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Valyaeva AA, Sheval EV. Nonspecific Interactions in Transcription Regulation and Organization of Transcriptional Condensates. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:688-700. [PMID: 38831505 DOI: 10.1134/s0006297924040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 06/05/2024]
Abstract
Eukaryotic cells are characterized by a high degree of compartmentalization of their internal contents, which ensures precise and controlled regulation of intracellular processes. During many processes, including different stages of transcription, dynamic membraneless compartments termed biomolecular condensates are formed. Transcription condensates contain various transcription factors and RNA polymerase and are formed by high- and low-specificity interactions between the proteins, DNA, and nearby RNA. This review discusses recent data demonstrating important role of nonspecific multivalent protein-protein and RNA-protein interactions in organization and regulation of transcription.
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Affiliation(s)
- Anna A Valyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Shin H, Leung A, Costello KR, Senapati P, Kato H, Moore RE, Lee M, Lin D, Tang X, Pirrotte P, Bouman Chen Z, Schones DE. Inhibition of DNMT1 methyltransferase activity via glucose-regulated O-GlcNAcylation alters the epigenome. eLife 2023; 12:e85595. [PMID: 37470704 PMCID: PMC10390045 DOI: 10.7554/elife.85595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/19/2023] [Indexed: 07/21/2023] Open
Abstract
The DNA methyltransferase activity of DNMT1 is vital for genomic maintenance of DNA methylation. We report here that DNMT1 function is regulated by O-GlcNAcylation, a protein modification that is sensitive to glucose levels, and that elevated O-GlcNAcylation of DNMT1 from high glucose environment leads to alterations to the epigenome. Using mass spectrometry and complementary alanine mutation experiments, we identified S878 as the major residue that is O-GlcNAcylated on human DNMT1. Functional studies in human and mouse cells further revealed that O-GlcNAcylation of DNMT1-S878 results in an inhibition of methyltransferase activity, resulting in a general loss of DNA methylation that preferentially occurs at partially methylated domains (PMDs). This loss of methylation corresponds with an increase in DNA damage and apoptosis. These results establish O-GlcNAcylation of DNMT1 as a mechanism through which the epigenome is regulated by glucose metabolism and implicates a role for glycosylation of DNMT1 in metabolic diseases characterized by hyperglycemia.
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Affiliation(s)
- Heon Shin
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Amy Leung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Kevin R Costello
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Parijat Senapati
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Hiroyuki Kato
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Roger E Moore
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center DuarteDuarteUnited States
| | - Michael Lee
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Dimitri Lin
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Xiaofang Tang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Patrick Pirrotte
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center DuarteDuarteUnited States
- Cancer & Cell Biology Division, Translational Genomics Research InstitutePhoenixUnited States
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
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Mechanisms of Long Non-Coding RNA in Breast Cancer. Int J Mol Sci 2023; 24:ijms24054538. [PMID: 36901971 PMCID: PMC10002950 DOI: 10.3390/ijms24054538] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
The landscape of pervasive transcription in eukaryotic genomes has made space for the identification of thousands of transcripts that are difficult to frame in a specific functional category. A new class has been broadly named as long non-coding RNAs (lncRNAs) and shortly defined as transcripts that are longer than 200 nucleotides with no or limited coding potential. So far, about 19,000 lncRNAs genes have been annotated in the human genome (Gencode 41), nearly matching the number of protein-coding genes. A key scientific priority is the functional characterization of lncRNAs, a major challenge in molecular biology that has encouraged many high-throughput efforts. LncRNA studies have been stimulated by the enormous clinical potential that these molecules promise and have been based on the characterization of their expression and functional mechanisms. In this review, we illustrate some of these mechanisms as they have been pictured in the context of breast cancer.
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Abstract
PURPOSE OF REVIEW Intervertebral disc degeneration is a contributor to chronic back pain. While a part of the natural aging process, early or rapid intervertebral disc degeneration is highly heritable. In this review, we summarize recent progress towards unraveling the genetics associated with this degenerative process. RECENT FINDINGS Use of large cohorts of patient data to conduct genome-wide association studies (GWAS) for intervertebral disc disease, and to lesser extent for aspects of this process, such as disc height, has resulted in a large increase in our understanding of the genetic etiology. Genetic correlation suggests that intervertebral disc disease is pleiotropic with risk factors for other diseases such as osteoporosis. The use of Mendelian Randomization is slowly establishing what are the causal relationships between intervertebral disc disease and factors previously correlated with this disease. The results from these human genetic studies highlight the complex nature of this disease and have the potential to lead to improved clinical management of intervertebral disc disease. Much additional work should now be focused on characterizing the causative relationship various co-morbid conditions have with intervertebral disc degeneration and on finding interventions to slow or halt this disease.
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Affiliation(s)
- David C Ou-Yang
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado, Anschutz Medical Campus, 12800 E 19th Ave, MS8343, Aurora, CO, 80045, USA
| | - Christopher J Kleck
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado, Anschutz Medical Campus, 12800 E 19th Ave, MS8343, Aurora, CO, 80045, USA
| | - Cheryl L Ackert-Bicknell
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado, Anschutz Medical Campus, 12800 E 19th Ave, MS8343, Aurora, CO, 80045, USA.
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Yang Z, Xu F, Teschendorff AE, Zhao Y, Yao L, Li J, He Y. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci 2022; 9:1067406. [PMID: 36533073 PMCID: PMC9755597 DOI: 10.3389/fmolb.2022.1067406] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feng Xu
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yao
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Li
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yungang He
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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DNA Methyltransferases: From Evolution to Clinical Applications. Int J Mol Sci 2022; 23:ijms23168994. [PMID: 36012258 PMCID: PMC9409253 DOI: 10.3390/ijms23168994] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an epigenetic mark that living beings have used in different environments. The MTases family catalyzes DNA methylation. This process is conserved from archaea to eukaryotes, from fertilization to every stage of development, and from the early stages of cancer to metastasis. The family of DNMTs has been classified into DNMT1, DNMT2, and DNMT3. Each DNMT has been duplicated or deleted, having consequences on DNMT structure and cellular function, resulting in a conserved evolutionary reaction of DNA methylation. DNMTs are conserved in the five kingdoms of life: bacteria, protists, fungi, plants, and animals. The importance of DNMTs in whether methylate or not has a historical adaptation that in mammals has been discovered in complex regulatory mechanisms to develop another padlock to genomic insurance stability. The regulatory mechanisms that control DNMTs expression are involved in a diversity of cell phenotypes and are associated with pathologies transcription deregulation. This work focused on DNA methyltransferases, their biology, functions, and new inhibitory mechanisms reported. We also discuss different approaches to inhibit DNMTs, the use of non-coding RNAs and nucleoside chemical compounds in recent studies, and their importance in biological, clinical, and industry research.
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LncRNA-mediated DNA methylation: an emerging mechanism in cancer and beyond. J Exp Clin Cancer Res 2022; 41:100. [PMID: 35292092 PMCID: PMC8922926 DOI: 10.1186/s13046-022-02319-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/08/2022] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms to regulate gene expression, which is highly dynamic during development and specifically maintained in somatic cells. Aberrant DNA methylation patterns are strongly associated with human diseases including cancer. How are the cell-specific DNA methylation patterns established or disturbed is a pivotal question in developmental biology and cancer epigenetics. Currently, compelling evidence has emerged that long non-coding RNA (lncRNA) mediates DNA methylation in both physiological and pathological conditions. In this review, we provide an overview of the current understanding of lncRNA-mediated DNA methylation, with emphasis on the roles of this mechanism in cancer, which to the best of our knowledge, has not been systematically summarized. In addition, we also discuss the potential clinical applications of this mechanism in RNA-targeting drug development.
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