Project A: The Genetics of Epigenetics

Fernando Pardo-Manuel de Villena (UNC), Wei Wang (UCLA), Leonard McMillan (UNC)


DNA methylation is a widespread epigenetic mark that plays critical roles in development, gene by environment interaction and disease susceptibility in mammals. DNA methylation is a highly dynamic process that may affect ~20 million CpG dinucleotides present in a mammalian genome. Global and local DNA methylation patterns vary in both normal and pathological conditions. Our goal is to generate a comprehensive map of DNA methylation variation in mouse and to understand the role that genetic variation plays in epigenetic variation.

Center related publications

Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse
Didion JP, de Villena FP.
Mamm Genome. 2013 Feb;24(1-2):1-20. doi: 10.1007/s00335-012-9441-z. NIHMSID - NIHMS427610

Modeling host genetic regulation of influenza pathogenesis in the collaborative cross
Ferris MT, Aylor DL, Bottomly D, Whitmore AC, Aicher LD, Bell TA, Bradel-Tretheway B, Bryan JT, Buus RJ, Gralinski LE, Haagmans BL, McMillan L, Miller DR, Rosenzweig E, Valdar W, Wang J, Churchill GA, Threadgill DW, McWeeney SK, Katze MG, Pardo-Manuel de Villena F, Baric RS, Heise MT.
PLoS Pathog. 2013 Feb;9(2):e1003196. doi: 10.1371/journal.ppat.1003196. PMCID: PMC3585141 [ Full Text ]

Intronic parent-of-origin dependent differential methylation at the Actn1 gene is conserved in rodents but is not associated with imprinted expression
Calaway JD, Domínguez JI, Hanson ME, Cambranis EC, Pardo-Manuel de Villena F, de la Casa-Esperon E.
PLoS One. 2012;7(11):e48936. doi: 10.1371/journal.pone.0048936. PMCID: PMC3493592 [ Full Text ]

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
Didion JP, Yang H, Sheppard K, Fu CP, McMillan L, Pardo-Manuel de Villena F, Churchill GA
BMC Genomics. 2012 Jan 19;13(1):34. PMCID: PMC3305361 [ Full Text ] [ software ] [ datasets 1 ] [ datasets 2 ]

Genetic Analysis of Hematologic Parameters in Incipient Lines of the Collaborative Cross
Kelada SNP, Aylor DL, Peck BCE, Ryan JF, Tavarez U, Buus RJ, Miller DR, Chesler EJ, Threadgill DW, Churchill GA, Pardo-Manuel de Villena F, Collins FS.
G3 (Bethesda). 2012 Feb;2(2):157-65. PMCID: PMC3284323 [ Full Text ] [ datasets ]

High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population
Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA.
Genetics. 2012 Feb;190(2):437-47. PMCID: PMC3276626 [Available on 2013/2/1] [ datasets ]

Imputation of Single-Nucleotide Polymorphisms in Inbred Mice Using Local Phylogeny
Wang JR, Pardo-Manuel de Villena F, Lawson HA, Cheverud JM, Churchill GA, McMillan L.
Genetics. 2012 Feb;190(2):449-58. PMCID: PMC3276610 [ Full Text ] [ datasets ] [ software ]

Comparative analysis and visualization of multiple collinear genomes
Wang JR, de Villena FP, McMillan L.
BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S13. PMCID: PMC3311102 [ Full Text ]

Status and access to the Collaborative Cross population
Welsh CE, Miller DR, Manly KF, Wang J, McMillan L, Morahan G, Mott R, Iraqi FA, Threadgill DW, de Villena FP.
Mamm Genome. 2012 Oct;23(9-10):706-12. doi: 10.1007/s00335-012-9410-6. PMCID: PMC3463789 [ Full Text ]

HTreeQA: Using Semi-Perfect Phylogeny Trees in Quantitative Trait Loci Study on Genotype Data
Zhang Z, Zhang X, Wang W.
G3 (Bethesda). 2012 Feb;2(2):175-89. PMCID: PMC3284325 [ Full Text ]

The Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigates infection
Durrant C, Tayem H, Yalcin B, Osherov N, Pardo-Manuel de Villena F, Mott R, Iraqi FA.
Genome Res. 2011 Aug;21(8):1239-48. PMCID: PMC3149491. [ Full Text ]