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26
Dai X, Gonzalez G, Li L, Li J, You C, Miao W, Hu J, Fu L, Zhao Y, Li R, Li L, Chen X, Xu Y, Gu W, Wang Y. YTHDF2 Binds to 5-Methylcytosine in RNA and Modulates the Maturation of Ribosomal RNA. Anal Chem 2020;92:1346-1354. [PMID: 31815440 PMCID: PMC6949395 DOI: 10.1021/acs.analchem.9b04505] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
27
Liang Z, Riaz A, Chachar S, Ding Y, Du H, Gu X. Epigenetic Modifications of mRNA and DNA in Plants. MOLECULAR PLANT 2020;13:14-30. [PMID: 31863849 DOI: 10.1016/j.molp.2019.12.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/22/2019] [Accepted: 12/05/2019] [Indexed: 05/21/2023]
28
Hsu HK, Weng YI, Hsu PY, Huang THM, Huang YW. Detection of DNA Methylation by MeDIP and MBDCap Assays: An Overview of Techniques. Methods Mol Biol 2020;2102:225-234. [PMID: 31989558 DOI: 10.1007/978-1-0716-0223-2_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
29
Bhavsar-Jog YP, Van Dornshuld E, Brooks TA, Tschumper GS, Wadkins RM. Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells. Molecules 2019;24:molecules24193619. [PMID: 31597270 PMCID: PMC6804057 DOI: 10.3390/molecules24193619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/01/2019] [Accepted: 10/04/2019] [Indexed: 12/25/2022]  Open
30
Sun PP, Chen YB, Liu B, Gao YX, Han Y, He F, Ji JC. DeepMRMP: A new predictor for multiple types of RNA modification sites using deep learning. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2019;16:6231-6241. [PMID: 31698559 DOI: 10.3934/mbe.2019310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
31
Xue YM, Cheng HC, Wang JH, Wang W, Miao L. Cytosine 5-hydroxymethylation regulated kit gene expression in acute myeloid leukemia. J BIOL REG HOMEOS AG 2019;33:345-353. [PMID: 30972998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
32
Masiello I, Biggiogera M. Electron Microscope Detection of 5-Methylcytosine on DNA and RNA. Methods Mol Biol 2019;1870:165-177. [PMID: 30539554 DOI: 10.1007/978-1-4939-8808-2_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
33
Gu X, Liang Z. Transcriptome-Wide Mapping 5-Methylcytosine by m5C RNA Immunoprecipitation Followed by Deep Sequencing in Plant. Methods Mol Biol 2019;1933:389-394. [PMID: 30945199 DOI: 10.1007/978-1-4939-9045-0_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
34
Kochmanski J, Marchlewicz EH, Cavalcante RG, Sartor MA, Dolinoy DC. Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood. Epigenetics 2018;13:779-792. [PMID: 30079798 PMCID: PMC6224215 DOI: 10.1080/15592294.2018.1507198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/13/2018] [Accepted: 07/25/2018] [Indexed: 01/10/2023]  Open
35
Chu Y, Zhao Z, Sant DW, Zhu G, Greenblatt SM, Liu L, Wang J, Cao Z, Tho JC, Chen S, Liu X, Zhang P, Maciejewski JP, Nimer S, Wang G, Yuan W, Yang FC, Xu M. Tet2 Regulates Osteoclast Differentiation by Interacting with Runx1 and Maintaining Genomic 5-Hydroxymethylcytosine (5hmC). GENOMICS, PROTEOMICS & BIOINFORMATICS 2018;16:172-186. [PMID: 29908294 PMCID: PMC6076382 DOI: 10.1016/j.gpb.2018.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/29/2018] [Accepted: 04/16/2018] [Indexed: 12/13/2022]
36
Sussarellu R, Lebreton M, Rouxel J, Akcha F, Rivière G. Copper induces expression and methylation changes of early development genes in Crassostrea gigas embryos. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018;196:70-78. [PMID: 29353135 DOI: 10.1016/j.aquatox.2018.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 12/23/2017] [Accepted: 01/02/2018] [Indexed: 06/07/2023]
37
Islam F, Tang JC, Gopalan V, Lam AK. Epigenetics: DNA Methylation Analysis in Esophageal Adenocarcinoma. Methods Mol Biol 2018;1756:247-256. [PMID: 29600375 DOI: 10.1007/978-1-4939-7734-5_21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
38
Ji S, Shao H, Han Q, Seiler CL, Tretyakova NY. Reversible DNA-Protein Cross-Linking at Epigenetic DNA Marks. Angew Chem Int Ed Engl 2017;56:14130-14134. [PMID: 28898504 PMCID: PMC5796521 DOI: 10.1002/anie.201708286] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Indexed: 01/22/2023]
39
Schutsky EK, Nabel CS, Davis A, DeNizio JE, Kohli RM. APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA. Nucleic Acids Res 2017;45:7655-7665. [PMID: 28472485 PMCID: PMC5570014 DOI: 10.1093/nar/gkx345] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 04/18/2017] [Indexed: 12/21/2022]  Open
40
Yin X, Xu Y. Structure and Function of TET Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017;945:275-302. [PMID: 27826843 DOI: 10.1007/978-3-319-43624-1_12] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
41
Klungland A, Robertson AB. Oxidized C5-methyl cytosine bases in DNA: 5-Hydroxymethylcytosine; 5-formylcytosine; and 5-carboxycytosine. Free Radic Biol Med 2017;107:62-68. [PMID: 27890639 DOI: 10.1016/j.freeradbiomed.2016.11.038] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/17/2016] [Accepted: 11/23/2016] [Indexed: 01/31/2023]
42
Nguyen DB, Nguyen TD, Kim S, Joo SW. Raman spectroscopy and quantum-mechanical analysis of tautomeric forms in cytosine and 5-methylcytosine on gold surfaces. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017;174:183-188. [PMID: 27912177 DOI: 10.1016/j.saa.2016.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/16/2016] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
43
Amort T, Rieder D, Wille A, Khokhlova-Cubberley D, Riml C, Trixl L, Jia XY, Micura R, Lusser A. Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain. Genome Biol 2017;18:1. [PMID: 28077169 PMCID: PMC5225599 DOI: 10.1186/s13059-016-1139-1] [Citation(s) in RCA: 293] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/16/2016] [Indexed: 12/17/2022]  Open
44
Amort T, Sun X, Khokhlova-Cubberley D, Lusser A. Transcriptome-Wide Detection of 5-Methylcytosine by Bisulfite Sequencing. Methods Mol Biol 2017;1562:123-142. [PMID: 28349458 DOI: 10.1007/978-1-4939-6807-7_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
45
Riml C, Micura R. Automated Chemical Solid-Phase Synthesis and Deprotection of 5-Hydroxymethylcytosine-Containing RNA. Methods Mol Biol 2017;1562:295-302. [PMID: 28349469 DOI: 10.1007/978-1-4939-6807-7_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
46
Vander Zanden CM, Rowe RK, Broad AJ, Robertson AB, Ho PS. Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions. Biochemistry 2016;55:5781-5789. [PMID: 27653243 PMCID: PMC5258817 DOI: 10.1021/acs.biochem.6b00801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
47
Kizaki S, Zou T, Li Y, Han YW, Suzuki Y, Harada Y, Sugiyama H. Preferential 5-Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein. Chemistry 2016;22:16598-16601. [PMID: 27689340 DOI: 10.1002/chem.201602435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Indexed: 01/31/2023]
48
Li C, Liu B, Zhong S, Wang H. MEK inhibitor PD0325901 and vitamin C synergistically induce hypomethylation of mouse embryonic stem cells. Oncotarget 2016;7:39730-39739. [PMID: 27213595 PMCID: PMC5129966 DOI: 10.18632/oncotarget.9452] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/16/2016] [Indexed: 11/25/2022]  Open
49
Smith KE, House CH, Dworkin JP, Callahan MP. Spontaneous Oligomerization of Nucleotide Alternatives in Aqueous Solutions. ORIGINS LIFE EVOL B 2016;47:3-11. [PMID: 27029792 DOI: 10.1007/s11084-016-9484-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/23/2016] [Indexed: 11/25/2022]
50
Dan J, Chen T. Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016;945:123-150. [PMID: 27826837 DOI: 10.1007/978-3-319-43624-1_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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