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Mongelli A, Mengozzi A, Geiger M, Gorica E, Mohammed SA, Paneni F, Ruschitzka F, Costantino S. Mitochondrial epigenetics in aging and cardiovascular diseases. Front Cardiovasc Med 2023; 10:1204483. [PMID: 37522089 PMCID: PMC10382027 DOI: 10.3389/fcvm.2023.1204483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/29/2023] [Indexed: 08/01/2023] Open
Abstract
Mitochondria are cellular organelles which generate adenosine triphosphate (ATP) molecules for the maintenance of cellular energy through the oxidative phosphorylation. They also regulate a variety of cellular processes including apoptosis and metabolism. Of interest, the inner part of mitochondria-the mitochondrial matrix-contains a circular molecule of DNA (mtDNA) characterised by its own transcriptional machinery. As with genomic DNA, mtDNA may also undergo nucleotide mutations that have been shown to be responsible for mitochondrial dysfunction. During physiological aging, the mitochondrial membrane potential declines and associates with enhanced mitophagy to avoid the accumulation of damaged organelles. Moreover, if the dysfunctional mitochondria are not properly cleared, this could lead to cellular dysfunction and subsequent development of several comorbidities such as cardiovascular diseases (CVDs), diabetes, respiratory and cardiovascular diseases as well as inflammatory disorders and psychiatric diseases. As reported for genomic DNA, mtDNA is also amenable to chemical modifications, namely DNA methylation. Changes in mtDNA methylation have shown to be associated with altered transcriptional programs and mitochondrial dysfunction during aging. In addition, other epigenetic signals have been observed in mitochondria, in particular the interaction between mtDNA methylation and non-coding RNAs. Mitoepigenetic modifications are also involved in the pathogenesis of CVDs where oxygen chain disruption, mitochondrial fission, and ROS formation alter cardiac energy metabolism leading to hypertrophy, hypertension, heart failure and ischemia/reperfusion injury. In the present review, we summarize current evidence on the growing importance of epigenetic changes as modulator of mitochondrial function in aging. A better understanding of the mitochondrial epigenetic landscape may pave the way for personalized therapies to prevent age-related diseases.
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Affiliation(s)
- Alessia Mongelli
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Alessandro Mengozzi
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Martin Geiger
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Era Gorica
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Shafeeq Ahmed Mohammed
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Francesco Paneni
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Frank Ruschitzka
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sarah Costantino
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Wang M, Zhu J, Ye Y, Li P, Sun W, Zhang M. N6AMT1 is a novel potential diagnostic, prognostic and immunotherapy response biomarker in pan-cancer. Aging (Albany NY) 2023; 15:6526-6544. [PMID: 37437243 PMCID: PMC10373955 DOI: 10.18632/aging.204868] [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: 04/03/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND The N-6-adenine-specific DNA methyltransferase 1 (N6AMT1) is the only writer responsible for DNA 6mA modifications. At present, its role in cancer is still unclear, and further systematic pan-cancer analysis is needed to explore its value in diagnosis, prognosis and immunological function. METHODS The subcellular localization of N6AMT1 was explored by UniProt and HPA database. The expression data and prognosis data of N6AMT1 were downloaded from the UCSC (cohort: TCGA pan-cancer), and the diagnostic and prognostic value of N6AMT1 in pan-cancer was explored. The value of N6AMT1-guided immunotherapy was explored through three cohorts (GSE168204, GSE67501 and IMvigor210 cohort). The correlation between N6AMT1 expression and tumor immune microenvironment was explored using CIBERSORT and ESTIMATE calculation methods, combined with TISIDB database. The biological role of N6AMT1 in specific tumors was explored by GSEA method. Finally, we explored chemicals affecting N6AMT1 expression through the CTD. RESULTS N6AMT1 is mainly localized in the nucleus and differentially expressed in 9 cancer types. In addition, N6AMT1 showed early diagnostic value in 7 cancers and showed potential prognostic value in multiple cancer types. We also demonstrated that N6AMT1 expression was significantly associated with immunomodulator-related molecules, infiltration of lymphocyte subsets, and biomarkers of immunotherapy response. Furthermore, we show that N6AMT1 is differentially expressed in the immunotherapy cohort. Finally, we explored 43 chemicals that can affect N6AMT1 expression. CONCLUSIONS N6AMT1 has shown excellent diagnostic and prognostic capabilities in a variety of cancers, and it may reshape the tumor microenvironment and contribute to the ability to predict response to immunotherapy.
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Affiliation(s)
- Mingqi Wang
- Department of Chinese Integrative Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, Shushan, Hefei 230022, Anhui, China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Shushan, Hefei 230022, Anhui, China
| | - Jiajie Zhu
- Department of Gastroenterology, Tongde Hospital of Zhejiang Province, Xihu, Hangzhou 310012, Zhejiang, China
| | - Yingquan Ye
- Department of Chinese Integrative Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, Shushan, Hefei 230022, Anhui, China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Shushan, Hefei 230022, Anhui, China
| | - Ping Li
- Department of Chinese Integrative Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, Shushan, Hefei 230022, Anhui, China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Shushan, Hefei 230022, Anhui, China
| | - Weijie Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Shushan, Hefei 230022, Anhui, China
| | - Mei Zhang
- Department of Chinese Integrative Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, Shushan, Hefei 230022, Anhui, China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Shushan, Hefei 230022, Anhui, China
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53
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Sainty R, Silver MJ, Prentice AM, Monk D. The influence of early environment and micronutrient availability on developmental epigenetic programming: lessons from the placenta. Front Cell Dev Biol 2023; 11:1212199. [PMID: 37484911 PMCID: PMC10358779 DOI: 10.3389/fcell.2023.1212199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
DNA methylation is the most commonly studied epigenetic mark in humans, as it is well recognised as a stable, heritable mark that can affect genome function and influence gene expression. Somatic DNA methylation patterns that can persist throughout life are established shortly after fertilisation when the majority of epigenetic marks, including DNA methylation, are erased from the pre-implantation embryo. Therefore, the period around conception is potentially critical for influencing DNA methylation, including methylation at imprinted alleles and metastable epialleles (MEs), loci where methylation varies between individuals but is correlated across tissues. Exposures before and during conception can affect pregnancy outcomes and health throughout life. Retrospective studies of the survivors of famines, such as those exposed to the Dutch Hunger Winter of 1944-45, have linked exposures around conception to later disease outcomes, some of which correlate with DNA methylation changes at certain genes. Animal models have shown more directly that DNA methylation can be affected by dietary supplements that act as cofactors in one-carbon metabolism, and in humans, methylation at birth has been associated with peri-conceptional micronutrient supplementation. However, directly showing a role of micronutrients in shaping the epigenome has proven difficult. Recently, the placenta, a tissue with a unique hypomethylated methylome, has been shown to possess great inter-individual variability, which we highlight as a promising target tissue for studying MEs and mixed environmental exposures. The placenta has a critical role shaping the health of the fetus. Placenta-associated pregnancy complications, such as preeclampsia and intrauterine growth restriction, are all associated with aberrant patterns of DNA methylation and expression which are only now being linked to disease risk later in life.
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Affiliation(s)
- Rebecca Sainty
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Matt J. Silver
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - David Monk
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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Arkhipova IR, Yushenova IA, Rodriguez F. Shaping eukaryotic epigenetic systems by horizontal gene transfer. Bioessays 2023; 45:e2200232. [PMID: 37339822 PMCID: PMC10287040 DOI: 10.1002/bies.202200232] [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: 11/30/2022] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 06/22/2023]
Abstract
DNA methylation constitutes one of the pillars of epigenetics, relying on covalent bonds for addition and/or removal of chemically distinct marks within the major groove of the double helix. DNA methyltransferases, enzymes which introduce methyl marks, initially evolved in prokaryotes as components of restriction-modification systems protecting host genomes from bacteriophages and other invading foreign DNA. In early eukaryotic evolution, DNA methyltransferases were horizontally transferred from bacteria into eukaryotes several times and independently co-opted into epigenetic regulatory systems, primarily via establishing connections with the chromatin environment. While C5-methylcytosine is the cornerstone of plant and animal epigenetics and has been investigated in much detail, the epigenetic role of other methylated bases is less clear. The recent addition of N4-methylcytosine of bacterial origin as a metazoan DNA modification highlights the prerequisites for foreign gene co-option into the host regulatory networks, and challenges the existing paradigms concerning the origin and evolution of eukaryotic regulatory systems.
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Affiliation(s)
- Irina R Arkhipova
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, Massachusetts, USA
| | - Irina A Yushenova
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, Massachusetts, USA
| | - Fernando Rodriguez
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, Massachusetts, USA
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55
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Zhang XL, Chen XH, Xu B, Chen M, Zhu S, Meng N, Wang JZ, Zhu H, Chen D, Liu JB, Yan GR. K235 acetylation couples with PSPC1 to regulate the m 6A demethylation activity of ALKBH5 and tumorigenesis. Nat Commun 2023; 14:3815. [PMID: 37369679 DOI: 10.1038/s41467-023-39414-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
N6-methyladenosine (m6A) modification plays important roles in bioprocesses and diseases. AlkB homolog 5 (ALKBH5) is one of two m6A demethylases. Here, we reveal that ALKBH5 is acetylated at lysine 235 (K235) by lysine acetyltransferase 8 and deacetylated by histone deacetylase 7. K235 acetylation strengthens the m6A demethylation activity of ALKBH5 by increasing its recognition of m6A on mRNA. RNA-binding protein paraspeckle component 1 (PSCP1) is a regulatory subunit of ALKBH5 and preferentially interacts with K235-acetylated ALKBH5 to recruit and facilitate the recognition of m6A mRNA by ALKBH5, thereby promoting m6A erasure. Mitogenic signals promote ALKBH5 K235 acetylation. K235 acetylation of ALKBH5 is upregulated in cancers and promotes tumorigenesis. Thus, our findings reveal that the m6A demethylation activity of ALKBH5 is orchestrated by its K235 acetylation and regulatory subunit PSPC1 and that K235 acetylation is necessary for the m6A demethylase activity and oncogenic roles of ALKBH5.
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Affiliation(s)
- Xiao-Lan Zhang
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xin-Hui Chen
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Binwu Xu
- Blood Transfusion Department, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Min Chen
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Song Zhu
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Nan Meng
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Ji-Zhong Wang
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Huifang Zhu
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - De Chen
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Jin-Bao Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Guang-Rong Yan
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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56
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Mao F, Xie H, Shi Y, Jiang S, Wang S, Wu Y. The Global Changes of N6-methyldeoxyadenosine in Response to Low Temperature in Arabidopsis thaliana and Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2373. [PMID: 37375998 DOI: 10.3390/plants12122373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
N6-methyldeoxyadenosine (6mA) is a recently discovered DNA modification involved in regulating plant adaptation to abiotic stresses. However, the mechanisms and changes of 6mA under cold stress in plants are not yet fully understood. Here, we conducted a genome-wide analysis of 6mA and observed that 6mA peaks were predominantly present within the gene body regions under both normal and cold conditions. In addition, the global level of 6mA increased both in Arabidopsis and rice after the cold treatment. The genes that exhibited an up-methylation showed enrichment in various biological processes, whereas there was no significant enrichment observed among the down-methylated genes. The association analysis revealed a positive correlation between the 6mA level and the gene expression level. Joint analysis of the 6mA methylome and transcriptome of Arabidopsis and rice unraveled that fluctuations in 6mA levels caused by cold exposure were not correlated to changes in transcript levels. Furthermore, we discovered that orthologous genes modified by 6mA showed high expression levels; however, only a minor amount of differentially 6mA-methylated orthologous genes were shared between Arabidopsis and rice under low-temperature conditions. In conclusion, our study provides information on the role of 6mA in response to cold stress and reveals its potential for regulating the expression of stress-related genes.
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Affiliation(s)
- Fei Mao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Hairong Xie
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yucheng Shi
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shasha Jiang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufeng Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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Li Y, Liang ZY, Wang HL. N6-methyl-2'-deoxyadenosine promotes self-renewal of BFU-E progenitor in erythropoiesis. iScience 2023; 26:106924. [PMID: 37283807 PMCID: PMC10239700 DOI: 10.1016/j.isci.2023.106924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/08/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023] Open
Abstract
Red blood cells supply the oxygen required for all human cells and are in demand for emerging blood-loss therapy. Here we identified N6-methyl-2'-deoxyadenosine (6mdA) as an agonist that promotes the hyperproliferation of burst-forming unit erythroid (BFU-E) progenitor cells. In addition, 6mdA represses the apoptosis of erythroid progenitor cells (EPCs). Combined use of with SCF and EPO enabled cultures of isolated BFU-E to be expanded up to 5,000-fold. Transcriptome analysis showed that 6mdA upregulates the expression of the EPC-associated factors c-Kit, Myb, and Gata2 and downregulates that of the erythroid maturation-related transcription factors Gata1, Spi1, and Klf1. Mechanistic studies suggested that 6mdA enhances and prolongs the activation of erythropoiesis-associated master gene c-Kit and its downstream signaling, leading to expansion and accumulation of EPCs. Collectively, we demonstrate that 6mdA can efficiently stimulate the EPC hyperproliferation and provide a new regenerative medicine recipe to improve ex vivo generation of red blood cells.
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Affiliation(s)
- Yao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Yu Liang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Lin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Environment and Health, Jianghan University, Wuhan, Hubei 430056, China
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58
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Ding N, Lv Y, Su H, Wang Z, Kong X, Zhen J, Lv Z, Wang R. Vascular calcification in CKD: New insights into its mechanisms. J Cell Physiol 2023; 238:1160-1182. [PMID: 37269534 DOI: 10.1002/jcp.31021] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/28/2023] [Indexed: 06/05/2023]
Abstract
Vascular calcification (VC) is a common complication of chronic kidney disease (CKD) and contributes to an increased risk of cardiovascular morbidity and mortality. However, effective therapies are still unavailable at present. It has been well established that VC associated with CKD is not a passive process of calcium phosphate deposition, but an actively regulated and cell-mediated process that shares many similarities with bone formation. Additionally, numerous studies have suggested that CKD patients have specific risk factors and contributors to the development of VC, such as hyperphosphatemia, uremic toxins, oxidative stress and inflammation. Although research efforts in the past decade have greatly improved our knowledge of the multiple factors and mechanisms involved in CKD-related VC, many questions remain unanswered. Moreover, studies from the past decade have demonstrated that epigenetic modifications abnormalities, such as DNA methylation, histone modifications and noncoding RNAs, play an important role in the regulation of VC. This review seeks to provide an overview of the pathophysiological and molecular mechanisms of VC associated with CKD, mainly focusing on the involvement of epigenetic modifications in the initiation and progression of uremic VC, with the aim to develop promising therapies for CKD-related cardiovascular events in the future.
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Affiliation(s)
- Nannan Ding
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yaodong Lv
- Department of Neurology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Hong Su
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ziyang Wang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xianglei Kong
- Department of Nephrology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Junhui Zhen
- Department of Pathology, Shandong University, Jinan, China
| | - Zhimei Lv
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Rong Wang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023; 24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
Abstract
Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
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Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Kietzmann T. Vitamin C: From nutrition to oxygen sensing and epigenetics. Redox Biol 2023; 63:102753. [PMID: 37263060 DOI: 10.1016/j.redox.2023.102753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Vitamin C is unbeatable - at least when it comes to sales. Of all the vitamin preparations, those containing vitamin C sell best. This is surprising because vitamin C deficiency is extremely rare. Nevertheless, there is still controversy about whether the additional intake of vitamin C supplements is essential for our health. In this context, the possible additional benefit is in most cases merely reduced to the known effect as an antioxidant. However, new findings in recent years on the mechanisms of oxygen-sensing and epigenetic control underpin the multifaceted role of vitamin C in a biological context and have therefore renewed interest in it. In the present article, therefore, known facts are linked to these new key data. In addition, available clinical data on vitamin C use of cancer therapy are summarized.
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Affiliation(s)
- Thomas Kietzmann
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, P.O. Box 3000, 90014, Oulu, Finland.
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Pan B, Ye F, Li T, Wei F, Warren A, Wang Y, Gao S. Potential role of N 6-adenine DNA methylation in alternative splicing and endosymbiosis in Paramecium bursaria. iScience 2023; 26:106676. [PMID: 37182097 PMCID: PMC10173741 DOI: 10.1016/j.isci.2023.106676] [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: 05/21/2022] [Revised: 12/02/2022] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
N6-adenine DNA methylation (6mA), a rediscovered epigenetic mark in eukaryotic organisms, diversifies in abundance, distribution, and function across species, necessitating its study in more taxa. Paramecium bursaria is a typical model organism with endosymbiotic algae of the species Chlorella variabilis. This consortium therefore serves as a valuable system to investigate the functional role of 6mA in endosymbiosis, as well as the evolutionary importance of 6mA among eukaryotes. In this study, we report the first genome-wide, base pair-resolution map of 6mA in P. bursaria and identify its methyltransferase PbAMT1. Functionally, 6mA exhibits a bimodal distribution at the 5' end of RNA polymerase II-transcribed genes and possibly participates in transcription by facilitating alternative splicing. Evolutionarily, 6mA co-evolves with gene age and likely serves as a reverse mark of endosymbiosis-related genes. Our results offer new insights for the functional diversification of 6mA in eukaryotes as an important epigenetic mark.
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Affiliation(s)
- Bo Pan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Fei Ye
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Tao Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Fan Wei
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Yuanyuan Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- Corresponding author
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
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Sergeeva A, Davydova K, Perenkov A, Vedunova M. Mechanisms of human DNA methylation, alteration of methylation patterns in physiological processes and oncology. Gene 2023:147487. [PMID: 37211289 DOI: 10.1016/j.gene.2023.147487] [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: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
DNA methylation is one of the epigenetic modifications of the genome, the essence of which is the attachment of a methyl group to nitrogenous bases. In the eukaryote genome, cytosine is methylated in the vast majority of cases. About 98% of cytosines are methylated as part of CpG dinucleotides. They, in turn, form CpG islands, which are clusters of these dinucleotides. Islands located in the regulatory elements of genes are in particular interest. They are assumed to play an important role in the regulation of gene expression in humans. Besides that, cytosine methylation serves the functions of genomic imprinting, transposon suppression, epigenetic memory maintenance, X- chromosome inactivation, and embryonic development. Of particular interest are the enzymatic processes of methylation and demethylation. The methylation process always depends on the work of enzymatic complexes and is very precisely regulated. The methylation process largely depends on the functioning of three groups of enzymes: writers, readers and erasers. Writers include proteins of the DNMT family, readers are proteins containing the MBD, BTB/POZ or SET- and RING-associated domains and erasers are proteins of the TET family. Whereas demethylation can be performed not only by enzymatic complexes, but also passively during DNA replication. Hence, the maintenance of DNA methylation is important. Changes in methylation patterns are observed during embryonic development, aging, and cancers. In both aging and cancer, massive hypomethylation of the genome with local hypermethylation is observed. In this review, we will review the current understanding of the mechanisms of DNA methylation and demethylation in humans, the structure and distribution of CpG islands, the role of methylation in the regulation of gene expression, embryogenesis, aging, and cancer development.
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Affiliation(s)
- A Sergeeva
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - K Davydova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - A Perenkov
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - M Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
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Cai J, Shen W, Zhang G, Li X, Shen H, Li W, Tan C, Zhang T, Shi M, Yang Z, Li Y, Liu H, Zhao X. Xiao Chai Hu Tang alleviates the pancreatic tumorigenesis via improving the mtDNA N6-Methyladenine modification mediated mitochondrial dysfunction in Syrian hamster model. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154840. [PMID: 37172477 DOI: 10.1016/j.phymed.2023.154840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Pancreatic intraepithelial neoplasia (PanIN) is the most common precursor lesion of pancreatic ductal adenocarcinoma (PDAC), which is a highly malignant tumor and lack of effective treatment. Although Xiao Chai Hu Tang (XCHT) has a good therapeutic effect on pancreatic cancer patients with advanced stage, the effect and mechanism of XCHT remains unclear in pancreatic tumorigenesis. PURPOSE To assess the therapeutic effects of XCHT on the malignant transformation from PanIN to PDAC and to reveal its mechanisms of pancreatic tumorigenesis. METHODS Syrian golden hamster were induced by N-Nitrosobis (2-oxopropyl) amine (BOP) to establish the pancreatic tumorigenesis model. The morphological changes of pancreatic tissue were observed by H&E and Masson staining; the Gene ontology (GO) analysis the transcriptional profiling changes; the mitochondrial ATP generation, mitochondrial redox status, mitochondrial DNA (mtDNA) N6-methyladenine (6mA) level and relative mtDNA genes expressions were examined. In addition, immunofluorescence detect the cell localization of 6mA in human pancreatic cancer PANC1 cell. Using the TCGA database, the prognostic effect of mtDNA 6mA demethylation ALKBH1 expression on pancreatic cancer patients was analyzed. RESULTS We confirmed the mtDNA 6mA levels were gradually increased with the mitochondrial dysfunction in PanINs progression. XCHT showed the effect to inhibit the occurrence and development of pancreatic cancer in Syrian hamster pancreatic tumorigenesis model. In addition, the lack of ALKBH1 mediated mtDNA 6mA increase, mtDNA coded genes down-expression and abnormal redox status were rescued by XCHT. CONCLUSIONS ALKBH1/mtDNA 6mA mediated mitochondrial dysfunction to induce the occurrence and progression of pancreatic cancer. XCHT can improve ALKBH1 expression and mtDNA 6mA level, regulate the oxidative stress and expression of mtDNA coded genes. This study investigated a new molecular mechanism of pancreatic tumorigenesis, and revealed the therapeutic efficacy of XCHT in pancreatic tumorigenesis for the first time.
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Affiliation(s)
- Jun Cai
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China
| | - Wenyuan Shen
- Department of Spine Surgery, The Second Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China; International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, 154 Anshan Road, Tianjin, China
| | - Guixian Zhang
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China
| | - Xia Li
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China
| | - Hongsheng Shen
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China
| | - Wenchang Li
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China
| | - Cheng Tan
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China
| | - Ting Zhang
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China
| | - Mengrou Shi
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China
| | - Zibo Yang
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China
| | - Yuan Li
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
| | - Hongbin Liu
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China; Health Commission of Heping District, Tianjin, China.
| | - Xiumei Zhao
- Department of Cancer Pharmacology, Tianjin Institute of Medical and Pharmaceutical Sciences, Tianjin Medicine and Health Research Center, 79 Duolun Road, Tianjin, China.
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Lyu C, Wang HD, Lai W, Wang H. Identification and quantification of DNA N 6-methyladenine modification in mammals: A challenge to modern analytical technologies. Curr Opin Chem Biol 2023; 73:102259. [PMID: 36652775 DOI: 10.1016/j.cbpa.2022.102259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 01/18/2023]
Abstract
DNA N6-methyladenine modification (6mA) is a predominant epigenetic mark in prokaryotes but rarely present in multicellular metazoa. The analytical technologies have been developed for sensitive detection of 6mA, including ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-MS/MS) and single molecule real-time sequencing (SMRTseq). However, it remains challenging to detect 6mA at global level and/or in the context of sequence in multicellular metazoa (including mammals). This mini-review brings insights into current dilemma and potential solutions for the identification and quantifications of 6mA in mammals.
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Affiliation(s)
- Cong Lyu
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hui-Dong Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Weiyi Lai
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hailin Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China; University of Chinese Academy of Sciences, Beijing, China.
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Wang X, Wong CC, Chen H, Fu K, Shi L, Su H, Guo S, Gou H, Hu X, Zhang L, Ji J, Yu J. The N 6-methyladenine DNA demethylase ALKBH1 promotes gastric carcinogenesis by disrupting NRF1 binding capacity. Cell Rep 2023; 42:112279. [PMID: 36989111 DOI: 10.1016/j.celrep.2023.112279] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 01/20/2023] [Accepted: 03/03/2023] [Indexed: 03/30/2023] Open
Abstract
DNA N6-methyladenine (6mA) is an epigenetic modification that regulates various biological processes. Here, we show that gastric cancer (GC) cells and tumors display a marked reduction in 6mA levels compared with normal gastric tissues and cells. 6mA is abundant in the surrounding transcription start sites and occurs at consensus motifs. Among the 6mA regulators, ALKBH1, a demethylase, is significantly overexpressed in GC tissues compared with adjacent normal tissues. Moreover, high ALKBH1 expression is associated with poor survival of patients with GC. ALKBH1 knockout in mice impairs chemically induced gastric carcinogenesis. Mechanistically, ALKBH1 mediates DNA 6mA demethylation to repress gene expression. In particular, the 6mA sites are enriched in NRF1 binding sequences and targeted for demethylation by ALKBH1. ALKBH1-induced 6mA demethylation inhibits NRF1-driven transcription of downstream targets, including multiple genes involved in the AMP-activated protein kinase (AMPK) signaling pathway. Accordingly, ALKBH1 suppresses AMPK signaling, causing a metabolic shift toward the Warburg effect, which facilitates tumorigenesis.
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Affiliation(s)
- Xiaohong Wang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China; Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital and Institute, Beijing, China
| | - Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Huarong Chen
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kaili Fu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lingxue Shi
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hao Su
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shang Guo
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hongyan Gou
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiaoxu Hu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lianhai Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital and Institute, Beijing, China.
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Guo C, Liu Z, Zhang H. DNA 6mA demethylase ALKBH1 regulates DDX18 expression to promote proliferation of human head and neck squamous cell carcinoma. Cell Oncol (Dordr) 2023:10.1007/s13402-023-00800-1. [PMID: 36976498 DOI: 10.1007/s13402-023-00800-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2023] [Indexed: 03/29/2023] Open
Abstract
PURPOSE Human head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. Currently, surgical resection plus a combination of chemotherapy and radiotherapy is the standard treatment for HNSCC, and the 5-year survival rate of patients with HNSCC remains very low because of the higher incidence of metastasis with consequent recurrence. Here, we aimed to investigate the potential role of DNA N6-methyladenine (6mA) demethylase ALKBH1 in tumor cell proliferation in HNSCC. METHODS The expression of ALKBH1 in 10 pairs of HNSCC/normal tissues and 3 HNSCC cell lines were measured by qRT‒PCR and western blotting. Colony formation, flow cytometry, patient-derived HNSCC organoid assays were used to assess the role of ALKBH1 in HNSCC cell proliferation in cell lines and human HNSCC patients. MeDIP-seq, RNA sequencing, Dot blotting and western blotting were used to evaluate the regulatory effect of ALKBH1 on the expression of DEAD-box RNA helicase DDX18. A dual-luciferase reporter assay was used to assess the putative effect of DNA 6mA levels on DDX18 transcription. RESULTS ALKBH1 was highly expressed in HNSCC cells and patient tissues. Functional experiments revealed that ALKBH1 knockdown in SCC9, SCC25, and CAL27 cells inhibited their proliferation in vitro. Using patient-derived HNSCC organoid assay, we found that knockdown of ALKBH1 inhibited the proliferation and colony formation of HNSCC patients-derived organoids. Moreover, we found that ALKBH1 can enhance DDX18 expression by erasing DNA 6mA level and regulating its promoter activity. ALKBH1 deficiency blocked tumor cell proliferation by inhibiting DDX18 expression. Exogenous overexpression of DDX18 rescued the cell proliferation arrest caused by ALKBH1 knockdown. CONCLUSION Our data reveal the important role of ALKBH1 in regulating proliferation of HNSCC.
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Affiliation(s)
- Chengli Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Zheming Liu
- Cancer Center, Renmin Hospital, Wuhan University, No.185, East Lake Road, Wuhan, Hubei, 430071, China.
| | - Haojian Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China.
- Frontier Science Center for Immunology and Metabolism, Wuhan University, No.185, East Lake Road, Wuhan, Hubei, 430071, China.
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Li Q, Zhu Q. The role of demethylase AlkB homologs in cancer. Front Oncol 2023; 13:1153463. [PMID: 37007161 PMCID: PMC10060643 DOI: 10.3389/fonc.2023.1153463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
The AlkB family (ALKBH1-8 and FTO), a member of the Fe (II)- and α-ketoglutarate-dependent dioxygenase superfamily, has shown the ability to catalyze the demethylation of a variety of substrates, including DNA, RNA, and histones. Methylation is one of the natural organisms’ most prevalent forms of epigenetic modifications. Methylation and demethylation processes on genetic material regulate gene transcription and expression. A wide variety of enzymes are involved in these processes. The methylation levels of DNA, RNA, and histones are highly conserved. Stable methylation levels at different stages can coordinate the regulation of gene expression, DNA repair, and DNA replication. Dynamic methylation changes are essential for the abilities of cell growth, differentiation, and division. In some malignancies, the methylation of DNA, RNA, and histones is frequently altered. To date, nine AlkB homologs as demethylases have been identified in numerous cancers’ biological processes. In this review, we summarize the latest advances in the research of the structures, enzymatic activities, and substrates of the AlkB homologs and the role of these nine homologs as demethylases in cancer genesis, progression, metastasis, and invasion. We provide some new directions for the AlkB homologs in cancer research. In addition, the AlkB family is expected to be a new target for tumor diagnosis and treatment.
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Affiliation(s)
- Qiao Li
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Qingsan Zhu
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Qingsan Zhu,
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Liang X, Guo G, Wang Y, Wang M, Chen X, Zhang J, Li S, Liu L, Huang Q, Cui B, Zhang M, Sun G, Tang N, Zhang X, Zhang Q. Arsenic metabolism, N6AMT1 and AS3MT single nucleotide polymorphisms, and their interaction on gestational diabetes mellitus in Chinese pregnant women. ENVIRONMENTAL RESEARCH 2023; 221:115331. [PMID: 36681142 DOI: 10.1016/j.envres.2023.115331] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) in N6AMT1 and AS3MT are associated with arsenic (As) metabolism, and efficient As methylation capacity has been associated with diabetes. However, little is known about the gene-As interaction on gestational diabetes mellitus (GDM). OBJECTIVE This study aimed to explore the individual and combined effects of N6AMT1 and AS3MT SNPs with As metabolism on GDM. METHODS A cross-sectional study was performed among 385 Chinese pregnant women (86 GDM and 299 Non-GDM). Four SNPs in N6AMT1 (rs1997605 and rs1003671) and AS3MT (rs1046778 and rs11191453) were genotyped. Urinary inorganic arsenic (iAs), monomethylarsonic acid (MMA), and dimethylarsinic acid (DMA) were determined, and the percentages of As species (iAs%, MMA%, and DMA%) were calculated to assess the efficiency of As metabolism. RESULTS Pregnant women with N6AMT1 rs1997605 AA genotype had lower iAs% (B: 2.11; 95% CI: 4.08, -0.13) and MMA% (B: 0.21; 95% CI: 0.39, -0.04) than pregnant women with GG genotype. The AS3MT rs1046778 and rs11191453 C alleles were negatively associated with iAs% and MMA% but positively associated with DMA%. Higher urinary MMA% was significantly associated with a lower risk of GDM (OR: 0.54; 95% CI: 0.30, 0.97). The A allele in N6AMT1 rs1997605 (OR: 0.46; 95% CI: 0.26, 0.79) was associated with a decreased risk of GDM. The additive interactions between N6AMT1 rs1997605 GG genotypes and lower iAs% (AP: 0.50; 95% CI: 0.01, 0.99) or higher DMA% (AP: 0.52; 95% CI: 0.04, 0.99) were statistically significant. Similar additive interactions were also found between N6AMT1 rs1003671 GG genotypes and lower iAs% or higher DMA%. CONCLUSIONS Genetic variants in N6AMT1 and efficient As metabolism (indicated by lower iAs% and higher DMA%) can interact to influence GDM occurrence synergistically in Chinese pregnant women.
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Affiliation(s)
- Xiaoshan Liang
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China; Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China
| | - Guanshuai Guo
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China
| | - Yiyun Wang
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China
| | - Meng Wang
- Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China
| | - Xi Chen
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China
| | - Jingran Zhang
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China
| | - Shuying Li
- Department of Endocrinology, Tianjin Xiqing Hospital, Tianjin, 300380, China
| | - Liangpo Liu
- School of Public Health, Shanxi Medical University, Taiyuan, 030001 China
| | - Qingyu Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Bo Cui
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Tianjin, 300050, China
| | - Ming Zhang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China
| | - Guifan Sun
- Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, 110122, China
| | - Naijun Tang
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China
| | - Xumei Zhang
- Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China
| | - Qiang Zhang
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China.
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Falnes PØ, Małecki JM, Herrera MC, Bengtsen M, Davydova E. Human seven-β-strand (METTL) methyltransferases - conquering the universe of protein lysine methylation. J Biol Chem 2023; 299:104661. [PMID: 36997089 DOI: 10.1016/j.jbc.2023.104661] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
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Costa PMDS, Sales SLA, Pinheiro DP, Pontes LQ, Maranhão SS, Pessoa CDÓ, Furtado GP, Furtado CLM. Epigenetic reprogramming in cancer: From diagnosis to treatment. Front Cell Dev Biol 2023; 11:1116805. [PMID: 36866275 PMCID: PMC9974167 DOI: 10.3389/fcell.2023.1116805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
Disruption of the epigenetic program of gene expression is a hallmark of cancer that initiates and propagates tumorigenesis. Altered DNA methylation, histone modifications and ncRNAs expression are a feature of cancer cells. The dynamic epigenetic changes during oncogenic transformation are related to tumor heterogeneity, unlimited self-renewal and multi-lineage differentiation. This stem cell-like state or the aberrant reprogramming of cancer stem cells is the major challenge in treatment and drug resistance. Given the reversible nature of epigenetic modifications, the ability to restore the cancer epigenome through the inhibition of the epigenetic modifiers is a promising therapy for cancer treatment, either as a monotherapy or in combination with other anticancer therapies, including immunotherapies. Herein, we highlighted the main epigenetic alterations, their potential as a biomarker for early diagnosis and the epigenetic therapies approved for cancer treatment.
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Affiliation(s)
- Pedro Mikael da Silva Costa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Biotechnology Northeastern Network of Biotechnology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Sarah Leyenne Alves Sales
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Pharmacology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - Larissa Queiroz Pontes
- Oswaldo Cruz Foundation, FIOCRUZ-Ceará, Sector of Biotechnology, Eusebio, Ceará, Brazil,Postgraduation Program in Biotechnology and Natural Resources, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Sarah Sant’Anna Maranhão
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Claudia do Ó. Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Biotechnology Northeastern Network of Biotechnology, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Pharmacology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Gilvan Pessoa Furtado
- Oswaldo Cruz Foundation, FIOCRUZ-Ceará, Sector of Biotechnology, Eusebio, Ceará, Brazil,Postgraduation Program in Biotechnology and Natural Resources, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Cristiana Libardi Miranda Furtado
- Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil,Experimental Biology Center, University of Fortaleza, Fortaleza, Ceará, Brazil,*Correspondence: Cristiana Libardi Miranda Furtado,
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CRISPR-Cas9-Mediated Mutation of Methyltransferase METTL4 Results in Embryonic Defects in Silkworm Bombyx mori. Int J Mol Sci 2023; 24:ijms24043468. [PMID: 36834878 PMCID: PMC9965800 DOI: 10.3390/ijms24043468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
DNA N6-methyladenine (6mA) has recently been found to play regulatory roles in gene expression that links to various biological processes in eukaryotic species. The functional identification of 6mA methyltransferase will be important for understanding the underlying molecular mechanism of epigenetic 6mA methylation. It has been reported that the methyltransferase METTL4 can catalyze the methylation of 6mA; however, the function of METTL4 remains largely unknown. In this study, we aim to investigate the role of the Bombyx mori homolog METTL4 (BmMETTL4) in silkworm, a lepidopteran model insect. By using CRISPR-Cas9 system, we somatically mutated BmMETTL4 in silkworm individuates and found that disruption of BmMETTL4 caused the developmental defect of late silkworm embryo and subsequent lethality. We performed RNA-Seq and identified that there were 3192 differentially expressed genes in BmMETTL4 mutant including 1743 up-regulated and 1449 down-regulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that genes involved in molecular structure, chitin binding, and serine hydrolase activity were significantly affected by BmMETTL4 mutation. We further found that the expression of cuticular protein genes and collagens were clearly decreased while collagenases were highly increased, which had great contributions to the abnormal embryo and decreased hatchability of silkworm. Taken together, these results demonstrated a critical role of 6mA methyltransferase BmMETTL4 in regulating embryonic development of silkworm.
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72
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Wang D, Lin D, Feng G, Yang X, Deng L, Li P, Zhang Z, Zhang W, Guo Y, Wang Y, Fu S, Zhang N. Impact of chronic benzene poisoning on aberrant mitochondrial DNA methylation: A prospective observational study. Front Public Health 2023; 11:990051. [PMID: 36817889 PMCID: PMC9937586 DOI: 10.3389/fpubh.2023.990051] [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: 07/09/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Benzene is used as an industrial solvent, which may result in chronic benzene poisoning (CBP). Several studies suggested that CBP was associated with mitochondrial epigenetic regulation. This study aimed to explore the potential relation between CBP and mitochondrial DNA (mtDNA) methylation. This prospective observational study enrolled CBP patients admitted to Shenzhen Prevention and Treatment Center for Occupational Diseases hospital and healthy individuals between 2018 and 2021. The white blood cell (WBC), red blood cell (RBC), hemoglobin (HB), and platelet (PLT) counts and mtDNA methylation levels were measured using blood flow cytometry and targeted bisulfite sequencing, respectively. A total of 90 participants were recruited, including 30 cases of CBP (20 females, mean age 43.0 ± 8.0 years) and 60 healthy individuals (42 females, mean age 43.5 ± 11.5 years). This study detected 168 mitochondrial methylation sites >0 in all study subjects. The mtDNA methylation levels in the CBP cases were lower than the healthy individuals [median ± interquartile-range (IQR), 25th percentile, 75th percentile: (1.140 ± 0.570, 0.965, 1.535)% vs. median ± IQR, 25th percentile, 75th percentile: (1.705 ± 0.205,1.240,2.445)%, P < 0.05]. Additionally, the spearman correlation analysis showed that the mtDNA methylation levels were positively correlated with the counts of circulating leukocytes [WBC (r = 0.048, P = 0.036)] and platelets [PLT (r = 0.129, P < 0.01)]. We provided solid evidence of association between CBP and aberrant mtDNA methylation.
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Affiliation(s)
- Dianpeng Wang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China,*Correspondence: Dianpeng Wang ✉
| | - Dafeng Lin
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Gangquan Feng
- Medical Laboratory College, Hebei North University in China, Zhangjiakou, Hebei, China
| | - Xiangli Yang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lidan Deng
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Peimao Li
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Zhimin Zhang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Wen Zhang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Yan Guo
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Yue Wang
- Medical Laboratory College, Hebei North University in China, Zhangjiakou, Hebei, China
| | - Song Fu
- Medical Laboratory College, Hebei North University in China, Zhangjiakou, Hebei, China
| | - Naixing Zhang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China,Naixing Zhang ✉
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73
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Feng X, He C. Mammalian DNA N 6-methyladenosine: Challenges and new insights. Mol Cell 2023; 83:343-351. [PMID: 36736309 PMCID: PMC10182828 DOI: 10.1016/j.molcel.2023.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 02/05/2023]
Abstract
DNA N6-methyldeoxyadenosine (6mA) modification was first discovered in Bacterium coli in the 1950s. Over the next several decades, 6mA was recognized as a critical DNA modification in the genomes of prokaryotes and protists. While important in prokaryotes, less is known about the presence and functional roles of DNA 6mA in eukaryotes, particularly in mammals. Taking advantage of recent technology advances that made 6mA detection and sequencing possible, studies over the past several years have brought new insights into 6mA biology in mammals. In this perspective, we present recent progress, discuss challenges, and pose four questions for future research regarding mammalian DNA 6mA.
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Affiliation(s)
- Xinran Feng
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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74
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Broche J, Köhler AR, Kühnel F, Osteresch B, Chandrasekaran TT, Adam S, Brockmeyer J, Jeltsch A. Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression. Commun Biol 2023; 6:138. [PMID: 36732350 PMCID: PMC9895073 DOI: 10.1038/s42003-023-04466-1] [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: 08/06/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
While cytosine-C5 methylation of DNA is an essential regulatory system in higher eukaryotes, the presence and relevance of 6-methyladenine (m6dA) in human cells is controversial. To study the role of m6dA in human DNA, we introduced it in human cells at a genome-wide scale at GANTC and GATC sites by expression of bacterial DNA methyltransferases and observed concomitant reductions in cell viability, in particular after global GANTC methylation. We identified several genes that are directly regulated by m6dA in a GANTC context. Upregulated genes showed m6dA-dependent reduction of H3K27me3 suggesting that the PRC2 complex is inhibited by m6dA. Genes downregulated by m6dA showed enrichment of JUN family transcription factor binding sites. JUN binds m6dA containing DNA with reduced affinity suggesting that m6dA can reduce the recruitment of JUN transcription factors to target genes. Our study documents that global introduction of m6dA in human DNA has physiological effects. Furthermore, we identified a set of target genes which are directly regulated by m6dA in human cells, and we defined two molecular pathways with opposing effects by which artificially introduced m6dA in GANTC motifs can directly control gene expression and phenotypes of human cells.
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Affiliation(s)
- Julian Broche
- grid.5719.a0000 0004 1936 9713Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany ,grid.10392.390000 0001 2190 1447Present Address: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076 Tübingen, Germany
| | - Anja R. Köhler
- grid.5719.a0000 0004 1936 9713Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Fiona Kühnel
- grid.5719.a0000 0004 1936 9713Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Bernd Osteresch
- grid.5719.a0000 0004 1936 9713Institute of Biochemistry and Technical Biochemistry, Department of Food Chemistry, University of Stuttgart, Allmandring 5b, 70569 Stuttgart, Germany
| | - Thyagarajan T. Chandrasekaran
- grid.5719.a0000 0004 1936 9713Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Sabrina Adam
- grid.5719.a0000 0004 1936 9713Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jens Brockmeyer
- grid.5719.a0000 0004 1936 9713Institute of Biochemistry and Technical Biochemistry, Department of Food Chemistry, University of Stuttgart, Allmandring 5b, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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75
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Yang M, Leng D, Zeng B, Wang T, Xu Z, Li D. Characteristics and functions of DNA N(6)-methyladenine in embryonic chicken muscle development. Poult Sci 2023; 102:102528. [PMID: 36907131 PMCID: PMC10024188 DOI: 10.1016/j.psj.2023.102528] [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: 11/11/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
DNA N(6)-methyladenine (DNA-6mA) is a new epigenetic mark in eukaryotes, the distribution and functions of which in genomic DNA remain unknown. Although recent studies have suggested that 6mA is present in multiple model organisms and is dynamically regulated during development, the genomic features of 6mA in avian species have yet to be elucidated. 6mA immunoprecipitation sequencing approach was used to analysis the distribution and function of 6mA in the muscle genomic DNA during embryonic chicken development. 6mA immunoprecipitation sequencing was combined with transcriptomic sequencing to reveal the role of 6mA in the regulation of gene expression and to explore possible pathways by which 6mA is involved in muscle development. We here provide evidence that 6mA modification exists widely throughout the chicken genome, and show preliminary data regarding genome-wide distribution of this epigenetic mark. Gene expression was shown to be inhibited by 6mA modification in promoter regions. In addition, the promoters of some genes related to development were modified by 6mA, indicating that 6mA may be involved in embryonic chicken development. Furthermore, 6mA may participate in muscle development and immune function by regulating HSPB8 and OASL expression. Our study improves our understanding of the distribution and function of 6mA modification in higher organisms and provide new information about differences between mammals and other vertebrates. These findings demonstrate an epigenetic role for 6mA in gene expression and potential involvement in chicken muscle development. Furthermore, the results suggest a potential epigenetic role for 6mA in avian embryonic development.
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Affiliation(s)
- Maosen Yang
- School of Pharmacy, Chengdu University, Chengdu 610106, China; College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dong Leng
- School of Pharmacy, Chengdu University, Chengdu 610106, China; College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu 610106, China; College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongxian Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637002, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu 610106, China; College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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76
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Cadavid IC, Balbinott N, Margis R. Beyond transcription factors: more regulatory layers affecting soybean gene expression under abiotic stress. Genet Mol Biol 2023; 46:e20220166. [PMID: 36706026 PMCID: PMC9881580 DOI: 10.1590/1678-4685-gmb-2022-0166] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/18/2022] [Indexed: 01/28/2023] Open
Abstract
Abiotic stresses such as nutritional imbalance, salt, light intensity, and high and low temperatures negatively affect plant growth and development. Through the course of evolution, plants developed multiple mechanisms to cope with environmental variations, such as physiological, morphological, and molecular adaptations. Epigenetic regulation, transcription factor activity, and post-transcriptional regulation operated by RNA molecules are mechanisms associated with gene expression regulation under stress. Epigenetic regulation, including histone and DNA covalent modifications, triggers chromatin remodeling and changes the accessibility of transcription machinery leading to alterations in gene activity and plant homeostasis responses. Soybean is a legume widely produced and whose productivity is deeply affected by abiotic stresses. Many studies explored how soybean faces stress to identify key elements and improve productivity through breeding and genetic engineering. This review summarizes recent progress in soybean gene expression regulation through epigenetic modifications and circRNAs pathways, and points out the knowledge gaps that are important to study by the scientific community. It focuses on epigenetic factors participating in soybean abiotic stress responses, and chromatin modifications in response to stressful environments and draws attention to the regulatory potential of circular RNA in post-transcriptional processing.
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Affiliation(s)
- Isabel Cristina Cadavid
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre, Brazil
| | - Natalia Balbinott
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Porto Alegre, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Porto Alegre, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Biofisica, Porto Alegre, Brazil
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77
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Structural insights into DNA N 6-adenine methylation by the MTA1 complex. Cell Discov 2023; 9:8. [PMID: 36658132 PMCID: PMC9852454 DOI: 10.1038/s41421-022-00516-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/30/2022] [Indexed: 01/21/2023] Open
Abstract
N6-methyldeoxyadenine (6mA) has recently been reported as a prevalent DNA modification in eukaryotes. The Tetrahymena thermophila MTA1 complex consisting of four subunits, namely MTA1, MTA9, p1, and p2, is the first identified eukaryotic 6mA methyltransferase (MTase) complex. Unlike the prokaryotic 6mA MTases which have been biochemically and structurally characterized, the operation mode of the MTA1 complex remains largely elusive. Here, we report the cryogenic electron microscopy structures of the quaternary MTA1 complex in S-adenosyl methionine (SAM)-bound (2.6 Å) and S-adenosyl homocysteine (SAH)-bound (2.8 Å) states. Using an AI-empowered integrative approach based on AlphaFold prediction and chemical cross-linking mass spectrometry, we further modeled a near-complete structure of the quaternary complex. Coupled with biochemical characterization, we revealed that MTA1 serves as the catalytic core, MTA1, MTA9, and p1 likely accommodate the substrate DNA, and p2 may facilitate the stabilization of MTA1. These results together offer insights into the molecular mechanism underpinning methylation by the MTA1 complex and the potential diversification of MTases for N6-adenine methylation.
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78
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Han K, Wang J, Wang Y, Zhang L, Yu M, Xie F, Zheng D, Xu Y, Ding Y, Wan J. A review of methods for predicting DNA N6-methyladenine sites. Brief Bioinform 2023; 24:6887111. [PMID: 36502371 DOI: 10.1093/bib/bbac514] [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: 08/18/2022] [Revised: 10/07/2022] [Accepted: 10/27/2022] [Indexed: 12/14/2022] Open
Abstract
Deoxyribonucleic acid(DNA) N6-methyladenine plays a vital role in various biological processes, and the accurate identification of its site can provide a more comprehensive understanding of its biological effects. There are several methods for 6mA site prediction. With the continuous development of technology, traditional techniques with the high costs and low efficiencies are gradually being replaced by computer methods. Computer methods that are widely used can be divided into two categories: traditional machine learning and deep learning methods. We first list some existing experimental methods for predicting the 6mA site, then analyze the general process from sequence input to results in computer methods and review existing model architectures. Finally, the results were summarized and compared to facilitate subsequent researchers in choosing the most suitable method for their work.
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Affiliation(s)
- Ke Han
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China.,College of Pharmacy, Harbin University of Commerce, Harbin, 150076, China
| | - Jianchun Wang
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Yu Wang
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Lei Zhang
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Mengyao Yu
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Fang Xie
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Dequan Zheng
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Yaoqun Xu
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Yijie Ding
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China
| | - Jie Wan
- Laboratory for Space Environment and Physical Sciences, Harbin Institute of Technology, Harbin, 150001, China
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79
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Liu Y, Wan L, Ngai CK, Wang Y, Lam SL, Guo P. Structures and conformational dynamics of DNA minidumbbells in pyrimidine-rich repeats associated with neurodegenerative diseases. Comput Struct Biotechnol J 2023; 21:1584-1592. [PMID: 36874156 PMCID: PMC9975016 DOI: 10.1016/j.csbj.2023.02.010] [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: 09/26/2022] [Revised: 02/05/2023] [Accepted: 02/05/2023] [Indexed: 02/10/2023] Open
Abstract
Expansions of short tandem repeats (STRs) are associated with approximately 50 human neurodegenerative diseases. These pathogenic STRs are prone to form non-B DNA structure, which has been considered as one of the causative factors for repeat expansions. Minidumbbell (MDB) is a relatively new type of non-B DNA structure formed by pyrimidine-rich STRs. An MDB is composed of two tetraloops or pentaloops, exhibiting a highly compact conformation with extensive loop-loop interactions. The MDB structures have been found to form in CCTG tetranucleotide repeats associated with myotonic dystrophy type 2, ATTCT pentanucleotide repeats associated with spinocerebellar ataxia type 10, and the recently discovered ATTTT/ATTTC repeats associated with spinocerebellar ataxia type 37 and familial adult myoclonic epilepsy. In this review, we first introduce the structures and conformational dynamics of MDBs with a focus on the high-resolution structural information determined by nuclear magnetic resonance spectroscopy. Then we discuss the effects of sequence context, chemical environment, and nucleobase modification on the structure and thermostability of MDBs. Finally, we provide perspectives on further explorations of sequence criteria and biological functions of MDBs.
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Affiliation(s)
- Yuan Liu
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Liqi Wan
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheuk Kit Ngai
- Department of Chemistry, The Chinese University of Hong Kong, Shatin N.T., Hong Kong, China
| | - Yang Wang
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin N.T., Hong Kong, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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80
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Morel C, Schroeder H, Emond C, Turner JD, Lichtfouse E, Grova N. Brominated flame retardants, a cornelian dilemma. ENVIRONMENTAL CHEMISTRY LETTERS 2023; 21:9-14. [PMID: 35095379 PMCID: PMC8783781 DOI: 10.1007/s10311-022-01392-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Chloé Morel
- Calbinotox, Faculty of Science and Technology, University of Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Henri Schroeder
- Calbinotox, Faculty of Science and Technology, University of Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
- UMR Inserm 1256 nGERE, Nutrition-Génétique et Exposition aux risques environnementaux, Institute of Medical Research (Pôle BMS, University of Lorraine, B.P. 184, 54511 Vandoeuvre-lès-Nancy, France
| | - Claude Emond
- Calbinotox, Faculty of Science and Technology, University of Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
- PKSH Inc, Mascouche, QC Canada
- School of Public Health, DSEST, University of Montreal, Montreal, QC Canada
| | - Jonathan D. Turner
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-Sur-Alzette, Grand Duchy of Luxembourg
| | - Eric Lichtfouse
- Aix-Marseille Univ, CNRS, IRD, INRAE, CEREGE, 13100 Aix en Provence, France
| | - Nathalie Grova
- Calbinotox, Faculty of Science and Technology, University of Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
- UMR Inserm 1256 nGERE, Nutrition-Génétique et Exposition aux risques environnementaux, Institute of Medical Research (Pôle BMS, University of Lorraine, B.P. 184, 54511 Vandoeuvre-lès-Nancy, France
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-Sur-Alzette, Grand Duchy of Luxembourg
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81
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Sadler KC. Epigenetics across the evolutionary tree: New paradigms from non-model animals. Bioessays 2023; 45:e2200036. [PMID: 36403219 DOI: 10.1002/bies.202200036] [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: 02/13/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
Abstract
All animals have evolved solutions to manage their genomes, enabling the efficient organization of meters of DNA strands in the nucleus and allowing for nuanced regulation of gene expression while keeping transposable elements suppressed. Epigenetic modifications are central to accomplishing all these. Recent advances in sequencing technologies and the development of techniques that profile epigenetic marks and chromatin accessibility using reagents that can be used in any species has catapulted epigenomic studies in diverse animal species, shedding light on the multitude of epigenomic mechanisms utilized across the evolutionary tree. Now, comparative epigenomics is a rapidly growing field that is uncovering mechanistic aspects of epigenetic modifications and chromatin organization in non-model invertebrates, ranging from octopus to sponges. This review puts recent discoveries in the epigenetics of non-model invertebrates in historical context, and describes new insight into the patterning and functions of DNA methylation and other highly conserved epigenetic modifications.
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Affiliation(s)
- Kirsten C Sadler
- Program in Biology, New York University, Abu Dhabi, United Arab Emirates
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82
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Tsukiyama S, Hasan MM, Kurata H. CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction. Comput Struct Biotechnol J 2022; 21:644-654. [PMID: 36659917 PMCID: PMC9826936 DOI: 10.1016/j.csbj.2022.12.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022] Open
Abstract
N6-methyladenine (6mA) plays a critical role in various epigenetic processing including DNA replication, DNA repair, silencing, transcription, and diseases such as cancer. To understand such epigenetic mechanisms, 6 mA has been detected by high-throughput technologies on a genome-wide scale at single-base resolution, together with conventional methods such as immunoprecipitation, mass spectrometry and capillary electrophoresis, but these experimental approaches are time-consuming and laborious. To complement these problems, we have developed a CNN-based 6 mA site predictor, named CNN6mA, which proposed two new architectures: a position-specific 1-D convolutional layer and a cross-interactive network. In the position-specific 1-D convolutional layer, position-specific filters with different window sizes were applied to an inquiry sequence instead of sharing the same filters over all positions in order to extract the position-specific features at different levels. The cross-interactive network explored the relationships between all the nucleotide patterns within the inquiry sequence. Consequently, CNN6mA outperformed the existing state-of-the-art models in many species and created the contribution score vector that intelligibly interpret the prediction mechanism. The source codes and web application in CNN6mA are freely accessible at https://github.com/kuratahiroyuki/CNN6mA.git and http://kurata35.bio.kyutech.ac.jp/CNN6mA/, respectively.
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Key Words
- 6mA, N6-methyladenine
- AUCs, Area under the curves
- BERT, Bidirectional Encoder Representations from Transformers
- CNN
- CNN, Convolutional neural network
- DNA modification
- Deep learning
- Interpretable prediction
- LSTM, Long short-term memory
- MCC, Matthews correlation coefficient
- Machine learning
- N6-methyladenine
- RF, Random forest
- SMRT, Single-molecule real-time
- SN, Sensitivity
- SP, Specificity
- UMAP, Uniform manifold approximation and projection
- t-SNE, t-distributed stochastic neighbor embedding
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Affiliation(s)
- Sho Tsukiyama
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680–4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Md Mehedi Hasan
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680–4 Kawazu, Iizuka, Fukuoka 820-8502, Japan,Corresponding author.
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83
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Chen LQ, Zhang Z, Chen HX, Xi JF, Liu XH, Ma DZ, Zhong YH, Ng WH, Chen T, Mak DW, Chen Q, Chen YQ, Luo GZ. High-precision mapping reveals rare N 6-deoxyadenosine methylation in the mammalian genome. Cell Discov 2022; 8:138. [PMID: 36575183 PMCID: PMC9794812 DOI: 10.1038/s41421-022-00484-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 10/16/2022] [Indexed: 12/28/2022] Open
Abstract
N6-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more advanced investigations of 6mA. Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. We found that modified DNA bases are prone to form a local open region that allows capture by antibody, for example, via a DNA breathing or base-flipping mechanism. Specified endonuclease or exonuclease can recognize the antibody-stabilized mismatch-like structure and mark the exact modified sites for sequencing readout. Using this method, we examined the genomic positions of 6mA in bacteria (E. coli), green algae (C. reinhardtii), and mammalian cells (HEK239T, Huh7, and HeLa cells). In contrast to bacteria and green algae, human cells possess a very limited number of 6mA sites which are sporadically distributed across the genome of different cell types. After knocking out the RNA m6A methyltransferase METTL3 in mouse ES cells, 6mA becomes mostly diminished. Our results imply that rare 6mA in the mammalian genome is introduced by RNA m6A machinery via a non-targeted mechanism.
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Affiliation(s)
- Li-Qian Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China ,grid.410643.4Guangdong Cardiovascular Institute, Medical Research Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong China
| | - Zhang Zhang
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Hong-Xuan Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Jian-Fei Xi
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Xue-Hong Liu
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Dong-Zhao Ma
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Yu-Hao Zhong
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Wen Hui Ng
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Tao Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Daniel W. Mak
- grid.194645.b0000000121742757School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Qi Chen
- grid.12981.330000 0001 2360 039XSchool of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong China
| | - Yao-Qing Chen
- grid.12981.330000 0001 2360 039XSchool of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong China
| | - Guan-Zheng Luo
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
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84
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Song X, Song X, Lai W, Wang H. Hyperactive DNA Cutting for Unbiased UHPLC-MS/MS Quantification of Epigenetic DNA Marks by Engineering DNase I Mutants. Anal Chem 2022; 94:17670-17676. [PMID: 36490323 DOI: 10.1021/acs.analchem.2c04485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic DNA modifications, such as 5-methylcytosine, 5-hydroxymethylcytosine, and 5-formylcytosine, are associated with a variety of diseases and potential biomarkers for cancer diagnosis and therapy. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays are considered to be the gold standard for qualitative and quantitative detection of DNA modifications. DNA digestion for converting long DNA polymer into 2'-deoxynucleosides is an important preprocessing step to achieve sensitive and accurate LC-MS/MS quantification. Here, we showed that, as stimulated by divalent metal ions, Mg2+ and Mn2+, the engineered human DNase I Q9R:E13R:N74K mutant can efficiently digest DNA in the presence of monovalent metal ions at a high concentration (e.g., 1 M NaCl), showing hyperactivity on DNA cutting. We also found that the engineered DNase I mutants display exceptional DNA-cutting activity over a wider pH range (5.5-9.5). Due to their hyperactivity and high salt tolerance, the engineered DNase I mutants cut DNA 5mC and dC efficiently. Benefitting from this DNA-cutting hyperactivity, we demonstrated an LC-MS/MS assay for unbiased and accurate quantification of DNA 5mC.
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Affiliation(s)
- Xingrui Song
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xinyue Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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85
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Hsu KW, Lai JCY, Chang JS, Peng PH, Huang CH, Lee DY, Tsai YC, Chung CJ, Chang H, Chang CH, Chen JL, Pang ST, Hao Z, Cui XL, He C, Wu KJ. METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets. Genome Biol 2022; 23:249. [PMID: 36461076 PMCID: PMC9716733 DOI: 10.1186/s13059-022-02819-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND DNA N6-methyldeoxyadenosine (6mA) is rarely present in mammalian cells and its nuclear role remains elusive. RESULTS Here we show that hypoxia induces nuclear 6mA modification through a DNA methyltransferase, METTL4, in hypoxia-induced epithelial-mesenchymal transition (EMT) and tumor metastasis. Co-expression of METTL4 and 6mA represents a prognosis marker for upper tract urothelial cancer patients. By RNA sequencing and 6mA chromatin immunoprecipitation-exonuclease digestion followed by sequencing, we identify lncRNA RP11-390F4.3 and one novel HIF-1α co-activator, ZMIZ1, that are co-regulated by hypoxia and METTL4. Other genes involved in hypoxia-mediated phenotypes are also regulated by 6mA modification. Quantitative chromatin isolation by RNA purification assay shows the occupancy of lncRNA RP11-390F4.3 on the promoters of multiple EMT regulators, indicating lncRNA-chromatin interaction. Knockdown of lncRNA RP11-390F4.3 abolishes METTL4-mediated tumor metastasis. We demonstrate that ZMIZ1 is an essential co-activator of HIF-1α. CONCLUSIONS We show that hypoxia results in enriched 6mA levels in mammalian tumor cells through METTL4. This METTL4-mediated nuclear 6mA deposition induces tumor metastasis through activating multiple metastasis-inducing genes. METTL4 is characterized as a potential therapeutic target in hypoxic tumors.
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Affiliation(s)
- Kai-Wen Hsu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan ,Research Center for Cancer Biology, Taipei, Taiwan ,grid.254145.30000 0001 0083 6092Institute of Translational Medicine and New Drug Development, China Medical University, Taichung, 404 Taiwan
| | - Joseph Chieh-Yu Lai
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan ,grid.254145.30000 0001 0083 6092Institute of Biomedical Sciences, China Medical University, Taichung, 404 Taiwan
| | - Jeng-Shou Chang
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan
| | - Pei-Hua Peng
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan
| | - Ching-Hui Huang
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan
| | - Der-Yen Lee
- grid.254145.30000 0001 0083 6092Institute of Integrated Medicine, China Medical University, Taichung, 404 Taiwan
| | | | - Chi-Jung Chung
- grid.254145.30000 0001 0083 6092Department of Health Risk Management, College of Public Health, China Medical University, Taichung, 404 Taiwan
| | - Han Chang
- grid.411508.90000 0004 0572 9415Department of Pathology, China Medical University Hospital, Taichung, 404 Taiwan
| | - Chao-Hsiang Chang
- grid.411508.90000 0004 0572 9415Department of Urology, China Medical University Hospital, Taichung, 404 Taiwan
| | - Ji-Lin Chen
- grid.278247.c0000 0004 0604 5314Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, 112 Taiwan
| | - See-Tong Pang
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, 333 Taiwan
| | - Ziyang Hao
- grid.170205.10000 0004 1936 7822Departments of Chemistry & Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th St., Chicago, IL 60637 USA ,grid.24696.3f0000 0004 0369 153XSchool of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069 China
| | - Xiao-Long Cui
- grid.170205.10000 0004 1936 7822Departments of Chemistry & Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th St., Chicago, IL 60637 USA
| | - Chuan He
- grid.170205.10000 0004 1936 7822Departments of Chemistry & Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th St., Chicago, IL 60637 USA ,grid.170205.10000 0004 1936 7822Howard Hughes Medical Institute, The University of Chicago, 929 E. 57th St., Chicago, IL 60637 USA
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan
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86
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Zhang S, Meng Y, Zhou L, Qiu L, Wang H, Su D, Zhang B, Chan K, Han J. Targeting epigenetic regulators for inflammation: Mechanisms and intervention therapy. MedComm (Beijing) 2022; 3:e173. [PMID: 36176733 PMCID: PMC9477794 DOI: 10.1002/mco2.173] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 11/11/2022] Open
Abstract
Emerging evidence indicates that resolution of inflammation is a critical and dynamic endogenous process for host tissues defending against external invasive pathogens or internal tissue injury. It has long been known that autoimmune diseases and chronic inflammatory disorders are characterized by dysregulated immune responses, leading to excessive and uncontrol tissue inflammation. The dysregulation of epigenetic alterations including DNA methylation, posttranslational modifications to histone proteins, and noncoding RNA expression has been implicated in a host of inflammatory disorders and the immune system. The inflammatory response is considered as a critical trigger of epigenetic alterations that in turn intercede inflammatory actions. Thus, understanding the molecular mechanism that dictates the outcome of targeting epigenetic regulators for inflammatory disease is required for inflammation resolution. In this article, we elucidate the critical role of the nuclear factor‐κB signaling pathway, JAK/STAT signaling pathway, and the NLRP3 inflammasome in chronic inflammatory diseases. And we formulate the relationship between inflammation, coronavirus disease 2019, and human cancers. Additionally, we review the mechanism of epigenetic modifications involved in inflammation and innate immune cells. All that matters is that we propose and discuss the rejuvenation potential of interventions that target epigenetic regulators and regulatory mechanisms for chronic inflammation‐associated diseases to improve therapeutic outcomes.
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Affiliation(s)
- Su Zhang
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Yang Meng
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Lian Zhou
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Lei Qiu
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Heping Wang
- Department of Neurosurgery Tongji Hospital of Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Dan Su
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Bo Zhang
- Laboratory of Cancer Epigenetics and Genomics Department of Gastrointestinal Surgery Frontiers Science Center for Disease‐Related Molecular Network West China Hospital Sichuan University Chengdu China
| | - Kui‐Ming Chan
- Department of Biomedical Sciences City University of Hong Kong Hong Kong China
| | - Junhong Han
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
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87
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Cui C, Ma Z, Wan H, Gao J, Zhou B. GhALKBH10 negatively regulates salt tolerance in cotton. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 192:87-100. [PMID: 36215791 DOI: 10.1016/j.plaphy.2022.09.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/28/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The alpha-ketoglutarate-dependent dioxygenase (AlkB) gene family plays an essential role in regulating plant development and stress response. However, the AlkB gene family is still not well understood in cotton. In this study, 40 AlkB genes in cotton and Arabidopsis are identified and classified into three classes based on phylogenetic analysis. Their protein motifs and exon/intron structures are highly conserved. Chromosomal localization and synteny analysis suggested that segmental or whole-genome duplication and polyploidization events contributed to the expansion of the cotton AlkB gene family. Furthermore, the AlkB genes showed dynamic spatiotemporal expression patterns and diverse responses to abiotic stresses. Among them, GhALKBH10 was down-regulated under various abiotic stresses and its subcellular expression was localized in cytoplasm and nucleus. Silencing GhALKBH10 in cotton increased antioxidant capacity and reduced cytoplasmic Na+ concentration, thereby improved the plant tolerance to salinity. Conversely, overexpression (OE) of GhALKBH10 in Arabidopsis markedly weakened the plant tolerance to salinity. The global m6A levels measured in VIGS and OE transgenic lines showed that they were significantly higher in TRV: GhALKBH10 plants (VIGS) than in TRV: 00 plants but significantly lower in OE plants than wild-type plants under salt stress, which could be considered as a potential m6A demethylase in cotton. Our results suggest that the GhALKBH10 gene negatively regulates salt tolerance in plants, which provides information of the cotton AlkB family and an understanding of GhALKBH10 function under salt condition as well as a new gene for salt-tolerant cotton breeding.
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Affiliation(s)
- Changjiang Cui
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Zhifeng Ma
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Hui Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Jianbo Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China.
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88
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Zhou J, Wang X, Wei Z, Meng J, Huang D. 4acCPred: Weakly supervised prediction of N4-acetyldeoxycytosine DNA modification from sequences. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 30:337-345. [DOI: 10.1016/j.omtn.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
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89
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Szukiewicz D, Trojanowski S, Kociszewska A, Szewczyk G. Modulation of the Inflammatory Response in Polycystic Ovary Syndrome (PCOS)-Searching for Epigenetic Factors. Int J Mol Sci 2022; 23:ijms232314663. [PMID: 36498989 PMCID: PMC9736994 DOI: 10.3390/ijms232314663] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrine disorder in women of reproductive age. Despite its incidence, the syndrome is poorly understood and remains underdiagnosed, and female patients are diagnosed with a delay. The heterogenous nature of this complex disorder results from the combined occurrence of genetic, environmental, endocrine, and behavioral factors. Primary clinical manifestations of PCOS are derived from the excess of androgens (anovulation, polycystic ovary morphology, lack of or scanty, irregular menstrual periods, acne and hirsutism), whereas the secondary manifestations include multiple metabolic, cardiovascular, and psychological disorders. Dietary and lifestyle factors play important roles in the development and course of PCOS, which suggests strong epigenetic and environmental influences. Many studies have shown a strong association between PCOS and chronic, low-grade inflammation both in the ovarian tissue and throughout the body. In the vast majority of PCOS patients, elevated values of inflammatory markers or their gene markers have been reported. Development of the vicious cycle of the chronic inflammatory state in PCOS is additionally stimulated by hyperinsulinemia and obesity. Changes in DNA methylation, histone acetylation and noncoding RNA levels are presented in this review in the context of oxidative stress, reactive oxygen species, and inflammatory signaling in PCOS. Epigenetic modulation of androgenic activity in response to inflammatory signaling is also discussed.
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Affiliation(s)
- Dariusz Szukiewicz
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
- Correspondence:
| | - Seweryn Trojanowski
- Chair and Department of Obstetrics, Gynecology and Gynecological Oncology, Medical University of Warsaw, 03-242 Warsaw, Poland
| | - Anna Kociszewska
- Chair and Department of Obstetrics, Gynecology and Gynecological Oncology, Medical University of Warsaw, 03-242 Warsaw, Poland
| | - Grzegorz Szewczyk
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
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90
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Cui YH, Wilkinson E, Peterson J, He YY. ALKBH4 Stabilization Is Required for Arsenic-Induced 6mA DNA Methylation Inhibition, Keratinocyte Malignant Transformation, and Tumorigenicity. WATER 2022; 14:3595. [PMID: 37207134 PMCID: PMC10194016 DOI: 10.3390/w14223595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Inorganic arsenic is one of the well-known human skin carcinogens. However, the molecular mechanism by which arsenic promotes carcinogenesis remains unclear. Previous studies have established that epigenetic changes, including changes in DNA methylation, are among the critical mechanisms that drive carcinogenesis. N6-methyladenine (6mA) methylation on DNA is a widespread epigenetic modification that was initially found on bacterial and phage DNA. Only recently has 6mA been identified in mammalian genomes. However, the function of 6mA in gene expression and cancer development is not well understood. Here, we show that chronic low doses of arsenic induce malignant transformation and tumorigenesis in keratinocytes and lead to the upregulation of ALKBH4 and downregulation of 6mA on DNA. We found that reduced 6mA levels in response to low levels of arsenic were mediated by the upregulation of the 6mA DNA demethylase ALKBH4. Moreover, we found that arsenic increased ALKBH4 protein levels and that ALKBH4 deletion impaired arsenic-induced tumorigenicity in vitro and in mice. Mechanistically, we found that arsenic promoted ALKBH4 protein stability through reduced autophagy. Together, our findings reveal that the DNA 6mA demethylaseALKBH4 promotes arsenic tumorigenicity and establishes ALKBH4 as a promising target for arsenic-induced tumorigenesis.
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Affiliation(s)
- Yan-Hong Cui
- Section of Dermatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Emma Wilkinson
- Section of Dermatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jack Peterson
- The College, Biological Science Division, University of Chicago, Chicago, IL 60637, USA
| | - Yu-Ying He
- Section of Dermatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
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91
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Yang L, Zhang P, Wang Y, Hu G, Guo W, Gu X, Pu L. Plant synthetic epigenomic engineering for crop improvement. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2191-2204. [PMID: 35851940 DOI: 10.1007/s11427-021-2131-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Efforts have been directed to redesign crops with increased yield, stress adaptability, and nutritional value through synthetic biology-the application of engineering principles to biology. A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops, thus heralding the promise of "synthetic epigenetics." In this review, we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques, epigenetic editing, and deep learning-driven predictive tools can rapidly extend these insights. We also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.
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Affiliation(s)
- Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guihua Hu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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92
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Hu Y, Hong X, Yuan Z, Mu J, Zhang X, Fang Z, Yuan Y, Zheng S, Guo C. Pan-cancer analysis of DNA epigenetic modifications by hydrophilic interaction liquid chromatography-tandem mass spectrometry. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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93
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Epigenetic regulation of B cells and its role in autoimmune pathogenesis. Cell Mol Immunol 2022; 19:1215-1234. [PMID: 36220996 PMCID: PMC9622816 DOI: 10.1038/s41423-022-00933-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/19/2022] [Indexed: 11/05/2022] Open
Abstract
B cells play a pivotal role in the pathogenesis of autoimmune diseases. Although previous studies have shown many genetic polymorphisms associated with B-cell activation in patients with various autoimmune disorders, progress in epigenetic research has revealed new mechanisms leading to B-cell hyperactivation. Epigenetic mechanisms, including those involving histone modifications, DNA methylation, and noncoding RNAs, regulate B-cell responses, and their dysregulation can contribute to the pathogenesis of autoimmune diseases. Patients with autoimmune diseases show epigenetic alterations that lead to the initiation and perpetuation of autoimmune inflammation. Moreover, many clinical and animal model studies have shown the promising potential of epigenetic therapies for patients. In this review, we present an up-to-date overview of epigenetic mechanisms with a focus on their roles in regulating functional B-cell subsets. Furthermore, we discuss epigenetic dysregulation in B cells and highlight its contribution to the development of autoimmune diseases. Based on clinical and preclinical evidence, we discuss novel epigenetic biomarkers and therapies for patients with autoimmune disorders.
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94
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George S, Cassidy RN, Saintilnord WN, Fondufe-Mittendorf Y. Epigenomic reprogramming in iAs-mediated carcinogenesis. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 96:319-365. [PMID: 36858778 DOI: 10.1016/bs.apha.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Arsenic is a naturally occurring metal carcinogen found in the Earth's crust. Millions of people worldwide are chronically exposed to arsenic through drinking water and food. Exposure to inorganic arsenic has been implicated in many diseases ranging from acute toxicities to malignant transformations. Despite the well-known deleterious health effects of arsenic exposure, the molecular mechanisms in arsenic-mediated carcinogenesis are not fully understood. Since arsenic is non-mutagenic, the mechanism by which arsenic causes carcinogenesis is via alterations in epigenetic-regulated gene expression. There are two possible ways by which arsenic may modify the epigenome-indirectly through an arsenic-induced generation of reactive oxygen species which then impacts chromatin remodelers, or directly through interaction and modulation of chromatin remodelers. Whether directly or indirectly, arsenic modulates epigenetic gene regulation and our understanding of the direct effect of this modulation on chromatin structure is limited. In this chapter we will discuss the various ways by which inorganic arsenic affects the epigenome with consequences in health and disease.
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Affiliation(s)
- Smitha George
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States
| | - Richard N Cassidy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States
| | - Wesley N Saintilnord
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States; Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
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95
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Rube HT, Rastogi C, Feng S, Kribelbauer JF, Li A, Becerra B, Melo LAN, Do BV, Li X, Adam HH, Shah NH, Mann RS, Bussemaker HJ. Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning. Nat Biotechnol 2022; 40:1520-1527. [PMID: 35606422 PMCID: PMC9546773 DOI: 10.1038/s41587-022-01307-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 04/04/2022] [Indexed: 01/02/2023]
Abstract
Protein-ligand interactions are increasingly profiled at high throughput using affinity selection and massively parallel sequencing. However, these assays do not provide the biophysical parameters that most rigorously quantify molecular interactions. Here we describe a flexible machine learning method, called ProBound, that accurately defines sequence recognition in terms of equilibrium binding constants or kinetic rates. This is achieved using a multi-layered maximum-likelihood framework that models both the molecular interactions and the data generation process. We show that ProBound quantifies transcription factor (TF) behavior with models that predict binding affinity over a range exceeding that of previous resources; captures the impact of DNA modifications and conformational flexibility of multi-TF complexes; and infers specificity directly from in vivo data such as ChIP-seq without peak calling. When coupled with an assay called KD-seq, it determines the absolute affinity of protein-ligand interactions. We also apply ProBound to profile the kinetics of kinase-substrate interactions. ProBound opens new avenues for decoding biological networks and rationally engineering protein-ligand interactions.
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Affiliation(s)
- H Tomas Rube
- Department of Bioengineering, University of California, Merced, Merced, CA, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Siqian Feng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Allyson Li
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Basheer Becerra
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Lucas A N Melo
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Bach Viet Do
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Xiaoting Li
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Hammaad H Adam
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
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96
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Luo L, Liu Y, Nizigiyimana P, Ye M, Xiao Y, Guo Q, Su T, Luo X, Huang Y, Zhou H. DNA 6mA Demethylase ALKBH1 Orchestrates Fatty Acid Metabolism and Suppresses Diet-Induced Hepatic Steatosis. Cell Mol Gastroenterol Hepatol 2022; 14:1213-1233. [PMID: 36058506 PMCID: PMC9579408 DOI: 10.1016/j.jcmgh.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Nonalcoholic fatty liver disease (NAFLD) is a major cause of liver-related morbidity and mortality whereas the pathogenic mechanism remains largely elusive. DNA N6-methyladenosine (6mA) modification is a recently identified epigenetic mark indicative of transcription in eukaryotic genomes. Here, we aimed to investigate the role and mechanism of DNA 6mA modification in NAFLD progression. METHODS Dot blot and immunohistochemistry were used to detect DNA 6mA levels. Liver-specific AlkB homolog 1 (ALKBH1)-knockout mice and mice with ALKBH1 overexpression in liver were subjected to a high-fat diet or methionine choline-deficient diet to evaluate the critical role of ALKBH1-demethylated DNA 6mA modification in the pathogenesis of hepatic steatosis during NAFLD. RNA sequencing and chromatin immunoprecipitation sequencing were performed to investigate molecular mechanisms underlying this process. RESULTS The DNA 6mA level was increased significantly with hepatic steatosis, while ALKBH1 expression was down-regulated markedly in both mouse and human fatty liver. Deletion of ALKBH1 in hepatocytes increased genomic 6mA levels and accelerated diet-induced hepatic steatosis and metabolic dysfunction. Comprehensive analyses of transcriptome and chromatin immunoprecipitation sequencing data indicated that ALKBH1 directly bound to and exclusively demethylated 6mA levels of genes involved in fatty acid uptake and lipogenesis, leading to reduced hepatic lipid accumulation. Importantly, ALKBH1 overexpression was sufficient to suppress lipid uptake and synthesis, and alleviated diet-induced hepatic steatosis and insulin resistance. CONCLUSIONS Our findings show an indispensable role of ALKBH1 as an epigenetic suppressor of DNA 6mA in hepatic fatty acid metabolism and offer a potential therapeutic target for NAFLD treatment.
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Affiliation(s)
- Liping Luo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ya Liu
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Paul Nizigiyimana
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingsheng Ye
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ye Xiao
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qi Guo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tian Su
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xianghang Luo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Yan Huang
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Haiyan Zhou
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China,Correspondence Address correspondence to: Haiyan Zhou, PhD, Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital, Central South University, No 87, Xiangya Road, Changsha, Hunan Province 410008, China.
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97
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Application of Feature Selection and Deep Learning for Cancer Prediction Using DNA Methylation Markers. Genes (Basel) 2022; 13:genes13091557. [PMID: 36140725 PMCID: PMC9498757 DOI: 10.3390/genes13091557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is a process that can affect gene accessibility and therefore gene expression. In this study, a machine learning pipeline is proposed for the prediction of breast cancer and the identification of significant genes that contribute to the prediction. The current study utilized breast cancer methylation data from The Cancer Genome Atlas (TCGA), specifically the TCGA-BRCA dataset. Feature engineering techniques have been utilized to reduce data volume and make deep learning scalable. A comparative analysis of the proposed approach on Illumina 27K and 450K methylation data reveals that deep learning methodologies for cancer prediction can be coupled with feature selection models to enhance prediction accuracy. Prediction using 450K methylation markers can be accomplished in less than 13 s with an accuracy of 98.75%. Of the list of 685 genes in the feature selected 27K dataset, 578 were mapped to Ensemble Gene IDs. This reduced set was significantly (FDR < 0.05) enriched in five biological processes and one molecular function. Of the list of 1572 genes in the feature selected 450K data set, 1290 were mapped to Ensemble Gene IDs. This reduced set was significantly (FDR < 0.05) enriched in 95 biological processes and 17 molecular functions. Seven oncogene/tumor suppressor genes were common between the 27K and 450K feature selected gene sets. These genes were RTN4IP1, MYO18B, ANP32A, BRF1, SETBP1, NTRK1, and IGF2R. Our bioinformatics deep learning workflow, incorporating imputation and data balancing methods, is able to identify important methylation markers related to functionally important genes in breast cancer with high accuracy compared to deep learning or statistical models alone.
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98
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Rehman MU, Tayara H, Zou Q, Chong KT. i6mA-Caps: a CapsuleNet-based framework for identifying DNA N6-methyladenine sites. Bioinformatics 2022; 38:3885-3891. [PMID: 35771648 DOI: 10.1093/bioinformatics/btac434] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/19/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION DNA N6-methyladenine (6mA) has been demonstrated to have an essential function in epigenetic modification in eukaryotic species in recent research. 6mA has been linked to various biological processes. It's critical to create a new algorithm that can rapidly and reliably detect 6mA sites in genomes to investigate their biological roles. The identification of 6mA marks in the genome is the first and most important step in understanding the underlying molecular processes, as well as their regulatory functions. RESULTS In this article, we proposed a novel computational tool called i6mA-Caps which CapsuleNet based a framework for identifying the DNA N6-methyladenine sites. The proposed framework uses a single encoding scheme for numerical representation of the DNA sequence. The numerical data is then used by the set of convolution layers to extract low-level features. These features are then used by the capsule network to extract intermediate-level and later high-level features to classify the 6mA sites. The proposed network is evaluated on three datasets belonging to three genomes which are Rosaceae, Rice and Arabidopsis thaliana. Proposed method has attained an accuracy of 96.71%, 94% and 86.83% for independent Rosaceae dataset, Rice dataset and A.thaliana dataset respectively. The proposed framework has exhibited improved results when compared with the existing top-of-the-line methods. AVAILABILITY AND IMPLEMENTATION A user-friendly web-server is made available for the biological experts which can be accessed at: http://nsclbio.jbnu.ac.kr/tools/i6mA-Caps/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mobeen Ur Rehman
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea.,Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
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99
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Yang Y, Wang Z, Wang J, Dai X, You C. Next-Generation Sequencing-Based Analysis of the Effects of N1- and N6-Methyldeoxyadenosine Adducts on DNA Transcription. Anal Chem 2022; 94:11248-11254. [PMID: 35924299 DOI: 10.1021/acs.analchem.2c01764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA methylation can occur naturally or be induced by various environmental and chemotherapeutic agents. The regioisomeric N1- and N6-methyldeoxyadenosine (1mdA and 6mdA, respectively) represent an important class of methylated DNA adducts. In this study, we developed a shuttle vector- and next-generation sequencing-based assay to quantitatively assess the effects of 1mdA and 6mdA on the accuracy and efficiency of DNA transcription. Our results revealed that 1mdA can induce multiple types of mutant transcripts and strongly inhibit DNA transcription, whereas 6mdA is a nonmutagenic DNA adduct that can exhibit a subtle but significant inhibitory effect on DNA transcription in vitro and in human cells. Moreover, our results demonstrated that the transcription-coupled nucleotide excision repair pathway is dispensable for the removal of 1mdA and 6mdA from the template DNA strand in human cells. These findings provided new important insights into the functional interplay between DNA methylation modifications and transcription in mammalian cells.
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Affiliation(s)
- Ying Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Ziyu Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Juan Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xiaoxia Dai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Changjun You
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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100
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Wagner A, Kosnacova H, Chovanec M, Jurkovicova D. Mitochondrial Genetic and Epigenetic Regulations in Cancer: Therapeutic Potential. Int J Mol Sci 2022; 23:ijms23147897. [PMID: 35887244 PMCID: PMC9321253 DOI: 10.3390/ijms23147897] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Mitochondria are dynamic organelles managing crucial processes of cellular metabolism and bioenergetics. Enabling rapid cellular adaptation to altered endogenous and exogenous environments, mitochondria play an important role in many pathophysiological states, including cancer. Being under the control of mitochondrial and nuclear DNA (mtDNA and nDNA), mitochondria adjust their activity and biogenesis to cell demands. In cancer, numerous mutations in mtDNA have been detected, which do not inactivate mitochondrial functions but rather alter energy metabolism to support cancer cell growth. Increasing evidence suggests that mtDNA mutations, mtDNA epigenetics and miRNA regulations dynamically modify signalling pathways in an altered microenvironment, resulting in cancer initiation and progression and aberrant therapy response. In this review, we discuss mitochondria as organelles importantly involved in tumorigenesis and anti-cancer therapy response. Tumour treatment unresponsiveness still represents a serious drawback in current drug therapies. Therefore, studying aspects related to genetic and epigenetic control of mitochondria can open a new field for understanding cancer therapy response. The urgency of finding new therapeutic regimens with better treatment outcomes underlines the targeting of mitochondria as a suitable candidate with new therapeutic potential. Understanding the role of mitochondria and their regulation in cancer development, progression and treatment is essential for the development of new safe and effective mitochondria-based therapeutic regimens.
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Affiliation(s)
- Alexandra Wagner
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (A.W.); (H.K.); (M.C.)
- Department of Simulation and Virtual Medical Education, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Helena Kosnacova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (A.W.); (H.K.); (M.C.)
- Department of Simulation and Virtual Medical Education, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Miroslav Chovanec
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (A.W.); (H.K.); (M.C.)
| | - Dana Jurkovicova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (A.W.); (H.K.); (M.C.)
- Correspondence:
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