1
|
Khudaverdyan N, Lu J, Chen X, Herle G, Song J. The structure of DNA methyltransferase DNMT3C reveals an activity-tuning mechanism for DNA methylation. J Biol Chem 2024:107633. [PMID: 39098534 DOI: 10.1016/j.jbc.2024.107633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/20/2024] [Accepted: 07/26/2024] [Indexed: 08/06/2024] Open
Abstract
DNA methylation is one of the major epigenetic mechanisms crucial for gene regulation and genome stability. De novo DNA methyltransferase DNMT3C is required for silencing evolutionarily young transposons during mice spermatogenesis. Mutation of DNMT3C led to a sterility phenotype that cannot be rescued by its homologues DNMT3A and DNMT3B. However, the structural basis of DNMT3C-mediated DNA methylation remains unknown. Here, we report the structure and mechanism of DNMT3C-mediated DNA methylation. The DNMT3C methyltransferase domain recognizes CpG-containing DNA in a manner similar to that of DNMT3A and DNMT3B, in line with their high sequence similarity. However, two evolutionary covariation sites, C543 and E590, diversify the substrate interaction among DNMT3C, DNMT3A and DNMT3B, resulting in distinct DNA methylation activity and specificity between DNMT3C, DNMT3A and DNMT3B in vitro. In addition, our combined structural and biochemical analysis reveals that the disease-causing rahu mutation of DNMT3C compromises its oligomerization and DNA-binding activities, providing an explanation for the loss of DNA methylation activity caused by this mutation. This study provides a mechanistic insight into DNMT3C-mediated DNA methylation that complements DNMT3A- and DNMT3B-mediated DNA methylation in mice, unravelling a regulatory mechanism by which evolutionary conservation and diversification fine-tunes the activity of de novo DNA methyltransferases.
Collapse
Affiliation(s)
- Nelli Khudaverdyan
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Xinyi Chen
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Genevieve Herle
- Biophysics program, University of California, Riverside, CA 92521, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA 92521, USA; Biophysics program, University of California, Riverside, CA 92521, USA.
| |
Collapse
|
2
|
Han R, Zhu D, Sha J, Zhao B, Jin P, Meng C. Decoding the role of DNA methylation in allergic diseases: from pathogenesis to therapy. Cell Biosci 2024; 14:89. [PMID: 38965641 PMCID: PMC11225420 DOI: 10.1186/s13578-024-01270-0] [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: 02/08/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
Allergic diseases, characterized by a broad spectrum of clinical manifestations and symptoms, encompass a significant category of IgE-mediated atopic disorders, including asthma, allergic rhinitis, atopic dermatitis, and food allergies. These complex conditions arise from the intricate interplay between genetic and environmental factors and are known to contribute to socioeconomic burdens globally. Recent advancements in the study of allergic diseases have illuminated the crucial role of DNA methylation (DNAm) in their pathogenesis. This review explores the factors influencing DNAm in allergic diseases and delves into their mechanisms, offering valuable perspectives for clinicians. Understanding these epigenetic modifications aims to lay the groundwork for improved early prevention strategies. Moreover, our analysis of DNAm mechanisms in these conditions seeks to enhance diagnostic and therapeutic approaches, paving the way for more effective management of allergic diseases in the future.
Collapse
Affiliation(s)
- Ruiming Han
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Dongdong Zhu
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Precise Diagnosis and Treatment of Upper Airway Allergic Diseases, Changchun, China
| | - Jichao Sha
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Precise Diagnosis and Treatment of Upper Airway Allergic Diseases, Changchun, China
| | - Boning Zhao
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, 615 Michael ST NE, Atlanta, GA, 30322, USA.
| | - Cuida Meng
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China.
- Jilin Provincial Key Laboratory of Precise Diagnosis and Treatment of Upper Airway Allergic Diseases, Changchun, China.
| |
Collapse
|
3
|
Akanyibah FA, Zhu Y, Wan A, Ocansey DKW, Xia Y, Fang AN, Mao F. Effects of DNA methylation and its application in inflammatory bowel disease (Review). Int J Mol Med 2024; 53:55. [PMID: 38695222 DOI: 10.3892/ijmm.2024.5379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) is marked by persistent inflammation, and its development and progression are linked to environmental, genetic, immune system and gut microbial factors. DNA methylation (DNAm), as one of the protein modifications, is a crucial epigenetic process used by cells to control gene transcription. DNAm is one of the most common areas that has drawn increasing attention recently, with studies revealing that the interleukin (IL)‑23/IL‑12, wingless‑related integration site, IL‑6‑associated signal transducer and activator of transcription 3, suppressor of cytokine signaling 3 and apoptosis signaling pathways are involved in DNAm and in the pathogenesis of IBD. It has emerged that DNAm‑associated genes are involved in perpetuating the persistent inflammation that characterizes a number of diseases, including IBD, providing a novel therapeutic strategy for exploring their treatment. The present review discusses DNAm‑associated genes in the pathogenesis of IBD and summarizes their application as possible diagnostic, prognostic and therapeutic biomarkers in IBD. This may provide a reference for the particular form of IBD and its related methylation genes, aiding in clinical decision‑making and encouraging therapeutic alternatives.
Collapse
Affiliation(s)
- Francis Atim Akanyibah
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| | - Yi Zhu
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu 212300, P.R. China
| | - Aijun Wan
- Zhenjiang College, Zhenjiang, Jiangsu 212028, P.R. China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yuxuan Xia
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - An-Ning Fang
- Basic Medical School, Anhui Medical College, Hefei, Anhui 230061, P.R. China
| | - Fei Mao
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| |
Collapse
|
4
|
Lu J, Guo Y, Yin J, Chen J, Wang Y, Wang GG, Song J. Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations. Nat Commun 2024; 15:3111. [PMID: 38600075 PMCID: PMC11006857 DOI: 10.1038/s41467-024-47398-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.
Collapse
Affiliation(s)
- Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA
| | - Jianbin Chen
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Gang Greg Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA.
| |
Collapse
|
5
|
Mitchell W, Goeminne LJE, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. eLife 2024; 12:RP90579. [PMID: 38517750 PMCID: PMC10959535 DOI: 10.7554/elife.90579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
Collapse
Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Ludger JE Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Julie Y Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Kerry A Pierce
- Broad Institute of MIT and HarvardCambridgeUnited States
| | | | - Clary B Clish
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| |
Collapse
|
6
|
Bilgic Eltan S, Nain E, Catak MC, Ezen E, Sefer AP, Karimi N, Kiykim A, Kolukisa B, Baser D, Bulutoglu A, Kasap N, Yorgun Altunbas M, Yalcin Gungoren E, Kendir Demirkol Y, Kutlug S, Hancioglu G, Dilek F, Yildiran A, Ozen A, Karakoc-Aydiner E, Erman B, Baris S. Evaluation of Clinical and Immunological Alterations Associated with ICF Syndrome. J Clin Immunol 2023; 44:26. [PMID: 38129713 DOI: 10.1007/s10875-023-01620-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE Immunodeficiency with centromeric instability and facial anomalies (ICF) syndrome is a rare autosomal recessive combined immunodeficiency. The detailed immune responses are not explored widely. We investigated known and novel immune alterations in lymphocyte subpopulations and their association with clinical symptoms in a well-defined ICF cohort. METHODS We recruited the clinical findings from twelve ICF1 and ICF2 patients. We performed detailed immunological evaluation, including lymphocyte subset analyses, upregulation, and proliferation of T cells. We also determined the frequency of circulating T follicular helper (cTFH) and regulatory T (Treg) cells and their subtypes by flow cytometry. RESULTS There were ten ICF1 and two ICF2 patients. We identified two novel homozygous missense mutations in the ZBTB24 gene. Respiratory tract infections were the most common recurrent infections among the patients. Gastrointestinal system (GIS) involvements were observed in seven patients. All patients received intravenous immunoglobulin replacement therapy and antibacterial prophylaxis; two died during the follow-up period. Immunologically, CD4+ T-cell counts, percentages of recent thymic emigrant T cells, and naive CD4+ T decreased in two, five, and four patients, respectively. Impaired T-cell proliferation and reduced CD25 upregulation were detected in all patients. These changes were more prominent in CD8+ T cells. GIS involvements negatively correlated with CD3+ T-, CD3+CD4+ T-, CD16+CD56+ NK-cell counts, and CD4+/CD8+ T-cell ratios. Further, we observed expanded cTFH cells and reduced Treg and follicular regulatory T cells with a skewing to a TH2-like phenotype in all tested subpopulations. CONCLUSION The ICF syndrome encompasses various manifestations affecting multiple end organs. Perturbed T-cell responses with increased cTFH and decreased Treg cells may provide further insight into the immune aberrations observed in ICF syndrome.
Collapse
Affiliation(s)
- Sevgi Bilgic Eltan
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Ercan Nain
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Mehmet Cihangir Catak
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Ege Ezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Asena Pınar Sefer
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Nastaran Karimi
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayca Kiykim
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Burcu Kolukisa
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Dilek Baser
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Alper Bulutoglu
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Nurhan Kasap
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Melek Yorgun Altunbas
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Ezgi Yalcin Gungoren
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Yasemin Kendir Demirkol
- Division of Pediatric Genetics, Umraniye Education and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Seyhan Kutlug
- Division of Pediatric Immunology and Allergy, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Gonca Hancioglu
- Division of Pediatric Immunology and Allergy, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Fatih Dilek
- Department of Pediatrics, Faculty of Medicine, Atlas University, Istanbul, Turkey
| | - Alisan Yildiran
- Division of Pediatric Immunology and Allergy, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Ahmet Ozen
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Safa Baris
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey.
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey.
- Pediatric Allergy and Immunology, Marmara University Hospital, Istanbul, Turkey.
| |
Collapse
|
7
|
Lu J, Fang J, Zhu H, Liang KL, Khudaverdyan N, Song J. Structural basis for the allosteric regulation and dynamic assembly of DNMT3B. Nucleic Acids Res 2023; 51:12476-12491. [PMID: 37941146 PMCID: PMC10711551 DOI: 10.1093/nar/gkad972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/08/2023] [Accepted: 10/14/2023] [Indexed: 11/10/2023] Open
Abstract
Oligomerization of DNMT3B, a mammalian de novo DNA methyltransferase, critically regulates its chromatin targeting and DNA methylation activities. However, how the N-terminal PWWP and ADD domains interplay with the C-terminal methyltransferase (MTase) domain in regulating the dynamic assembly of DNMT3B remains unclear. Here, we report the cryo-EM structure of DNMT3B under various oligomerization states. The ADD domain of DNMT3B interacts with the MTase domain to form an autoinhibitory conformation, resembling the previously observed DNMT3A autoinhibition. Our combined structural and biochemical study further identifies a role for the PWWP domain and its associated ICF mutation in the allosteric regulation of DNMT3B tetramer, and a differential functional impact on DNMT3B by potential ADD-H3K4me0 and PWWP-H3K36me3 bindings. In addition, our comparative structural analysis reveals a coupling between DNMT3B oligomerization and folding of its substrate-binding sites. Together, this study provides mechanistic insights into the allosteric regulation and dynamic assembly of DNMT3B.
Collapse
Affiliation(s)
- Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Jian Fang
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Hongtao Zhu
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | | | - Nelli Khudaverdyan
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| |
Collapse
|
8
|
Mitchell W, Goeminne LJ, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.546730. [PMID: 37425825 PMCID: PMC10327104 DOI: 10.1101/2023.06.30.546730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
Collapse
Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Ludger J.E. Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Julie Y. Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 United States
| | - Kerry A. Pierce
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Angelina H. Choy
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 United States
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| |
Collapse
|
9
|
Westwood MN, Pilarski A, Johnson C, Mamoud S, Meints GA. Backbone Conformational Equilibrium in Mismatched DNA Correlates with Enzyme Activity. Biochemistry 2023; 62:2816-2827. [PMID: 37699121 PMCID: PMC10552547 DOI: 10.1021/acs.biochem.3c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/25/2023] [Indexed: 09/14/2023]
Abstract
T:G mismatches in mammals arise primarily from the deamination of methylated CpG sites or the incorporation of improper nucleotides. The process by which repair enzymes such as thymine DNA glycosylase (TDG) identify a canonical DNA base in the incorrect pairing context remains a mystery. However, the abundant contacts of the repair enzymes with the DNA backbone suggest a role for protein-phosphate interaction in the recognition and repair processes, where conformational properties may facilitate the proper interactions. We have previously used 31P NMR to investigate the energetics of DNA backbone BI-BII interconversion and the effect of a mismatch or lesion compared to canonical DNA and found stepwise differences in ΔG of 1-2 kcal/mol greater than equivalent steps in unmodified DNA. We have currently compared our results to substrate dependence for TDG, MBD4, M. HhaI, and CEBPβ, testing for correlations to sequence and base-pair dependence. We found strong correlations of our DNA phosphate backbone equilibrium (Keq) to different enzyme kinetics or binding parameters of these varied enzymes, suggesting that the backbone equilibrium may play an important role in mismatch recognition and/or conformational rearrangement and energetics during nucleotide flipping or other aspects of enzyme interrogation of the DNA substrate.
Collapse
Affiliation(s)
- M. N. Westwood
- Biophysics
Program, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - A. Pilarski
- Department
of Chemistry and Biochemistry, Missouri
State University, 901 S. National Ave., Springfield, Missouri 65897, United States
| | - C. Johnson
- Department
of Chemistry and Biochemistry, Missouri
State University, 901 S. National Ave., Springfield, Missouri 65897, United States
| | - S. Mamoud
- Department
of Chemistry and Biochemistry, Missouri
State University, 901 S. National Ave., Springfield, Missouri 65897, United States
| | - G. A. Meints
- Department
of Chemistry and Biochemistry, Missouri
State University, 901 S. National Ave., Springfield, Missouri 65897, United States
| |
Collapse
|
10
|
Cho CC, Lin CJ, Huang HH, Yang WZ, Fei CY, Lin HY, Lee MS, Yuan HS. Mechanistic Insights into Harmine-Mediated Inhibition of Human DNA Methyltransferases and Prostate Cancer Cell Growth. ACS Chem Biol 2023; 18:1335-1350. [PMID: 37188336 PMCID: PMC10278071 DOI: 10.1021/acschembio.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023]
Abstract
Mammalian DNA methyltransferases (DNMTs), including DNMT1, DNMT3A, and DNMT3B, are key DNA methylation enzymes and play important roles in gene expression regulation. Dysregulation of DNMTs is linked to various diseases and carcinogenesis, and therefore except for the two approved anticancer azanucleoside drugs, various non-nucleoside DNMT inhibitors have been identified and reported. However, the underlying mechanisms for the inhibitory activity of these non-nucleoside inhibitors still remain largely unknown. Here, we systematically tested and compared the inhibition activities of five non-nucleoside inhibitors toward the three human DNMTs. We found that harmine and nanaomycin A blocked the methyltransferase activity of DNMT3A and DNMT3B more efficiently than resveratrol, EGCG, and RG108. We further determined the crystal structure of harmine in complex with the catalytic domain of the DNMT3B-DNMT3L tetramer revealing that harmine binds at the adenine cavity of the SAM-binding pocket in DNMT3B. Our kinetics assays confirm that harmine competes with SAM to competitively inhibit DNMT3B-3L activity with a Ki of 6.6 μM. Cell-based studies further show that harmine treatment inhibits castration-resistant prostate cancer cell (CRPC) proliferation with an IC50 of ∼14 μM. The CPRC cells treated with harmine resulted in reactivating silenced hypermethylated genes compared to the untreated cells, and harmine cooperated with an androgen antagonist, bicalutamide, to effectively inhibit the proliferation of CRPC cells. Our study thus reveals, for the first time, the inhibitory mechanism of harmine on DNMTs and highlights new strategies for developing novel DNMT inhibitors for cancer treatment.
Collapse
Affiliation(s)
- Chao-Cheng Cho
- Institute
of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic
of China
| | - Chun-Jung Lin
- Institute
of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic
of China
- Graduate
Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, Republic of China
| | - Hsun-Ho Huang
- Institute
of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic
of China
- Graduate
Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, Republic of China
| | - Wei-Zen Yang
- Institute
of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic
of China
| | - Cheng-Yin Fei
- Institute
of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic
of China
| | - Hsin-Ying Lin
- Graduate
Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, Republic of China
| | - Ming-Shyue Lee
- Graduate
Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, Republic of China
| | - Hanna S. Yuan
- Institute
of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic
of China
- Graduate
Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, Republic of China
| |
Collapse
|
11
|
Stillson NJ, Anderson KE, Reich NO. In silico study of selective inhibition mechanism of S-adenosyl-L-methionine analogs for human DNA methyltransferase 3A. Comput Biol Chem 2023; 102:107796. [PMID: 36495748 DOI: 10.1016/j.compbiolchem.2022.107796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
Epigenetic mechanisms leading to transcriptional regulation, including DNA methylation, are frequently dysregulated in diverse cancers. Interfering with aberrant DNA methylation performed by DNA cytosine methyltransferases (DNMTs) is a clinically validated approach. In particular, the selective inhibition of the de novo DNMT3A and DNMT3B enzymes, whose expression is limited to early embryogenesis, adult stem cells, and in cancers, is particularly attractive; such selectivity is likely to attenuate the dose limiting toxicity shown by current, non-selective DNMT inhibitors. We use molecular dynamics (MD) based computational analysis to study known small molecule binders of DNMT3A, then propose reversible, tight binding, and selective inhibitors that exploit the Asn1192/Arg688 difference between the maintenance DNMT1 and DNMT3A near the active site. A similar strategy exploiting the presence of a unique active site cysteine Cys666 is used to propose DNMT3A-selective irreversible inhibitors. We report our results of relative binding energies of the known and proposed compounds estimated using MM/GBSA and umbrella sampling (US) techniques, and our evaluation of other end-point binding free energy calculation methods for these receptors. These calculations offer insight into the potential for small molecules to selectively target the active site of DNMT3A.
Collapse
Affiliation(s)
- Nathaniel J Stillson
- The Department of Chemistry and Biochemistry University of California, Santa Barbara 93106-9510, USA
| | - Kyle E Anderson
- The Department of Chemistry and Biochemistry University of California, Santa Barbara 93106-9510, USA
| | - Norbert O Reich
- The Department of Chemistry and Biochemistry University of California, Santa Barbara 93106-9510, USA.
| |
Collapse
|
12
|
Loaeza-Loaeza J, Cerecedo-Castillo AJ, Rodríguez-Ruiz HA, Castro-Coronel Y, Del Moral-Hernández O, Recillas-Targa F, Hernández-Sotelo D. DNMT3B overexpression downregulates genes with CpG islands, common motifs, and transcription factor binding sites that interact with DNMT3B. Sci Rep 2022; 12:20839. [PMID: 36460706 PMCID: PMC9718745 DOI: 10.1038/s41598-022-24186-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
DNA methylation is a key epigenetic modification to regulate gene expression in mammalian cells. Abnormal DNA methylation in gene promoters is common across human cancer types. DNMT3B is the main de novo methyltransferase enhanced in several primary tumors. How de novo methylation is established in genes related to cancer is poorly understood. CpG islands (CGIs), common sequences, and transcription factors (TFs) that interact with DNMT3B have been associated with abnormal de novo methylation. We initially identified cis elements associated with DNA methylation to investigate the contribution of DNMT3B overexpression to the deregulation of its possible target genes in an epithelial cell model. In a set of downregulated genes (n = 146) from HaCaT cells with DNMT3B overexpression, we found CGI, common sequences, and TFs Binding Sites that interact with DNMT3B (we called them P-down-3B). PPL1, VAV3, IRF1, and BRAF are P-down-3B genes that are downregulated and increased their methylation in DNMT3B presence. Together these findings suggest that methylated promoters aberrantly have some cis elements that could conduce de novo methylation by DNMT3B.
Collapse
Affiliation(s)
- Jaqueline Loaeza-Loaeza
- grid.412856.c0000 0001 0699 2934Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070 Chilpancingo, Guerrero Mexico
| | - Angel Josué Cerecedo-Castillo
- grid.9486.30000 0001 2159 0001Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Hugo Alberto Rodríguez-Ruiz
- grid.412856.c0000 0001 0699 2934Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070 Chilpancingo, Guerrero Mexico
| | - Yaneth Castro-Coronel
- grid.412856.c0000 0001 0699 2934Laboratorio de Citopatología e Inmunohistoquímica, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070 Chilpancingo, Guerrero Mexico
| | - Oscar Del Moral-Hernández
- grid.412856.c0000 0001 0699 2934Laboratorio de Virus y Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070 Chilpancingo, Guerrero Mexico
| | - Félix Recillas-Targa
- grid.9486.30000 0001 2159 0001Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Daniel Hernández-Sotelo
- grid.412856.c0000 0001 0699 2934Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070 Chilpancingo, Guerrero Mexico
| |
Collapse
|
13
|
Abstract
DNMT1 is an essential enzyme that maintains genomic DNA methylation, and its function is regulated by mechanisms that are not yet fully understood. Here, we report the cryo-EM structure of human DNMT1 bound to its two natural activators: hemimethylated DNA and ubiquitinated histone H3. We find that a hitherto unstudied linker, between the RFTS and CXXC domains, plays a key role for activation. It contains a conserved α-helix which engages a crucial "Toggle" pocket, displacing a previously described inhibitory linker, and allowing the DNA Recognition Helix to spring into the active conformation. This is accompanied by large-scale reorganization of the inhibitory RFTS and CXXC domains, allowing the enzyme to gain full activity. Our results therefore provide a mechanistic basis for the activation of DNMT1, with consequences for basic research and drug design.
Collapse
|
14
|
Chao L, Yang S, Li H, Long C, Xi Q, Zuo Y. Competitive binding of TET1 and DNMT3A/B cooperates the DNA methylation pattern in human embryonic stem cells. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194861. [PMID: 35998875 DOI: 10.1016/j.bbagrm.2022.194861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 08/06/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
DNMT3A/B and TET1 play indispensable roles in regulating DNA methylation that undergoes extensive reprogramming during mammalian embryogenesis. Yet the competitive and cooperative relationships between TET1 and DNMT3A/B remain largely unknown in the human embryonic stem cells. Here, we revealed that the main DNA-binding domain of TET1 contains more positive charges by using charge reduction of amino acid alphabet, followed by DNMT3A and DNMT3B. The genome-wide binding profiles showed that TET1 prefers binding to the proximal promoters and CpG islands compared with DNMT3A/B. Moreover, the binding regions of these three transcription factors can be divided into specific and co-binding regions. And a stronger inhibitory effect of DNMT3A on TET1 demethylation was observed in co-binding regions. Furthermore, we integrated TET1 knockout data to further discuss the competitive binding patterns of TET1 and DNMT3A/B. The lack of TET1 increased the occupation of DNMT3A/B at the specific binding regions of TET1 causing focal hypermethylation. The knockout of TET1 was also accompanied by a reduction of DNMT3A/B binding in the co-binding regions, further confirming the cooperative binding function between TET1 and DNMT3A/B. In conclusion, our studies found that the competitive binding of TET1 and DNMT3A/B cooperatively shapes the global DNA methylation pattern in human embryonic stem cells.
Collapse
Affiliation(s)
- Lemuge Chao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Siqi Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Hanshuang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Chunshen Long
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Qilemuge Xi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China..
| |
Collapse
|
15
|
Cheng X, Blumenthal RM. Mediating and maintaining methylation while minimizing mutation: Recent advances on mammalian DNA methyltransferases. Curr Opin Struct Biol 2022; 75:102433. [PMID: 35914495 PMCID: PMC9620438 DOI: 10.1016/j.sbi.2022.102433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/08/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022]
Abstract
Mammalian genomes are methylated on carbon-5 of many cytosines, mostly in CpG dinucleotides. Methylation patterns are maintained during mitosis via DNMT1, and regulatory factors involved in processes that include histone modifications. Methylation in a sequence longer than CpG can influence the binding of sequence-specific transcription factors, thus affecting gene expression. 5-Methylcytosine deamination results in C-to-T transition. While some mutations are beneficial, most are not; so boosting C-to-T transitions can be dangerous. Given the role of DNMT3A in establishing de novo DNA methylation during development, it is this CpG methylation and deamination that provide the major mutagenic impetus in the DNMT3A gene itself, including the R882H dominant-negative substitution associated with two diseases: germline mutations in DNMT3A overgrowth syndrome, and somatic mutations in clonal hematopoiesis that can initiate acute myeloid leukemia. We discuss recent developments in therapeutics targeting DNMT1, the role of noncatalytic isoform DNMT3B3 in regulating de novo methylation by DNMT3A, and structural characterization of DNMT3A in various configurations.
Collapse
Affiliation(s)
- Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| |
Collapse
|
16
|
Gao L, Guo Y, Biswal M, Lu J, Yin J, Fang J, Chen X, Shao Z, Huang M, Wang Y, Wang GG, Song J. Structure of DNMT3B homo-oligomer reveals vulnerability to impairment by ICF mutations. Nat Commun 2022; 13:4249. [PMID: 35869095 PMCID: PMC9307851 DOI: 10.1038/s41467-022-31933-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 07/04/2022] [Indexed: 02/05/2023] Open
Abstract
DNA methyltransferase DNMT3B plays an essential role in establishment of DNA methylation during embryogenesis. Mutations of DNMT3B are associated with human diseases, notably the immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome. How ICF mutations affect DNMT3B activity is not fully understood. Here we report the homo-oligomeric structure of DNMT3B methyltransferase domain, providing insight into DNMT3B-mediated DNA methylation in embryonic stem cells where the functional regulator DNMT3L is dispensable. The interplay between one of the oligomer interfaces (FF interface) and the catalytic loop renders DNMT3B homo-oligomer a conformation and activity distinct from the DNMT3B-DNMT3L heterotetramer, and a greater vulnerability to certain ICF mutations. Biochemical and cellular analyses further reveal that the ICF mutations of FF interface impair the DNA binding and heterochromatin targeting of DNMT3B, leading to reduced DNA methylation in cells. Together, this study provides a mechanistic understanding of DNMT3B-mediated DNA methylation and its dysregulation in disease.
Collapse
Affiliation(s)
- Linfeng Gao
- Environmental Toxicology Graduate Program, University of California, Riverside, 92521, CA, USA
| | - Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, 27599, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Mahamaya Biswal
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, 92521, CA, USA
| | - Jian Fang
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Xinyi Chen
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Zengyu Shao
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Mengjiang Huang
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, 92521, CA, USA
- Department of Chemistry, University of California, Riverside, 92521, CA, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, 27599, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, 27599, NC, USA.
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, 27599, NC, USA.
| | - Jikui Song
- Environmental Toxicology Graduate Program, University of California, Riverside, 92521, CA, USA.
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA.
| |
Collapse
|
17
|
Fang J, Jiang J, Leichter SM, Liu J, Biswal M, Khudaverdyan N, Zhong X, Song J. Mechanistic basis for maintenance of CHG DNA methylation in plants. Nat Commun 2022; 13:3877. [PMID: 35790763 PMCID: PMC9256654 DOI: 10.1038/s41467-022-31627-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 06/26/2022] [Indexed: 11/08/2022] Open
Abstract
DNA methylation is an evolutionarily conserved epigenetic mechanism essential for transposon silencing and heterochromatin assembly. In plants, DNA methylation widely occurs in the CG, CHG, and CHH (H = A, C, or T) contexts, with the maintenance of CHG methylation mediated by CMT3 chromomethylase. However, how CMT3 interacts with the chromatin environment for faithful maintenance of CHG methylation is unclear. Here we report structure-function characterization of the H3K9me2-directed maintenance of CHG methylation by CMT3 and its Zea mays ortholog ZMET2. Base-specific interactions and DNA deformation coordinately underpin the substrate specificity of CMT3 and ZMET2, while a bivalent readout of H3K9me2 and H3K18 allosterically stimulates substrate binding. Disruption of the interaction with DNA or H3K9me2/H3K18 led to loss of CMT3/ZMET2 activity in vitro and impairment of genome-wide CHG methylation in vivo. Together, our study uncovers how the intricate interplay of CMT3, repressive histone marks, and DNA sequence mediates heterochromatic CHG methylation.
Collapse
Affiliation(s)
- Jian Fang
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Jianjun Jiang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Sarah M Leichter
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Jie Liu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Mahamaya Biswal
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Nelli Khudaverdyan
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA.
| |
Collapse
|
18
|
Boyko K, Arkova O, Nikolaeva A, Popov VO, Georgiev P, Bonchuk A. Structure of the DNMT3B ADD domain suggests the absence of a DNMT3A-like autoinhibitory mechanism. Biochem Biophys Res Commun 2022; 619:124-129. [PMID: 35760008 DOI: 10.1016/j.bbrc.2022.06.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/02/2022]
Abstract
De novo DNA methylation in early mammalian development depends on the activity of the DNMT3 methyltransferase family. An autoinhibitory mechanism involving the interaction between ADD and the catalytic domains of DNMT3A has been described. ADD is a zinc-coordinating histone-binding domain. The ADD domain of DNMT3A, when bound to a K4-unmethylated histone H3 tail, switches the enzyme to its catalytically active state. DNMT3B is another de novo methyltransferase enzyme with a more strict tissue- and stage-specific expression profile and a slightly different site specificity, lacking cooperative DNA methylation activity. Here, we obtained the crystal structure of the DNMT3B ADD domain, which demonstrated the extended conformation of the autoinhibitory loop even in the absence of the histone H3 tail. The lack of interaction between DNMT3B ADD and the methyltransferase domain was confirmed using an in vitro pull-down assay. The structural rearrangements in the loop also created an additional protein interaction interface leading to the formation of trimers in crystal, which may reflect their possible involvement in some unknown protein-protein interactions. Our results suggest that DNMT3B, in contrast to DNMT3A, has different modes of regulation of its activity that are independent of H3K4 methylation status.
Collapse
Affiliation(s)
- Konstantin Boyko
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia; Bach Institute of Biochemistry, Research Center of Biotechnology Russian Academy of Sciences, Leninsky pr-t, 33, Bld. 2, Moscow, 119071, Russia
| | - Olga Arkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Alena Nikolaeva
- National Research Center «Kurchatov Institute», Moscow, Russia
| | - Vladimir O Popov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia; National Research Center «Kurchatov Institute», Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Artem Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia.
| |
Collapse
|
19
|
Singh J, Raina R, Vinothkumar KR, Anand R. Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases. ACS Chem Biol 2022; 17:829-839. [PMID: 35316014 DOI: 10.1021/acschembio.1c00732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methylation of specific nucleotides is integral for ribosomal biogenesis and also serves as a common mechanism to confer antibiotic resistance by pathogenic bacteria. Here, by determining the high-resolution structure of the 30S-KsgA complex by cryo-electron microscopy, a state was captured, where KsgA juxtaposes between helices h44 and h45 of the 30S ribosome, separating them, thereby enabling remodeling of the surrounded rRNA and allowing the cognate site to enter the methylation pocket. With the structure as a guide, several mutant versions of the ribosomes, where interacting bases in the catalytic helix h45 and surrounding helices h44, h24, and h27, were mutated and evaluated for their methylation efficiency revealing factors that direct the enzyme to its cognate site with high fidelity. The biochemical studies show that the three-dimensional environment of the ribosome enables the interaction of select loop regions in KsgA with the ribosome helices paramount to maintain selectivity.
Collapse
Affiliation(s)
- Juhi Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Rahul Raina
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru560065, India
| | - Kutti R. Vinothkumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru560065, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
- DBT-Wellcome Trust India Alliance Senior Fellow, Mumbai400076, India
| |
Collapse
|
20
|
Jin Y, Liu T, Luo H, Liu Y, Liu D. Targeting Epigenetic Regulatory Enzymes for Cancer Therapeutics: Novel Small-Molecule Epidrug Development. Front Oncol 2022; 12:848221. [PMID: 35419278 PMCID: PMC8995554 DOI: 10.3389/fonc.2022.848221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Dysregulation of the epigenetic enzyme-mediated transcription of oncogenes or tumor suppressor genes is closely associated with the occurrence, progression, and prognosis of tumors. Based on the reversibility of epigenetic mechanisms, small-molecule compounds that target epigenetic regulation have become promising therapeutics. These compounds target epigenetic regulatory enzymes, including DNA methylases, histone modifiers (methylation and acetylation), enzymes that specifically recognize post-translational modifications, chromatin-remodeling enzymes, and post-transcriptional regulators. Few compounds have been used in clinical trials and exhibit certain therapeutic effects. Herein, we summarize the classification and therapeutic roles of compounds that target epigenetic regulatory enzymes in cancer treatment. Finally, we highlight how the natural compounds berberine and ginsenosides can target epigenetic regulatory enzymes to treat cancer.
Collapse
Affiliation(s)
- Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Tianjia Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Haoming Luo
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yangyang Liu
- Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Da Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| |
Collapse
|
21
|
Tajima S, Suetake I, Takeshita K, Nakagawa A, Kimura H, Song J. Domain Structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:45-68. [PMID: 36350506 PMCID: PMC11025882 DOI: 10.1007/978-3-031-11454-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In mammals, three major DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b, have been identified. Dnmt3a and Dnmt3b are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. Dnmt3-like (Dnmt3l), which is a member of the Dnmt3 family but does not possess DNA methylation activity, was reported to be indispensable for global methylation in germ cells. Once the DNA methylation patterns are established, maintenance-type DNA methyltransferase Dnmt1 faithfully propagates them to the next generation via replication. All Dnmts possess multiple domains. For instance, Dnmt3a and Dnmt3b each contain a Pro-Trp-Trp-Pro (PWWP) domain that recognizes the histone H3K36me2/3 mark, an Atrx-Dnmt3-Dnmt3l (ADD) domain that recognizes unmodified histone H3 tail, and a catalytic domain that methylates CpG sites. Dnmt1 contains an N-terminal independently folded domain (NTD) that interacts with a variety of regulatory factors, a replication foci-targeting sequence (RFTS) domain that recognizes the histone H3K9me3 mark and H3 ubiquitylation, a CXXC domain that recognizes unmodified CpG DNA, two tandem Bromo-Adjacent-homology (BAH1 and BAH2) domains that read the H4K20me3 mark with BAH1, and a catalytic domain that preferentially methylates hemimethylated CpG sites. In this chapter, the structures and functions of these domains are described.
Collapse
Affiliation(s)
- Shoji Tajima
- Institute for Protein Research, Osaka University, Osaka, Japan.
| | - Isao Suetake
- Department of Nutritional Sciences, Faculty of Nutritional Sciences, Nakamura Gakuen University, Fukuoka, Japan
| | | | - Atsushi Nakagawa
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hironobu Kimura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Jikui Song
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA.
| |
Collapse
|
22
|
Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:1-19. [DOI: 10.1007/978-3-031-11454-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
23
|
Recent Advances on DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:295-315. [DOI: 10.1007/978-3-031-11454-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
24
|
Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:69-110. [DOI: 10.1007/978-3-031-11454-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
25
|
Mensah IK, Norvil AB, AlAbdi L, McGovern S, Petell CJ, He M, Gowher H. Misregulation of the expression and activity of DNA methyltransferases in cancer. NAR Cancer 2021; 3:zcab045. [PMID: 34870206 PMCID: PMC8634572 DOI: 10.1093/narcan/zcab045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In mammals, DNA methyltransferases DNMT1 and DNMT3's (A, B and L) deposit and maintain DNA methylation in dividing and nondividing cells. Although these enzymes have an unremarkable DNA sequence specificity (CpG), their regional specificity is regulated by interactions with various protein factors, chromatin modifiers, and post-translational modifications of histones. Changes in the DNMT expression or interacting partners affect DNA methylation patterns. Consequently, the acquired gene expression may increase the proliferative potential of cells, often concomitant with loss of cell identity as found in cancer. Aberrant DNA methylation, including hypermethylation and hypomethylation at various genomic regions, therefore, is a hallmark of most cancers. Additionally, somatic mutations in DNMTs that affect catalytic activity were mapped in Acute Myeloid Leukemia cancer cells. Despite being very effective in some cancers, the clinically approved DNMT inhibitors lack specificity, which could result in a wide range of deleterious effects. Elucidating distinct molecular mechanisms of DNMTs will facilitate the discovery of alternative cancer therapeutic targets. This review is focused on: (i) the structure and characteristics of DNMTs, (ii) the prevalence of mutations and abnormal expression of DNMTs in cancer, (iii) factors that mediate their abnormal expression and (iv) the effect of anomalous DNMT-complexes in cancer.
Collapse
Affiliation(s)
- Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
26
|
Liu A, Zhou K, Martínez MA, Lopez-Torres B, Martínez M, Martínez-Larrañaga MR, Wang X, Anadón A, Ares I. A "Janus" face of the RASSF4 signal in cell fate. J Cell Physiol 2021; 237:466-479. [PMID: 34553373 DOI: 10.1002/jcp.30592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/06/2021] [Accepted: 09/11/2021] [Indexed: 12/19/2022]
Abstract
RASSF4 (Ras-association domain family 4) is a protein-coding gene, regarded as a tumor suppressor regulated by DNA methylation. However, RASSF4 acts as a "Janus" in cell fate: death and survival. This review article focuses on the regulatory mechanisms of RASSF4 on cell death and cell survival and puts forward a comprehensive analysis of the relevant signaling pathways. The participation of RASSF4 in the regulation of intracellular store-operated Ca2+ entry also affects cell survival. Moreover, the mechanism of inducing abnormal expression of RASSF4 was summarized. We highlight recent advances in our knowledge of RASSF4 function in the development of cancer and other clinical diseases, which may provide insight into the controversial functions of RASSF4 and its potential application in disease therapy.
Collapse
Affiliation(s)
- Aimei Liu
- Department of National Reference, Laboratory of Veterinary Drug Residues (HZAU) and MOA Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China.,Department of MOA, Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, Hubei, China
| | - Kaixiang Zhou
- Department of National Reference, Laboratory of Veterinary Drug Residues (HZAU) and MOA Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China.,Department of MOA, Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, Hubei, China
| | - María Aránzazu Martínez
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid(UCM), and Research Institute Hospital 12 de October (i+12), Madrid, Spain
| | - Bernardo Lopez-Torres
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid(UCM), and Research Institute Hospital 12 de October (i+12), Madrid, Spain
| | - Marta Martínez
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid(UCM), and Research Institute Hospital 12 de October (i+12), Madrid, Spain
| | - María-Rosa Martínez-Larrañaga
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid(UCM), and Research Institute Hospital 12 de October (i+12), Madrid, Spain
| | - Xu Wang
- Department of National Reference, Laboratory of Veterinary Drug Residues (HZAU) and MOA Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China.,Department of MOA, Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, Hubei, China
| | - Arturo Anadón
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid(UCM), and Research Institute Hospital 12 de October (i+12), Madrid, Spain
| | - Irma Ares
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid(UCM), and Research Institute Hospital 12 de October (i+12), Madrid, Spain
| |
Collapse
|
27
|
Khan AH, Smith DJ. Cost-Effective Mapping of Genetic Interactions in Mammalian Cells. Front Genet 2021; 12:703738. [PMID: 34434222 PMCID: PMC8381747 DOI: 10.3389/fgene.2021.703738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022] Open
Abstract
Comprehensive maps of genetic interactions in mammalian cells are daunting to construct because of the large number of potential interactions, ~ 2 × 108 for protein coding genes. We previously used co-inheritance of distant genes from published radiation hybrid (RH) datasets to identify genetic interactions. However, it was necessary to combine six legacy datasets from four species to obtain adequate statistical power. Mapping resolution was also limited by the low density PCR genotyping. Here, we employ shallow sequencing of nascent human RH clones as an economical approach to constructing interaction maps. In this initial study, 15 clones were analyzed, enabling construction of a network with 225 genes and 2,359 interactions (FDR < 0.05). Despite its small size, the network showed significant overlap with the previous RH network and with a protein-protein interaction network. Consumables were ≲$50 per clone, showing that affordable, high quality genetic interaction maps are feasible in mammalian cells.
Collapse
Affiliation(s)
- Arshad H Khan
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Desmond J Smith
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
28
|
Deep enzymology studies on DNA methyltransferases reveal novel connections between flanking sequences and enzyme activity. J Mol Biol 2021; 433:167186. [PMID: 34375615 DOI: 10.1016/j.jmb.2021.167186] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 11/22/2022]
Abstract
DNA interacting enzymes recognize their target sequences embedded in variable flanking sequence context. The influence of flanking sequences on enzymatic activities of DNA methyltransferases (DNMTs) can be systematically studied with "deep enzymology" approaches using pools of double-stranded DNA substrates, which contain target sites in random flanking sequence context. After incubation with DNMTs and bisulfite conversion, the methylation states and flanking sequences of individual DNA molecules are determined by NGS. Deep enzymology studies with different human and mouse DNMTs revealed strong influences of flanking sequences on the CpG and non-CpG methylation activity and structure of DNMT-DNA complexes. Differences in flanking sequence preferences of DNMT3A and DNMT3B were shown to be related to the prominent role of DNMT3B in the methylation of human SATII repeat elements. Mutational studies in DNMT3B discovered alternative interaction networks between the enzyme and the DNA leading to a partial equalization of the effects of different flanking sequences. Structural studies in DNMT1 revealed striking correlations between enzymatic activities and flanking sequence dependent conformational changes upon DNA binding. Correlation of the biochemical data with cellular methylation patterns demonstrated that flanking sequence preferences are an important parameter that influences genomic DNA methylation patterns together with other mechanisms targeting DNMTs to genomic sites.
Collapse
|
29
|
Insights into S-adenosyl-l-methionine (SAM)-dependent methyltransferase related diseases and genetic polymorphisms. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108396. [PMID: 34893161 DOI: 10.1016/j.mrrev.2021.108396] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022]
Abstract
Enzymatic methylation catalyzed by methyltransferases has a significant impact on many human biochemical reactions. As the second most ubiquitous cofactor in humans, S-adenosyl-l-methionine (SAM or AdoMet) serves as a methyl donor for SAM-dependent methyltransferases (MTases), which transfer a methyl group to a nucleophilic acceptor such as O, As, N, S, or C as the byproduct. SAM-dependent methyltransferases can be grouped into different types based on the substrates. Here we systematically reviewed eight types of methyltransferases associated with human diseases. Catechol O-methyltransferase (COMT), As(III) S-adenosylmethionine methyltransferase (AS3MT), indolethylamine N-methyltransferase (INMT), phenylethanolamine N-methyltransferase (PNMT), histamine N-methyltransferase (HNMT), nicotinamide N-methyltransferase (NNMT), thiopurine S-methyltransferase (TPMT) and DNA methyltansferase (DNMT) are classic SAM-dependent MTases. Correlations between genotypes and disease susceptibility can be partially explained by genetic polymorphisms. The physiological function, substrate specificity, genetic variants and disease susceptibility associated with these eight SAM-dependent methyltransferases are discussed in this review.
Collapse
|
30
|
Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X, Song J. Substrate deformation regulates DRM2-mediated DNA methylation in plants. SCIENCE ADVANCES 2021; 7:eabd9224. [PMID: 34078593 PMCID: PMC8172135 DOI: 10.1126/sciadv.abd9224] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
DNA methylation is a major epigenetic mechanism critical for gene expression and genome stability. In plants, domains rearranged methyltransferase 2 (DRM2) preferentially mediates CHH (H = C, T, or A) methylation, a substrate specificity distinct from that of mammalian DNA methyltransferases. However, the underlying mechanism is unknown. Here, we report structure-function characterization of DRM2-mediated methylation. An arginine finger from the catalytic loop intercalates into the nontarget strand of DNA through the minor groove, inducing large DNA deformation that affects the substrate preference of DRM2. The target recognition domain stabilizes the enlarged major groove via shape complementarity rather than base-specific interactions, permitting substrate diversity. The engineered DRM2 C397R mutation introduces base-specific contacts with the +2-flanking guanine, thereby shifting the substrate specificity of DRM2 toward CHG DNA. Together, this study uncovers DNA deformation as a mechanism in regulating the specificity of DRM2 toward diverse CHH substrates and illustrates methylome complexity in plants.
Collapse
Affiliation(s)
- Jian Fang
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Sarah M Leichter
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Jianjun Jiang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Mahamaya Biswal
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Zhi-Min Zhang
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Wendan Ren
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Jixian Zhai
- Department of Biology and Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA.
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
| |
Collapse
|
31
|
Yusuf AP, Abubakar MB, Malami I, Ibrahim KG, Abubakar B, Bello MB, Qusty N, Elazab ST, Imam MU, Alexiou A, Batiha GES. Zinc Metalloproteins in Epigenetics and Their Crosstalk. Life (Basel) 2021; 11:186. [PMID: 33652690 PMCID: PMC7996840 DOI: 10.3390/life11030186] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
More than half a century ago, zinc was established as an essential micronutrient for normal human physiology. In silico data suggest that about 10% of the human proteome potentially binds zinc. Many proteins with zinc-binding domains (ZBDs) are involved in epigenetic modifications such as DNA methylation and histone modifications, which regulate transcription in physiological and pathological conditions. Zinc metalloproteins in epigenetics are mainly zinc metalloenzymes and zinc finger proteins (ZFPs), which are classified into writers, erasers, readers, editors, and feeders. Altogether, these classes of proteins engage in crosstalk that fundamentally maintains the epigenome's modus operandi. Changes in the expression or function of these proteins induced by zinc deficiency or loss of function mutations in their ZBDs may lead to aberrant epigenetic reprogramming, which may worsen the risk of non-communicable chronic diseases. This review attempts to address zinc's role and its proteins in natural epigenetic programming and artificial reprogramming and briefly discusses how the ZBDs in these proteins interact with the chromatin.
Collapse
Affiliation(s)
- Abdurrahman Pharmacy Yusuf
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
| | - Murtala Bello Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Ibrahim Malami
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Kasimu Ghandi Ibrahim
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Bilyaminu Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Naeem Qusty
- Medical Laboratories Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Mecca 21955, Saudi Arabia;
| | - Sara T. Elazab
- Department of Pharmacology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Dakahlia 35516, Egypt;
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
- AFNP Med, Haidingergasse 29, 1030 Vienna, Austria
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, AlBeheira 22511, Egypt
| |
Collapse
|
32
|
Mallona I, Ilie IM, Karemaker ID, Butz S, Manzo M, Caflisch A, Baubec T. Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Res 2021; 49:145-157. [PMID: 33290556 PMCID: PMC7797059 DOI: 10.1093/nar/gkaa1168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/22/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Mammalian de novo DNA methyltransferases (DNMT) are responsible for the establishment of cell-type-specific DNA methylation in healthy and diseased tissues. Through genome-wide analysis of de novo methylation activity in murine stem cells we uncover that DNMT3A prefers to methylate CpGs followed by cytosines or thymines, while DNMT3B predominantly methylates CpGs followed by guanines or adenines. These signatures are further observed at non-CpG sites, resembling methylation context observed in specialised cell types, including neurons and oocytes. We further show that these preferences result from structural differences in the catalytic domains of the two de novo DNMTs and are not a consequence of differential recruitment to the genome. Molecular dynamics simulations suggest that, in case of human DNMT3A, the preference is due to favourable polar interactions between the flexible Arg836 side chain and the guanine that base-pairs with the cytosine following the CpG. By exchanging arginine to a lysine, the corresponding side chain in DNMT3B, the sequence preference is reversed, confirming the requirement for arginine at this position. This context-dependent enzymatic activity provides additional insights into the complex regulation of DNA methylation patterns.
Collapse
Affiliation(s)
- Izaskun Mallona
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich 8057, Switzerland
| | - Ioana Mariuca Ilie
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Ino Dominiek Karemaker
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
| | - Stefan Butz
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Massimiliano Manzo
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
| |
Collapse
|
33
|
Dukatz M, Adam S, Biswal M, Song J, Bashtrykov P, Jeltsch A. Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase. Nucleic Acids Res 2020; 48:11495-11509. [PMID: 33105482 PMCID: PMC7672481 DOI: 10.1093/nar/gkaa938] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
DNA methyltransferases interact with their CpG target sites in the context of variable flanking sequences. We investigated DNA methylation by the human DNMT3B catalytic domain using substrate pools containing CpX target sites in randomized flanking context and identified combined effects of CpG recognition and flanking sequence interaction together with complex contact networks involved in balancing the interaction with different flanking sites. DNA methylation rates were more affected by flanking sequences at non-CpG than at CpG sites. We show that T775 has an essential dynamic role in the catalytic mechanism of DNMT3B. Moreover, we identify six amino acid residues in the DNA-binding interface of DNMT3B (N652, N656, N658, K777, N779, and R823), which are involved in the equalization of methylation rates of CpG sites in favored and disfavored sequence contexts by forming compensatory interactions to the flanking residues including a CpG specific contact to an A at the +1 flanking site. Non-CpG flanking preferences of DNMT3B are highly correlated with non-CpG methylation patterns in human cells. Comparison of the flanking sequence preferences of human and mouse DNMT3B revealed subtle differences suggesting a co-evolution of flanking sequence preferences and cellular DNMT targets.
Collapse
Affiliation(s)
- Michael Dukatz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Sabrina Adam
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Mahamaya Biswal
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| |
Collapse
|
34
|
Loaeza-Loaeza J, Beltran AS, Hernández-Sotelo D. DNMTs and Impact of CpG Content, Transcription Factors, Consensus Motifs, lncRNAs, and Histone Marks on DNA Methylation. Genes (Basel) 2020; 11:genes11111336. [PMID: 33198240 PMCID: PMC7696963 DOI: 10.3390/genes11111336] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022] Open
Abstract
DNA methyltransferases (DNMTs) play an essential role in DNA methylation and transcriptional regulation in the genome. DNMTs, along with other poorly studied elements, modulate the dynamic DNA methylation patterns of embryonic and adult cells. We summarize the current knowledge on the molecular mechanism of DNMTs’ functional targeting to maintain genome-wide DNA methylation patterns. We focus on DNMTs’ intrinsic characteristics, transcriptional regulation, and post-transcriptional modifications. Furthermore, we focus special attention on the DNMTs’ specificity for target sites, including key cis-regulatory factors such as CpG content, common motifs, transcription factors (TF) binding sites, lncRNAs, and histone marks to regulate DNA methylation. We also review how complexes of DNMTs/TFs or DNMTs/lncRNAs are involved in DNA methylation in specific genome regions. Understanding these processes is essential because the spatiotemporal regulation of DNA methylation modulates gene expression in health and disease.
Collapse
Affiliation(s)
- Jaqueline Loaeza-Loaeza
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, NC 39087 Chilpancingo, Mexico;
| | - Adriana S. Beltran
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Daniel Hernández-Sotelo
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, NC 39087 Chilpancingo, Mexico;
- Correspondence:
| |
Collapse
|
35
|
Zeng Y, Ren R, Kaur G, Hardikar S, Ying Z, Babcock L, Gupta E, Zhang X, Chen T, Cheng X. The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation. Genes Dev 2020; 34:1546-1558. [PMID: 33004415 PMCID: PMC7608744 DOI: 10.1101/gad.341925.120] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
The de novo DNA methyltransferases Dnmt3a and Dnmt3b play crucial roles in developmental and cellular processes. Their enzymatic activities are stimulated by a regulatory protein Dnmt3L (Dnmt3-like) in vitro. However, genetic evidence indicates that Dnmt3L functions predominantly as a regulator of Dnmt3a in germ cells. How Dnmt3a and Dnmt3b activities are regulated during embryonic development and in somatic cells remains largely unknown. Here we show that Dnmt3b3, a catalytically inactive Dnmt3b isoform expressed in differentiated cells, positively regulates de novo methylation by Dnmt3a and Dnmt3b with a preference for Dnmt3b. Dnmt3b3 is equally potent as Dnmt3L in stimulating the activities of Dnmt3a2 and Dnmt3b2 in vitro. Like Dnmt3L, Dnmt3b3 forms a complex with Dnmt3a2 with a stoichiometry of 2:2. However, rescue experiments in Dnmt3a/3b/3l triple-knockout (TKO) mouse embryonic stem cells (mESCs) reveal that Dnmt3b3 prefers Dnmt3b2 over Dnmt3a2 in remethylating genomic sequences. Dnmt3a2, an active isoform that lacks the N-terminal uncharacterized region of Dnmt3a1 including a nuclear localization signal, has very low activity in TKO mESCs, indicating that an accessory protein is absolutely required for its function. Our results suggest that Dnmt3b3 and perhaps similar Dnmt3b isoforms facilitate de novo DNA methylation during embryonic development and in somatic cells.
Collapse
Affiliation(s)
- Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zhengzhou Ying
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Lance Babcock
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Esha Gupta
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|