The placental imprinted DLK1-DIO3 domain: a new link to prenatal and postnatal growth in humans

Abstract

The developmentally important DLK1-DIO3 imprinted domain on human chromosome 14 is regulated by 2 differentially methylated regions, the intergenic differentially methylated region and the MEG3 differentially methylated region. The aim was to determine the natural variation in DNA methylation at these differentially methylated regions in human placentas, and to determine its link to gene expression levels at the domain. The second goal was to explore whether the domain's methylation and gene expression correlate with prenatal and early postnatal growth of the conceptus. Using pyrosequencing, we determined methylation levels at CpG dinucleotides across the 2 regulatory differentially methylated regions in placentas from 91 healthy mothers. At birth, placentas and infants were weighed (gestational age 39 ± 1 weeks; birthweight SD score 0.1 ± 0.8) and placental biopsies were collected. RNA expression was quantitated by real-time polymerase chain reaction. Infants' weights and lengths were followed up monthly during the first year. Methylation levels at the 2 regulatory differentially methylated regions were linked and varied considerably between placentas. MEG3 promoter differentially methylated region methylation correlated negatively with weight increase (β= -0.406, P= .001, R2= 0.206) andlength increase (β= -0.363, P= .002, R2= 0.230) during the firstpostnatal year. The methylation level of the intergenic differentially methylated region correlated with DIO3 expression (β= 0.313, P= .032, R2= 0.152). Furthermore, the expression of both DIO3 and RTL1 (bothimprinted genes within the DLK1-DIO3 domain) was negatively associated with birthweight (β= -0.331, P= .002, R2= 0.165; and β=-0.307, P= .005, R2= 0.159, respectively). RTL1 expression, in addition, was negatively linked to birth length (β= -0.306, P= .007, R2= 0.162). Our combined findings strongly suggest that placental DNA methylation at the DLK1-DIO3 domain's intergenic differentially methylated region and MEG3 promoter differentially methylated region relates to measures of early human growth, and may thus contribute to its control.