Intrauterine growth retardation (IUGR) is associated with development of type 2 diabetes in adulthood. Using a rat model of IUGR induced by bilateral uterine artery ligation, we performed RNA-Seq and HELP-TagSeq, a restriction enzyme-based genome-wide approach, to assess the association of DNA methylation changes in islets at 2 weeks of age, prior to the onset of diabetes. We identified over 2,000 transcripts differentially expressed in IUGR (q<0.05 vs. control) and 512 differentially methylated regions (DMRs->3 contiguous CpGs within 500 bp) mapped to 481 genes (q <0.05). 23 and 489 loci showed significantly increased and decreased DNA methylation in IUGR islets, respectively (q <0.05). Integrating methylome and transcriptome datasets showed alterations in multiple genes and canonical pathways that are critical for normal islet function. DMRs were enriched with transcription factor binding motifs, such as Elk1, Etv1, Foxa1, Foxa2, Pax7, Stat3, Hnf1, and AR. These transcription factors were also identified as top upstream regulators by Ingenuity Pathway Analysis of islet transcriptomes. To determine if identified DMRs represented regulatory regions for non-proximal genes, we performed in silico analysis of 3D chromosomal interactions between conserved DMRs and interacting regions of the genome using published human pancreas and islet Hi-C datasets. Hi-C analysis identified interactions between 14 highly conserved DMRs and 35 genes (key islet genes) with expression changes (q < 0.05). Changes in gene expression for many of these persisted until adulthood. In adulthood, there were far more HiC interaction genes associated with altered expression and most of these were key islet genes. Our findings have identified novel DMRs with potential distal regulatory functions, and suggest alterations of DNA methylation in key transcription factor binding motifs and genes in early life that may contribute to gene dysregulation and an abnormal islet phenotype in IUGR rats.
Y. Lien: None. X.M. Lu: None. R.A. Simmons: None.
National Institutes of Health (DK114054)