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For: Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schübeler D, Vinson C, Taipale J. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 2018;356:356/6337/eaaj2239. [PMID: 28473536 DOI: 10.1126/science.aaj2239] [Citation(s) in RCA: 679] [Impact Index Per Article: 113.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/09/2017] [Indexed: 12/17/2022]
Number Cited by Other Article(s)
601
Liu Y, Shen J, Yang X, Sun Q, Yang X. Folic Acid Reduced Triglycerides Deposition in Primary Chicken Hepatocytes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018;66:13162-13172. [PMID: 30484310 DOI: 10.1021/acs.jafc.8b05193] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
602
Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C, Greenleaf WJ, Chang HY. The chromatin accessibility landscape of primary human cancers. Science 2018;362:362/6413/eaav1898. [PMID: 30361341 DOI: 10.1126/science.aav1898] [Citation(s) in RCA: 621] [Impact Index Per Article: 103.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022]
603
Xiong T, Rohm D, Workman RE, Roundtree L, Novina CD, Timp W, Ostermeier M. Protein engineering strategies for improving the selective methylation of target CpG sites by a dCas9-directed cytosine methyltransferase in bacteria. PLoS One 2018;13:e0209408. [PMID: 30562388 PMCID: PMC6298699 DOI: 10.1371/journal.pone.0209408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/05/2018] [Indexed: 12/22/2022]  Open
604
Laisné M, Gupta N, Kirsh O, Pradhan S, Defossez PA. Mechanisms of DNA Methyltransferase Recruitment in Mammals. Genes (Basel) 2018;9:genes9120617. [PMID: 30544749 PMCID: PMC6316769 DOI: 10.3390/genes9120617] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022]  Open
605
Feng W, Zhou L, Wang H, Hu Z, Wang X, Fu J, Wang A, Liu JF. Functional analysis of DNA methylation of the PACSIN1 promoter in pig peripheral blood mononuclear cells. J Cell Biochem 2018;120:10118-10127. [PMID: 30537176 DOI: 10.1002/jcb.28295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022]
606
Lussier AA, Bodnar TS, Mingay M, Morin AM, Hirst M, Kobor MS, Weinberg J. Prenatal Alcohol Exposure: Profiling Developmental DNA Methylation Patterns in Central and Peripheral Tissues. Front Genet 2018;9:610. [PMID: 30568673 PMCID: PMC6290329 DOI: 10.3389/fgene.2018.00610] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022]  Open
607
Tobi EW, van den Heuvel J, Zwaan BJ, Lumey L, Heijmans BT, Uller T. Selective Survival of Embryos Can Explain DNA Methylation Signatures of Adverse Prenatal Environments. Cell Rep 2018;25:2660-2667.e4. [DOI: 10.1016/j.celrep.2018.11.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 09/18/2018] [Accepted: 11/02/2018] [Indexed: 12/21/2022]  Open
608
Effect of hypermethylation in ovarian cancer: Computational approach. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
609
Parker HR, Orjuela S, Martinho Oliveira A, Cereatti F, Sauter M, Heinrich H, Tanzi G, Weber A, Komminoth P, Vavricka S, Albanese L, Buffoli F, Robinson MD, Marra G. The proto CpG island methylator phenotype of sessile serrated adenomas/polyps. Epigenetics 2018;13:1088-1105. [PMID: 30398409 PMCID: PMC6342079 DOI: 10.1080/15592294.2018.1543504] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
610
Jeltsch A, Broche J, Bashtrykov P. Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes. Genes (Basel) 2018;9:genes9110566. [PMID: 30469440 PMCID: PMC6266221 DOI: 10.3390/genes9110566] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022]  Open
611
Shen SY, Singhania R, Fehringer G, Chakravarthy A, Roehrl MHA, Chadwick D, Zuzarte PC, Borgida A, Wang TT, Li T, Kis O, Zhao Z, Spreafico A, Medina TDS, Wang Y, Roulois D, Ettayebi I, Chen Z, Chow S, Murphy T, Arruda A, O'Kane GM, Liu J, Mansour M, McPherson JD, O'Brien C, Leighl N, Bedard PL, Fleshner N, Liu G, Minden MD, Gallinger S, Goldenberg A, Pugh TJ, Hoffman MM, Bratman SV, Hung RJ, De Carvalho DD. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature 2018;563:579-583. [PMID: 30429608 DOI: 10.1038/s41586-018-0703-0] [Citation(s) in RCA: 509] [Impact Index Per Article: 84.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 09/25/2018] [Indexed: 12/16/2022]
612
Transcriptional Landscape of PARs in Epithelial Malignancies. Int J Mol Sci 2018;19:ijms19113451. [PMID: 30400241 PMCID: PMC6275037 DOI: 10.3390/ijms19113451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/22/2018] [Accepted: 10/27/2018] [Indexed: 12/24/2022]  Open
613
Sardina JL, Collombet S, Tian TV, Gómez A, Di Stefano B, Berenguer C, Brumbaugh J, Stadhouders R, Segura-Morales C, Gut M, Gut IG, Heath S, Aranda S, Di Croce L, Hochedlinger K, Thieffry D, Graf T. Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate. Cell Stem Cell 2018;23:727-741.e9. [DOI: 10.1016/j.stem.2018.08.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/07/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022]
614
Lin KN, Grandhi TSP, Goklany S, Rege K. Chemotherapeutic Drug-Conjugated Microbeads Demonstrate Preferential Binding to Methylated Plasmid DNA. Biotechnol J 2018;13:e1700701. [DOI: 10.1002/biot.201700701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/25/2018] [Indexed: 11/08/2022]
615
Hudson NO, Whitby FG, Buck-Koehntop BA. Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38. J Biol Chem 2018;293:19835-19843. [PMID: 30355731 DOI: 10.1074/jbc.ra118.005147] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/16/2018] [Indexed: 02/05/2023]  Open
616
Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM. Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. Nat Biotechnol 2018;36:nbt.4204. [PMID: 30295673 PMCID: PMC6453757 DOI: 10.1038/nbt.4204] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/03/2018] [Indexed: 12/17/2022]
617
Hudson NO, Buck-Koehntop BA. Zinc Finger Readers of Methylated DNA. Molecules 2018;23:E2555. [PMID: 30301273 PMCID: PMC6222495 DOI: 10.3390/molecules23102555] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/07/2023]  Open
618
Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells. Cancers (Basel) 2018;10:cancers10100371. [PMID: 30301163 PMCID: PMC6210734 DOI: 10.3390/cancers10100371] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/01/2018] [Indexed: 01/18/2023]  Open
619
Liu Y, Huang R, Liu Y, Song W, Wang Y, Yang Y, Dong S, Yang X. Insights from multidimensional analyses of the pan-cancer DNA methylome heterogeneity and the uncanonical CpG-gene associations. Int J Cancer 2018;143:2814-2827. [PMID: 30121964 DOI: 10.1002/ijc.31810] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/18/2018] [Accepted: 08/13/2018] [Indexed: 12/28/2022]
620
Gatzmann F, Falckenhayn C, Gutekunst J, Hanna K, Raddatz G, Carneiro VC, Lyko F. The methylome of the marbled crayfish links gene body methylation to stable expression of poorly accessible genes. Epigenetics Chromatin 2018;11:57. [PMID: 30286795 PMCID: PMC6172769 DOI: 10.1186/s13072-018-0229-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/28/2018] [Indexed: 12/22/2022]  Open
621
Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Res 2018;78:5538-5547. [PMID: 30275053 PMCID: PMC6169995 DOI: 10.1158/0008-5472.can-18-0454] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/04/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022]
622
Luo C, Hajkova P, Ecker JR. Dynamic DNA methylation: In the right place at the right time. Science 2018;361:1336-1340. [PMID: 30262495 PMCID: PMC6197482 DOI: 10.1126/science.aat6806] [Citation(s) in RCA: 379] [Impact Index Per Article: 63.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
623
The interaction landscape between transcription factors and the nucleosome. Nature 2018;562:76-81. [PMID: 30250250 PMCID: PMC6173309 DOI: 10.1038/s41586-018-0549-5] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 08/06/2018] [Indexed: 01/01/2023]
624
Goodman SJ, Roubinov DS, Bush NR, Park M, Farré P, Emberly E, Hertzman C, Essex MJ, Kobor MS, Boyce WT. Children's biobehavioral reactivity to challenge predicts DNA methylation in adolescence and emerging adulthood. Dev Sci 2018;22:e12739. [PMID: 30176105 PMCID: PMC6433477 DOI: 10.1111/desc.12739] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/08/2018] [Indexed: 12/21/2022]
625
Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. eLife 2018;7:36187. [PMID: 30188322 PMCID: PMC6126923 DOI: 10.7554/elife.36187] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/21/2018] [Indexed: 02/06/2023]  Open
626
Rogers JM, Bulyk ML. Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018;10:e1423. [PMID: 29694718 PMCID: PMC6202284 DOI: 10.1002/wsbm.1423] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/23/2018] [Accepted: 03/11/2018] [Indexed: 01/17/2023]
627
The role of epigenetics in cardiovascular health and ageing: A focus on physical activity and nutrition. Mech Ageing Dev 2018;174:76-85. [DOI: 10.1016/j.mad.2017.11.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/08/2017] [Accepted: 11/15/2017] [Indexed: 02/06/2023]
628
Lead induces the up-regulation of the protein arginine methyltransferase 5 possibly by its promoter demethylation. Biochem J 2018;475:2653-2666. [PMID: 30054435 DOI: 10.1042/bcj20180009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/24/2018] [Accepted: 07/27/2018] [Indexed: 01/10/2023]
629
The effect of maternal care on gene expression and DNA methylation in a subsocial bee. Nat Commun 2018;9:3468. [PMID: 30150650 PMCID: PMC6110825 DOI: 10.1038/s41467-018-05903-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022]  Open
630
Chen F, Zhang Q, Deng X, Zhang X, Chen C, Lv D, Li Y, Li D, Zhang Y, Li P, Diao Y, Kang L, Owen GI, Chen J, Li Z. Conflicts of CpG density and DNA methylation are proximally and distally involved in gene regulation in human and mouse tissues. Epigenetics 2018;13:721-741. [PMID: 30009687 DOI: 10.1080/15592294.2018.1500057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
631
Oyinlade O, Wei S, Kammers K, Liu S, Wang S, Ma D, Huang ZY, Qian J, Zhu H, Wan J, Xia S. Analysis of KLF4 regulated genes in cancer cells reveals a role of DNA methylation in promoter- enhancer interactions. Epigenetics 2018;13:751-768. [PMID: 30058478 DOI: 10.1080/15592294.2018.1504592] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
632
Catuogno S, Esposito CL, Ungaro P, de Franciscis V. Nucleic Acid Aptamers Targeting Epigenetic Regulators: An Innovative Therapeutic Option. Pharmaceuticals (Basel) 2018;11:ph11030079. [PMID: 30149585 PMCID: PMC6161095 DOI: 10.3390/ph11030079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022]  Open
633
Hui T, Cao Q, Wegrzyn-Woltosz J, O'Neill K, Hammond CA, Knapp DJHF, Laks E, Moksa M, Aparicio S, Eaves CJ, Karsan A, Hirst M. High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations. Stem Cell Reports 2018;11:578-592. [PMID: 30078558 PMCID: PMC6093082 DOI: 10.1016/j.stemcr.2018.07.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 02/06/2023]  Open
634
Johnson TE, Lee JH, Myler LR, Zhou Y, Mosley TJ, Yang SH, Uprety N, Kim J, Paull TT. Homeodomain Proteins Directly Regulate ATM Kinase Activity. Cell Rep 2018;24:1471-1483. [PMID: 30089259 PMCID: PMC6127865 DOI: 10.1016/j.celrep.2018.06.089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 04/18/2018] [Accepted: 06/20/2018] [Indexed: 12/17/2022]  Open
635
Pathak R, Feil R. Environmental effects on chromatin repression at imprinted genes and endogenous retroviruses. Curr Opin Chem Biol 2018;45:139-147. [DOI: 10.1016/j.cbpa.2018.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/05/2018] [Accepted: 04/24/2018] [Indexed: 12/26/2022]
636
Grasse S, Lienhard M, Frese S, Kerick M, Steinbach A, Grimm C, Hussong M, Rolff J, Becker M, Dreher F, Schirmer U, Boerno S, Ramisch A, Leschber G, Timmermann B, Grohé C, Lüders H, Vingron M, Fichtner I, Klein S, Odenthal M, Büttner R, Lehrach H, Sültmann H, Herwig R, Schweiger MR. Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance. Genome Med 2018;10:55. [PMID: 30029672 PMCID: PMC6054719 DOI: 10.1186/s13073-018-0562-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/21/2018] [Indexed: 12/31/2022]  Open
637
Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 2018;53:88-99. [PMID: 30031306 DOI: 10.1016/j.sbi.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
638
Zhang J, Han X, Gao C, Xing Y, Qi Z, Liu R, Wang Y, Zhang X, Yang YG, Li X, Sun B, Tian X. 5-Hydroxymethylome in Circulating Cell-free DNA as A Potential Biomarker for Non-small-cell Lung Cancer. GENOMICS PROTEOMICS & BIOINFORMATICS 2018;16:187-199. [PMID: 30010036 PMCID: PMC6076378 DOI: 10.1016/j.gpb.2018.06.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 02/06/2023]
639
Soulsbury CD, Lipponen A, Wood K, Mein CA, Hoffman JI, Lebigre C. Age- and quality-dependent DNA methylation correlate with melanin-based coloration in a wild bird. Ecol Evol 2018;8:6547-6557. [PMID: 30038756 PMCID: PMC6053554 DOI: 10.1002/ece3.4132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 12/11/2022]  Open
640
Marjonen H, Auvinen P, Kahila H, Tšuiko O, Kõks S, Tiirats A, Viltrop T, Tuuri T, Söderström-Anttila V, Suikkari AM, Salumets A, Tiitinen A, Kaminen-Ahola N. rs10732516 polymorphism at the IGF2/H19 locus associates with genotype-specific effects on placental DNA methylation and birth weight of newborns conceived by assisted reproductive technology. Clin Epigenetics 2018;10:80. [PMID: 29946374 PMCID: PMC6006593 DOI: 10.1186/s13148-018-0511-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/01/2018] [Indexed: 11/10/2022]  Open
641
Apostolou E, Stadtfeld M. Cellular trajectories and molecular mechanisms of iPSC reprogramming. Curr Opin Genet Dev 2018;52:77-85. [PMID: 29925040 DOI: 10.1016/j.gde.2018.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/24/2018] [Accepted: 06/04/2018] [Indexed: 12/30/2022]
642
Pflueger C, Tan D, Swain T, Nguyen T, Pflueger J, Nefzger C, Polo JM, Ford E, Lister R. A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Genome Res 2018;28:1193-1206. [PMID: 29907613 PMCID: PMC6071642 DOI: 10.1101/gr.233049.117] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/06/2018] [Indexed: 12/15/2022]
643
Kweon SM, Zhu B, Chen Y, Aravind L, Xu SY, Feldman DE. Erasure of Tet-Oxidized 5-Methylcytosine by a SRAP Nuclease. Cell Rep 2018;21:482-494. [PMID: 29020633 DOI: 10.1016/j.celrep.2017.09.055] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/15/2017] [Accepted: 09/18/2017] [Indexed: 12/15/2022]  Open
644
Huang J, Zheng J, Yuan H, McGinnis K. Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize. BMC PLANT BIOLOGY 2018;18:111. [PMID: 29879919 PMCID: PMC6040155 DOI: 10.1186/s12870-018-1329-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/24/2018] [Indexed: 05/22/2023]
645
Holtzman L, Gersbach CA. Editing the Epigenome: Reshaping the Genomic Landscape. Annu Rev Genomics Hum Genet 2018;19:43-71. [PMID: 29852072 DOI: 10.1146/annurev-genom-083117-021632] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
646
Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome Res 2018;28:998-1007. [PMID: 29844026 PMCID: PMC6028135 DOI: 10.1101/gr.228833.117] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 05/23/2018] [Indexed: 12/22/2022]
647
Albert M, Huttner WB. Epigenetic and Transcriptional Pre-patterning-An Emerging Theme in Cortical Neurogenesis. Front Neurosci 2018;12:359. [PMID: 29896084 PMCID: PMC5986960 DOI: 10.3389/fnins.2018.00359] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/08/2018] [Indexed: 01/08/2023]  Open
648
Identification of rare de novo epigenetic variations in congenital disorders. Nat Commun 2018;9:2064. [PMID: 29802345 PMCID: PMC5970273 DOI: 10.1038/s41467-018-04540-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 05/08/2018] [Indexed: 01/05/2023]  Open
649
A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility. Nat Biotechnol 2018;36:521-529. [DOI: 10.1038/nbt.4138] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/23/2018] [Indexed: 12/29/2022]
650
Khabiri M, Freddolino PL. Expression of Concern for "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes". J Phys Chem B 2018;124:1115–1123. [PMID: 29741907 DOI: 10.1021/acs.jpcb.8b04187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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