title: Epigenetic modifications are associated with  inter-species gene expression variation in  primates.
abstract: BACKGROUND
  Changes in gene regulation have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels, yet we know much less about the extent to which regulatory mechanisms differ between species.
  
  
  RESULTS
  To begin addressing this gap, we perform a comparative epigenetic study in primate lymphoblastoid cell lines, to query the contribution of RNA polymerase II and four histone modifications, H3K4me1, H3K4me3, H3K27ac, and H3K27me3, to inter-species variation in gene expression levels. We find that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also find that first-order interactions among the five marks, as well as chromatin states, do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution.
  
  
  CONCLUSIONS
  Our observations suggest that epigenetic modifications are substantially associated with changes in gene expression levels among primates and may represent important molecular mechanisms in primate evolution.
authors.forename: Xiang
authors.initials: X
authors.lastname: Zhou
authors.forename: Carolyn E
authors.initials: CE
authors.lastname: Cain
authors.forename: Marsha
authors.initials: M
authors.lastname: Myrthil
authors.forename: Noah
authors.initials: N
authors.lastname: Lewellen
authors.forename: Katelyn
authors.initials: K
authors.lastname: Michelini
authors.forename: Emily R
authors.initials: ER
authors.lastname: Davenport
authors.forename: Matthew
authors.initials: M
authors.lastname: Stephens
authors.forename: Jonathan K
authors.initials: JK
authors.lastname: Pritchard
authors.forename: Yoav
authors.initials: Y
authors.lastname: Gilad
mesh_terms: D000818:Animals; D002460:Cell Line; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation; D006657:Histones / Q000378:metabolism; D006801:Humans; D008214:Lymphocytes / Q000378:metabolism; D011323:Primates / Q000145:classification* / Q000235:genetics*; D012333:RNA, Messenger / Q000032:analysis; D017423:Sequence Analysis, RNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D006657:Histones; D012333:RNA, Messenger