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DNA methylation, genotype and gene expression: who is driving and who is along for the ride?

Jones MJ, Fejes AP, Kobor MS.

Genome Biol. 2013 Jul 29;14(7):126. doi: 10.1186/gb-2013-14-7-126.


Passive and active DNA methylation and the interplay with genetic variation in gene regulation.

Gutierrez-Arcelus M, Lappalainen T, Montgomery SB, Buil A, Ongen H, Yurovsky A, Bryois J, Giger T, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Padioleau I, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET.

Elife. 2013 Jun 4;2:e00523. doi: 10.7554/eLife.00523. Erratum in: Elife. 2013;2:e01045.


Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects.

van Eijk KR, de Jong S, Boks MP, Langeveld T, Colas F, Veldink JH, de Kovel CG, Janson E, Strengman E, Langfelder P, Kahn RS, van den Berg LH, Horvath S, Ophoff RA.

BMC Genomics. 2012 Nov 17;13:636. doi: 10.1186/1471-2164-13-636.


Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens.

Nätt D, Rubin CJ, Wright D, Johnsson M, Beltéky J, Andersson L, Jensen P.

BMC Genomics. 2012 Feb 4;13:59. doi: 10.1186/1471-2164-13-59.


Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model.

Wang F, Zhang S, Wen Y, Wei Y, Yan H, Liu H, Su J, Zhang Y, Che J.

Brief Bioinform. 2014 Nov;15(6):1028-43. doi: 10.1093/bib/bbt076.


Epigenetic and genetic influences on DNA methylation variation in maize populations.

Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, Waters AJ, Starr E, West PT, Tiffin P, Myers CL, Vaughn MW, Springer NM.

Plant Cell. 2013 Aug;25(8):2783-97. doi: 10.1105/tpc.113.114793.


The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts.

Wagner JR, Busche S, Ge B, Kwan T, Pastinen T, Blanchette M.

Genome Biol. 2014 Feb 20;15(2):R37. doi: 10.1186/gb-2014-15-2-r37.


An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver.

Xie L, Weichel B, Ohm JE, Zhang K.

BMC Syst Biol. 2011;5 Suppl 3:S4. doi: 10.1186/1752-0509-5-S3-S4.


Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state.

Lafon-Placette C, Faivre-Rampant P, Delaunay A, Street N, Brignolas F, Maury S.

New Phytol. 2013 Jan;197(2):416-30. doi: 10.1111/nph.12026.


Natural variation of histone modification and its impact on gene expression in the rat genome.

Rintisch C, Heinig M, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colomé-Tatché M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, Hubner N.

Genome Res. 2014 Jun;24(6):942-53. doi: 10.1101/gr.169029.113.


Genome-wide association between DNA methylation and alternative splicing in an invertebrate.

Flores K, Wolschin F, Corneveaux JJ, Allen AN, Huentelman MJ, Amdam GV.

BMC Genomics. 2012 Sep 15;13:480. doi: 10.1186/1471-2164-13-480.


Genetic effects on DNA methylation and its potential relevance for obesity in Mexican Americans.

Carless MA, Kulkarni H, Kos MZ, Charlesworth J, Peralta JM, Göring HH, Curran JE, Almasy L, Dyer TD, Comuzzie AG, Mahaney MC, Blangero J.

PLoS One. 2013 Sep 13;8(9):e73950. doi: 10.1371/journal.pone.0073950.


DNA methylation and epigenotypes.

Holliday R.

Biochemistry (Mosc). 2005 May;70(5):500-4. Review.


Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.

Zeng J, Konopka G, Hunt BG, Preuss TM, Geschwind D, Yi SV.

Am J Hum Genet. 2012 Sep 7;91(3):455-65. doi: 10.1016/j.ajhg.2012.07.024.


An integrated workflow for DNA methylation analysis.

Li P, Demirci F, Mahalingam G, Demirci C, Nakano M, Meyers BC.

J Genet Genomics. 2013 May 20;40(5):249-60. doi: 10.1016/j.jgg.2013.03.010. Review.


Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation.

Lou S, Lee HM, Qin H, Li JW, Gao Z, Liu X, Chan LL, Kl Lam V, So WY, Wang Y, Lok S, Wang J, Ma RC, Tsui SK, Chan JC, Chan TF, Yip KY.

Genome Biol. 2014 Jul 30;15(7):408. doi: 10.1186/s13059-014-0408-0.


Targeting DNA methylation to the genome.

Lo PC.

Biotechniques. 2014 Sep 1;57(3):106-10. doi: 10.2144/000114203.


Methylation of p15INK4b and expression of ANRIL on chromosome 9p21 are associated with coronary artery disease.

Zhuang J, Peng W, Li H, Wang W, Wei Y, Li W, Xu Y.

PLoS One. 2012;7(10):e47193. doi: 10.1371/journal.pone.0047193.


Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.

Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T.

Genome Res. 2013 Sep;23(9):1541-53. doi: 10.1101/gr.152231.112.


Extensive variation and low heritability of DNA methylation identified in a twin study.

Gervin K, Hammerø M, Akselsen HE, Moe R, Nygård H, Brandt I, Gjessing HK, Harris JR, Undlien DE, Lyle R.

Genome Res. 2011 Nov;21(11):1813-21. doi: 10.1101/gr.119685.110.

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