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Fan H, Zhao Z, Cheng Y, Cui H, Qiao F, Wang L, Hu J, Wu H, Song W. Genome-wide profiling of DNA methylation reveals preferred sequences of DNMTs in hepatocellular carcinoma cells. Tumour Biol 2016; 37:877-85. [PMID: 26254611 DOI: 10.1007/s13277-015-3202-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 02/03/2015] [Indexed: 02/03/2023] Open
Abstract
Aberrant DNA methylation of CpG site is among the earliest and most frequent alterations in developmental process and diseases including cancer. To elucidate the functional preferred site of DNMTs, we analyzed the feature of distinct methylated sequences and established the defined relationship between DNMTs and preference genomic DNA sequences. Small interfering RNA (siRNA) construct of DNTM1, DNMT3A, and DNMT3B was transfected into the human hepatocellular carcinoma cell line SMMC-7721, respectively. Distinguishing methylated fragments pool was enriched by SHH method in cells which is knocked down DNMT1, DNMT3A, DNMT3B, separately. The defined binding transcription factors (TFs) containing of 5'CpG islands were obtained with bioinformatics software and website. In SMMC-7721 hepatocellular carcinoma (HCC) cell line, DNMT1, DNMT3A, and DNMT3B were specific suppressed by their corresponding siRNA construct, separately. A 46, 42, 67 distinctive methylated fragments from three different DNMTs were evaluated according to genomic DNA database. Those separated fragments were distributed among genomic DNA regions of all chromosome complements, including coding genes, repeat sequences, and genes with unknown function. The majority of coding genes contain CpG islands in their promoter region. Cluster analysis demonstrated all of preference sequences identified by three DNMTs shares their own conserved sequences. In depleting of different DNMTs cells, 80 % of 103 upregulation genes induced by DNMT1 knock-down contain CpG sites; 76 % of 25 upregulation genes induced by DNMT3A knock-down contain CpG sites; 63 % of 126 upregulation genes induced by DNMT3B knock-down contain CpG sites. Our findings suggested that distinctive DNMTs targeted DNA methylation site to their preference sequences, and this targeting might be associated with diverse roles of DNMTs in tumorigenesis. Meanwhile, the analysis of preference sequences provides an alternative way to find out the individual function of DNMTs.
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Affiliation(s)
- Hong Fan
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China.
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.
| | - Zhujiang Zhao
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Yuchao Cheng
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - He Cui
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Fengchang Qiao
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Ling Wang
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Jiaojiao Hu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Huzhang Wu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Wei Song
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
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Richa R, Sinha RP. Hydroxymethylation of DNA: an epigenetic marker. EXCLI J 2014; 13:592-610. [PMID: 26417286 DOI: 10.17877/de290r-181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/08/2003] [Indexed: 05/25/2023]
Affiliation(s)
- Rajneesh Richa
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi-221005, India
| | - Rajeshwar P Sinha
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi-221005, India
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Harrison IF, Dexter DT. Epigenetic targeting of histone deacetylase: therapeutic potential in Parkinson's disease? Pharmacol Ther 2013; 140:34-52. [PMID: 23711791 DOI: 10.1016/j.pharmthera.2013.05.010] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/09/2013] [Indexed: 12/12/2022]
Abstract
Parkinson's disease (PD) is the most common movement disorder affecting more than 4million people worldwide. The primary motor symptoms of the disease are due to degeneration of dopaminergic nigrostriatal neurons. Dopamine replacement therapies have therefore revolutionised disease management by partially controlling these symptoms. However these drugs can produce debilitating side effects when used long term and do not protect degenerating neurons against death. Recent evidence has highlighted a pathological imbalance in PD between the acetylation and deacetylation of the histone proteins around which deoxyribonucleic acid (DNA) is coiled, in favour of excessive histone deacetylation. This mechanism of adding/removing acetyl groups to histone lysine residues is one of many epigenetic regulatory processes which control the expression of genes, many of which will be essential for neuronal survival. Hence, such epigenetic modifications may have a pathogenic role in PD. It has therefore been hypothesised that if this pathological imbalance can be corrected with the use of histone deacetylase inhibiting agents then neurodegeneration observed in PD can be ameliorated. This article will review the current literature with regard to epigenetic changes in PD and the use of histone deacetylase inhibitors (HDACIs) in PD: examining the evidence of the neuroprotective effects of numerous HDACIs in cellular and animal models of Parkinsonian cell death. Ultimately answering the question: does epigenetic targeting of histone deacetylases hold therapeutic potential in PD?
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Affiliation(s)
- Ian F Harrison
- Parkinson's Disease Research Group, Centre for Neuroinflammation and Neurodegeneration, Division of Brain Sciences, Department of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK.
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