1
|
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
|
2
|
Mensah IK, Norvil AB, He M, Lendy E, Hjortland N, Tan H, Pomerantz RT, Mesecar A, Gowher H. Development of a sensitive microplate assay for characterizing RNA methyltransferase activity: Implications for epitranscriptomics and drug development. J Biol Chem 2023; 299:105257. [PMID: 37716702 PMCID: PMC10582764 DOI: 10.1016/j.jbc.2023.105257] [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: 01/25/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/18/2023] Open
Abstract
RNA methylation is a ubiquitous post-transcriptional modification found in diverse RNA classes and is a critical regulator of gene expression. In this study, we used Zika virus RNA methyltransferase (MTase) to develop a highly sensitive microplate assay that uses a biotinylated RNA substrate and radiolabeled AdoMet coenzyme. The assay is fast, highly reproducible, exhibits linear progress-curve kinetics under multiple turnover conditions, has high sensitivity in competitive inhibition assays, and significantly lower background levels compared with the currently used method. Using our newly developed microplate assay, we observed no significant difference in the catalytic constants of the full-length nonstructural protein 5 enzyme and the truncated MTase domain. These data suggest that, unlike the Zika virus RNA-dependent RNA polymerase activity, the MTase activity is unaffected by RNA-dependent RNA polymerase-MTase interdomain interaction. Given its quantitative nature and accuracy, this method can be used to characterize various RNA MTases, and, therefore, significantly contribute to the field of epitranscriptomics and drug development against infectious diseases.
Collapse
Affiliation(s)
- Isaiah K Mensah
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Allison B Norvil
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Ming He
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Emma Lendy
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Nicole Hjortland
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Hern Tan
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Richard T Pomerantz
- Department Biochemistry and Molecular Biology, Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania, USA
| | - Andrew Mesecar
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA.
| |
Collapse
|
3
|
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
|
4
|
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
|
5
|
Mack A, Emperle M, Schnee P, Adam S, Pleiss J, Bashtrykov P, Jeltsch A. Preferential self-interaction of DNA methyltransferase DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence preferences. J Mol Biol 2022; 434:167482. [DOI: 10.1016/j.jmb.2022.167482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 11/30/2022]
|
6
|
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
|
7
|
Liu W, Mohan SP, Nagaraj NR, Sundar Jaganathan S, Wen Y, Ramasubramanyan S, Irudayaraj J. Epigenetic alterations associated with dexamethasone sodium phosphate through DNMT and TET in RPE cells. Mol Vis 2021; 27:643-655. [PMID: 34924744 PMCID: PMC8645185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 11/18/2021] [Indexed: 11/29/2022] Open
Abstract
PURPOSE To elucidate the mechanism behind epigenetic alteration associated with dexamethasone (DEX) sodium phosphate treatment. METHODS We performed enzyme-linked immunosorbent assay to quantify changes in global DNA methylation and hydroxymethylation, quantitative real-time PCR (qRT-PCR) of the DNA methylation- and hydroxymethylation-related gene, in vitro DNA methyltransferase (DNMT) enzymatic activity assays with purified DNMTs, and DNA hydroxymethylation pattern with super-resolution imaging. RESULTS We identified global DNA hypomethylation and hyper-hydroxymethylation upon DEX treatment, associated with aberrant mRNA expression levels of DNMT and ten-eleven translocation (TET) proteins. Additionally, DEX exposure could directly hinder DNMT activities. CONCLUSIONS We showed that DEX-induced epigenetic alterations are linked to aberrant DNMT and TET expression, potentially through an essential role of DNMT.
Collapse
Affiliation(s)
- Wenjie Liu
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory. University of Illinois at Urbana-Champaign, Urbana, IL,Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL
| | - Sruthi Priya Mohan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, KBIRVO, Vision Research Foundation, Chennai, TN, India
| | | | - Shyam Sundar Jaganathan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, KBIRVO, Vision Research Foundation, Chennai, TN, India
| | - Yi Wen
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory. University of Illinois at Urbana-Champaign, Urbana, IL,Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL
| | - Sharada Ramasubramanyan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, KBIRVO, Vision Research Foundation, Chennai, TN, India
| | - Joseph Irudayaraj
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory. University of Illinois at Urbana-Champaign, Urbana, IL,Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL
| |
Collapse
|
8
|
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
|
9
|
Abstract
The genetic information of human cells is stored in the context of chromatin, which is subjected to DNA methylation and various histone modifications. Such a 'language' of chromatin modification constitutes a fundamental means of gene and (epi)genome regulation, underlying a myriad of cellular and developmental processes. In recent years, mounting evidence has demonstrated that miswriting, misreading or mis-erasing of the modification language embedded in chromatin represents a common, sometimes early and pivotal, event across a wide range of human cancers, contributing to oncogenesis through the induction of epigenetic, transcriptomic and phenotypic alterations. It is increasingly clear that cancer-related metabolic perturbations and oncohistone mutations also directly impact chromatin modification, thereby promoting cancerous transformation. Phase separation-based deregulation of chromatin modulators and chromatin structure is also emerging to be an important underpinning of tumorigenesis. Understanding the various molecular pathways that underscore a misregulated chromatin language in cancer, together with discovery and development of more effective drugs to target these chromatin-related vulnerabilities, will enhance treatment of human malignancies.
Collapse
Affiliation(s)
- Shuai Zhao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| |
Collapse
|
10
|
Huo X, Jin S, Wang Y, Ma L. DNA methylation in chronic obstructive pulmonary disease. Epigenomics 2021; 13:1145-1155. [PMID: 34142873 DOI: 10.2217/epi-2021-0111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), a complex disease with polygenetic tendency, is one of the most important health problems in the world. Recently, in the study of the pathogenesis of the COPD, epigenetic changes caused by environmental factors, such as DNA methylation, started to attract more attention than genetic factors. In this review, we discuss the main features of DNA methylation, such as DNA methyltransferases and the methylation sites that modulate the DNA methylation level, and their roles in COPD progression. Finally, to promote new ideas for the prevention and treatment of COPD, we focus on the potential of DNA methylation as a COPD therapeutic target.
Collapse
Affiliation(s)
- XinXin Huo
- School of Public Health, Lanzhou University, Lanzhou, China
| | - SiHui Jin
- School of Public Health, Lanzhou University, Lanzhou, China
| | - YiGe Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Li Ma
- School of Public Health, Lanzhou University, Lanzhou, China
| |
Collapse
|
11
|
Rugowska A, Starosta A, Konieczny P. Epigenetic modifications in muscle regeneration and progression of Duchenne muscular dystrophy. Clin Epigenetics 2021; 13:13. [PMID: 33468200 PMCID: PMC7814631 DOI: 10.1186/s13148-021-01001-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a multisystemic disorder that affects 1:5000 boys. The severity of the phenotype varies dependent on the mutation site in the DMD gene and the resultant dystrophin expression profile. In skeletal muscle, dystrophin loss is associated with the disintegration of myofibers and their ineffective regeneration due to defective expansion and differentiation of the muscle stem cell pool. Some of these phenotypic alterations stem from the dystrophin absence-mediated serine-threonine protein kinase 2 (MARK2) misplacement/downregulation in activated muscle stem (satellite) cells and neuronal nitric oxide synthase loss in cells committed to myogenesis. Here, we trace changes in DNA methylation, histone modifications, and expression of regulatory noncoding RNAs during muscle regeneration, from the stage of satellite cells to myofibers. Furthermore, we describe the abrogation of these epigenetic regulatory processes due to changes in signal transduction in DMD and point to therapeutic treatments increasing the regenerative potential of diseased muscles based on this acquired knowledge.
Collapse
Affiliation(s)
- Anna Rugowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Alicja Starosta
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Patryk Konieczny
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland.
| |
Collapse
|
12
|
Venugopal K, Feng Y, Shabashvili D, Guryanova OA. Alterations to DNMT3A in Hematologic Malignancies. Cancer Res 2021; 81:254-263. [PMID: 33087320 PMCID: PMC7855745 DOI: 10.1158/0008-5472.can-20-3033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
In the last decade, large-scale genomic studies in patients with hematologic malignancies identified recurrent somatic alterations in epigenetic modifier genes. Among these, the de novo DNA methyltransferase DNMT3A has emerged as one of the most frequently mutated genes in adult myeloid as well as lymphoid malignancies and in clonal hematopoiesis. In this review, we discuss recent advances in our understanding of the biochemical and structural consequences of DNMT3A mutations on DNA methylation catalysis and binding interactions and summarize their effects on epigenetic patterns and gene expression changes implicated in the pathogenesis of hematologic malignancies. We then review the role played by mutant DNMT3A in clonal hematopoiesis, accompanied by its effect on immune cell function and inflammatory responses. Finally, we discuss how this knowledge informs therapeutic approaches for hematologic malignancies with mutant DNMT3A.
Collapse
Affiliation(s)
- Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Yang Feng
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Daniil Shabashvili
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Olga A Guryanova
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida.
- University of Florida Health Cancer Center, Gainesville, Florida
| |
Collapse
|
13
|
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
|
14
|
Norvil AB, AlAbdi L, Liu B, Tu YH, Forstoffer NE, Michie A, Chen T, Gowher H. The acute myeloid leukemia variant DNMT3A Arg882His is a DNMT3B-like enzyme. Nucleic Acids Res 2020; 48:3761-3775. [PMID: 32123902 PMCID: PMC7144950 DOI: 10.1093/nar/gkaa139] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 12/31/2022] Open
Abstract
We have previously shown that the highly prevalent acute myeloid leukemia (AML) mutation, Arg882His, in DNMT3A disrupts its cooperative mechanism and leads to reduced enzymatic activity, thus explaining the genomic hypomethylation in AML cells. However, the underlying cause of the oncogenic effect of Arg882His in DNMT3A is not fully understood. Here, we discovered that DNMT3A WT enzyme under conditions that favor non-cooperative kinetic mechanism as well as DNMT3A Arg882His variant acquire CpG flanking sequence preference akin to that of DNMT3B, which is non-cooperative. We tested if DNMT3A Arg882His could preferably methylate DNMT3B-specific target sites in vivo. Rescue experiments in Dnmt3a/3b double knockout mouse embryonic stem cells show that the corresponding Arg878His mutation in mouse DNMT3A severely impairs its ability to methylate major satellite DNA, a DNMT3A-preferred target, but has no overt effect on the ability to methylate minor satellite DNA, a DNMT3B-preferred target. We also observed a previously unappreciated CpG flanking sequence bias in major and minor satellite repeats that is consistent with DNMT3A and DNMT3B specificity suggesting that DNA methylation patterns are guided by the sequence preference of these enzymes. We speculate that aberrant methylation of DNMT3B target sites could contribute to the oncogenic potential of DNMT3A AML variant.
Collapse
Affiliation(s)
- Allison B Norvil
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Lama AlAbdi
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Bigang Liu
- Department of Epigenetics and Molecular Carcinogenesis, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yu Han Tu
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Nicole E Forstoffer
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Amie R Michie
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
15
|
Lin CC, Chen YP, Yang WZ, Shen JCK, Yuan H. Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B. Nucleic Acids Res 2020; 48:3949-3961. [PMID: 32083663 PMCID: PMC7144912 DOI: 10.1093/nar/gkaa111] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/07/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
DNA methyltransferases are primary enzymes for cytosine methylation at CpG sites of epigenetic gene regulation in mammals. De novo methyltransferases DNMT3A and DNMT3B create DNA methylation patterns during development, but how they differentially implement genomic DNA methylation patterns is poorly understood. Here, we report crystal structures of the catalytic domain of human DNMT3B-3L complex, noncovalently bound with and without DNA of different sequences. Human DNMT3B uses two flexible loops to enclose DNA and employs its catalytic loop to flip out the cytosine base. As opposed to DNMT3A, DNMT3B specifically recognizes DNA with CpGpG sites via residues Asn779 and Lys777 in its more stable and well-ordered target recognition domain loop to facilitate processive methylation of tandemly repeated CpG sites. We also identify a proton wire water channel for the final deprotonation step, revealing the complete working mechanism for cytosine methylation by DNMT3B and providing the structural basis for DNMT3B mutation-induced hypomethylation in immunodeficiency, centromere instability and facial anomalies syndrome.
Collapse
Affiliation(s)
- Chien-Chu Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ping Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - James C K Shen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei 10048, Taiwan
| |
Collapse
|
16
|
Luck A, Giehr P, Nordstrom K, Walter J, Wolf V. Hidden Markov Modelling Reveals Neighborhood Dependence of Dnmt3a and 3b Activity. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1598-1609. [PMID: 31027045 DOI: 10.1109/tcbb.2019.2910814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA methylation is an epigenetic mark whose important role in development has been widely recognized. This epigenetic modification results in heritable information not encoded by the DNA sequence. The underlying mechanisms controlling DNA methylation are only partly understood. Several mechanistic models of enzyme activities responsible for DNA methylation have been proposed. Here, we extend existing Hidden Markov Models (HMMs) for DNA methylation by describing the occurrence of spatial methylation patterns over time and propose several models with different neighborhood dependences. Furthermore, we investigate correlations between the neighborhood dependence and other genomic information. We perform numerical analysis of the HMMs applied to comprehensive hairpin and non-hairpin bisulfite sequencing measurements and accurately predict wild-type data. We find evidence that the activities of Dnmt3a and Dnmt3b responsible for de novo methylation depend on 5' (left) but not on 3' (right) neighboring CpGs in a sequencing string.
Collapse
|
17
|
Effect of Disease-Associated Germline Mutations on Structure Function Relationship of DNA Methyltransferases. Genes (Basel) 2019; 10:genes10050369. [PMID: 31091831 PMCID: PMC6562416 DOI: 10.3390/genes10050369] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 12/21/2022] Open
Abstract
Despite a large body of evidence supporting the role of aberrant DNA methylation in etiology of several human diseases, the fundamental mechanisms that regulate the activity of mammalian DNA methyltransferases (DNMTs) are not fully understood. Recent advances in whole genome association studies have helped identify mutations and genetic alterations of DNMTs in various diseases that have a potential to affect the biological function and activity of these enzymes. Several of these mutations are germline-transmitted and associated with a number of hereditary disorders, which are potentially caused by aberrant DNA methylation patterns in the regulatory compartments of the genome. These hereditary disorders usually cause neurological dysfunction, growth defects, and inherited cancers. Biochemical and biological characterization of DNMT variants can reveal the molecular mechanism of these enzymes and give insights on their specific functions. In this review, we introduce roles and regulation of DNA methylation and DNMTs. We discuss DNMT mutations that are associated with rare diseases, the characterized effects of these mutations on enzyme activity and provide insights on their potential effects based on the known crystal structure of these proteins.
Collapse
|
18
|
Gowher H, Jeltsch A. Mammalian DNA methyltransferases: new discoveries and open questions. Biochem Soc Trans 2018; 46:1191-1202. [PMID: 30154093 PMCID: PMC6581191 DOI: 10.1042/bst20170574] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 11/17/2022]
Abstract
As part of the epigenetic network, DNA methylation is a major regulator of chromatin structure and function. In mammals, it mainly occurs at palindromic CpG sites, but asymmetric methylation at non-CpG sites is also observed. Three enzymes are involved in the generation and maintenance of DNA methylation patterns. DNMT1 has high preference for hemimethylated CpG sites, and DNMT3A and DNMT3B equally methylate unmethylated and hemimethylated DNA, and also introduce non-CpG methylation. Here, we review recent observations and novel insights into the structure and function of mammalian DNMTs (DNA methyltransferases), including new structures of DNMT1 and DNMT3A, data on their mechanism, regulation by post-translational modifications and on the function of DNMTs in cells. In addition, we present news findings regarding the allosteric regulation and targeting of DNMTs by chromatin modifications and chromatin proteins. In combination, the recent publications summarized here impressively illustrate the intensity of ongoing research in this field. They provide a deeper understanding of key mechanistic properties of DNMTs, but they also document still unsolved issues, which need to be addressed in future research.
Collapse
Affiliation(s)
- Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| |
Collapse
|
19
|
Ravichandran M, Jurkowska RZ, Jurkowski TP. Target specificity of mammalian DNA methylation and demethylation machinery. Org Biomol Chem 2018; 16:1419-1435. [DOI: 10.1039/c7ob02574b] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.
Collapse
Affiliation(s)
| | | | - T. P. Jurkowski
- Universität Stuttgart
- Abteilung Biochemie
- Institute für Biochemie und Technische Biochemie
- Stuttgart D-70569
- Germany
| |
Collapse
|