of histone modifications close to the nucleosome core.
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Affiliation(s)
- Rick van Nuland
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University Utrecht, Padualaan 8, Utrecht, CH, 3854, The Netherlands.
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Eidahl JO, Crowe BL, North JA, McKee CJ, Shkriabai N, Feng L, Plumb M, Graham RL, Gorelick RJ, Hess S, Poirier MG, Foster MP, Kvaratskhelia M. Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes. Nucleic Acids Res 2013; 41:3924-36. [PMID: 23396443 PMCID: PMC3616739 DOI: 10.1093/nar/gkt074] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/27/2012] [Accepted: 01/18/2013] [Indexed: 01/19/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) tethers lentiviral preintegration complexes (PICs) to chromatin and is essential for effective HIV-1 replication. LEDGF/p75 interactions with lentiviral integrases are well characterized, but the structural basis for how LEDGF/p75 engages chromatin is unknown. We demonstrate that cellular LEDGF/p75 is tightly bound to mononucleosomes (MNs). Our proteomic experiments indicate that this interaction is direct and not mediated by other cellular factors. We determined the solution structure of LEDGF PWWP and monitored binding to the histone H3 tail containing trimethylated Lys36 (H3K36me3) and DNA by NMR. Results reveal two distinct functional interfaces of LEDGF PWWP: a well-defined hydrophobic cavity, which selectively interacts with the H3K36me3 peptide and adjacent basic surface, which non-specifically binds DNA. LEDGF PWWP exhibits nanomolar binding affinity to purified native MNs, but displays markedly lower affinities for the isolated H3K36me3 peptide and DNA. Furthermore, we show that LEDGF PWWP preferentially and tightly binds to in vitro reconstituted MNs containing a tri-methyl-lysine analogue at position 36 of H3 and not to their unmodified counterparts. We conclude that cooperative binding of the hydrophobic cavity and basic surface to the cognate histone peptide and DNA wrapped in MNs is essential for high-affinity binding to chromatin.
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Affiliation(s)
- Jocelyn O. Eidahl
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Brandon L. Crowe
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Justin A. North
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher J. McKee
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Nikoloz Shkriabai
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Lei Feng
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew Plumb
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert L. Graham
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert J. Gorelick
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sonja Hess
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Michael G. Poirier
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mark P. Foster
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mamuka Kvaratskhelia
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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Struck AW, Thompson ML, Wong LS, Micklefield J. S-Adenosyl-Methionine-Dependent Methyltransferases: Highly Versatile Enzymes in Biocatalysis, Biosynthesis and Other Biotechnological Applications. Chembiochem 2012. [DOI: 10.1002/cbic.201200556] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Shindo H, Suzuki R, Tsuchiya W, Taichi M, Nishiuchi Y, Yamazaki T. PHD finger of the SUMO ligase Siz/PIAS family in rice reveals specific binding for methylated histone H3 at lysine 4 and arginine 2. FEBS Lett 2012; 586:1783-9. [PMID: 22626555 DOI: 10.1016/j.febslet.2012.04.063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 04/27/2012] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
Abstract
We determined the three-dimensional structure of the PHD finger of the rice Siz/PIAS-type SUMO ligase, OsSiz1, by NMR spectroscopy and investigated binding ability for a variety of methylated histone H3 tails, showing that OsSiz1-PHD primarily recognizes dimethylated Arg2 of the histone H3 and that methylations at Arg2 and Lys4 reveal synergy effect on binding to OsSiz1-PHD. The K4 cage of OsSiz1-PHD for trimethylated Lys4 of H3K4me3 was similar to that of the BPTF-PHD finger, while the R2 pocket for Arg2 was different. It is intriguing that the PHD module of Siz/PIAS plays an important role, with collaboration with the DNA binding domain SAP, in gene regulation through SUMOylation of a variety of effectors associated with the methylated arginine-riched chromatin domains.
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Affiliation(s)
- Heisaburo Shindo
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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