title: DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth.
abstract: BACKGROUND
  Gestational age at birth strongly predicts neonatal, adolescent and adult morbidity and mortality through mostly unknown mechanisms. Identification of specific genes that are undergoing regulatory change prior to birth, such as through changes in DNA methylation, would increase our understanding of developmental changes occurring during the third trimester and consequences of pre-term birth (PTB).
  
  
  METHODS
  We performed a genome-wide analysis of DNA methylation (using microarrays, specifically CHARM 2.0) in 141 newborns collected in Baltimore, MD, using novel statistical methodology to identify genomic regions associated with gestational age at birth. Bisulphite pyrosequencing was used to validate significant differentially methylated regions (DMRs), and real-time PCR was performed to assess functional significance of differential methylation in a subset of newborns.
  
  
  RESULTS
  We identified three DMRs at genome-wide significance levels adjacent to the NFIX, RAPGEF2 and MSRB3 genes. All three regions were validated by pyrosequencing, and RAGPEF2 also showed an inverse correlation between DNA methylation levels and gene expression levels. Although the three DMRs appear very dynamic with gestational age in our newborn sample, adult DNA methylation levels at these regions are stable and of equal or greater magnitude than the oldest neonate, directionally consistent with the gestational age results.
  
  
  CONCLUSIONS
  We have identified three differentially methylated regions associated with gestational age at birth. All three nearby genes play important roles in the development of several organs, including skeletal muscle, brain and haematopoietic system. Therefore, they may provide initial insight into the basis of PTB's negative health outcomes. The genome-wide custom DNA methylation array technology and novel statistical methods employed in this study could constitute a model for epidemiologic studies of epigenetic variation.
authors.affiliation: Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Hwajin
authors.initials: H
authors.lastname: Lee
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Jaffe
authors.forename: Jason I
authors.initials: JI
authors.lastname: Feinberg
authors.forename: Rakel
authors.initials: R
authors.lastname: Tryggvadottir
authors.forename: Shannon
authors.initials: S
authors.lastname: Brown
authors.forename: Carolina
authors.initials: C
authors.lastname: Montano
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Aryee
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Irizarry
authors.forename: Julie
authors.initials: J
authors.lastname: Herbstman
authors.forename: Frank R
authors.initials: FR
authors.lastname: Witter
authors.forename: Lynn R
authors.initials: LR
authors.lastname: Goldman
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Feinberg
authors.forename: M Daniele
authors.initials: MD
authors.lastname: Fallin
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D005260:Female; D055106:Genome-Wide Association Study; D005865:Gestational Age; D020662:Guanine Nucleotide Exchange Factors / Q000235:genetics*; D006801:Humans; D007231:Infant, Newborn; D008297:Male; D051150:Methionine Sulfoxide Reductases / Q000235:genetics*; D008875:Middle Aged; D051839:NFI Transcription Factors / Q000235:genetics*; D009419:Nerve Tissue Proteins / Q000235:genetics*; D055815:Young Adult
chemical_list: D020662:Guanine Nucleotide Exchange Factors; D051839:NFI Transcription Factors; D009419:Nerve Tissue Proteins; C403525:RAPGEF2 protein, human; D051150:Methionine Sulfoxide Reductases; C524352:MSRB3 protein, human