Transcriptomics

Dataset Information

4

Genome-wide DNA methylation in normal and IUGR pancreatic islets


ABSTRACT: Intrauterine growth restriction (IUGR) increases susceptibility to age-related diseases including type 2 diabetes (T2DM), and is associated with permanent and progressive changes in gene expression and epigenetic regulation. We studied cytosine methylation throughout the genome in pancreatic islets from a rat model of uteroplacental insufficiency, providing a novel and detailed assessment of the genomic distribution and locus-specific patterns of DNA methylation in normal islets as well as the changes that occur as a consequence of IUGR. Utilizing a high throughput approach to study DNA methylation at almost 1 million unique sites throughout the genome, we found ~1,400 changes in methylation (IUGR compared to control) with an estimated false discovery rate of 4.2%. These epigenetic differences were observed in IUGR male rats at 7 weeks of age, preceding the development of diabetes in this model. Therefore, these epigenetic differences represent candidates for mediating the pathogenesis of metabolic disease that occurs later in life in these animals. Moreover, many of the changes we identify are located near genes that regulate processes known to be abnormal in IUGR islets, such as vascularization, β-cell proliferation, insulin secretion, and cell death. Consistent changes in mRNA expression were identified at some of the epigenetically-dysregulated genes including Fgfr1, Gch1, Pcsk5, and Vgf. Globally, epigenetic dysregulation occurred preferentially at conserved intergenic sequences, which are candidate cis-regulatory elements driving differential expression of nearby genes. These results provide insights into the complex developmental consequences of IUGR, and suggest that changes in DNA methylation could mediate a constellation of changes in both gene expression and pancreatic islet development and function, with relevance to T2DM. Direct comparison of DNA methylation in 8 samples consisting of isolated, pooled pancreatic islets from 7-week-old male offspring belonging to 4 IUGR and 4 control litters (Sprague-Dawley rats). Each microarray consists of a two-color comparison of a methylation-sensitive representation of the genome (HpaII) with an internal methylation-insensitive control/reference (MspI).

ORGANISM(S): Rattus norvegicus  

SUBMITTER: Nir Barzilai  Melissa J Fazzari  Reid F Thompson  Rebecca A Simmons  Hong S Niu  John M Greally 

PROVIDER: E-GEOD-16839 | ArrayExpress | 2010-06-24

SECONDARY ACCESSION(S): GSE16839PRJNA117605

REPOSITORIES: GEO, ArrayExpress

altmetric image

Publications

Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats.

Thompson Reid F RF   Fazzari Melissa J MJ   Niu Hongshun H   Barzilai Nir N   Simmons Rebecca A RA   Greally John M JM  

The Journal of biological chemistry 20100301 20


Intrauterine growth restriction (IUGR) increases susceptibility to age-related diseases, including type 2 diabetes (T2DM), and is associated with permanent and progressive changes in gene expression. Our study was designed to test whether epigenomic dysregulation mediates the cellular memory of this intrauterine event. To test this hypothesis, we isolated pancreatic islets from control and IUGR (induced by bilateral uterine artery ligation at day 18 of fetal life) animals at 7 weeks of age. Usin  ...[more]

Similar Datasets

2010-02-17 | E-GEOD-17727 | ArrayExpress
2013-08-19 | E-GEOD-46167 | ArrayExpress
2015-05-20 | E-GEOD-60233 | ArrayExpress
2013-06-27 | E-GEOD-38295 | ArrayExpress
2010-05-01 | E-GEOD-17332 | ArrayExpress
2013-06-27 | E-GEOD-44860 | ArrayExpress
2014-02-07 | E-GEOD-52151 | ArrayExpress
2010-03-09 | GSE16839 | GEO
2008-04-01 | E-GEOD-10894 | ArrayExpress
2012-12-05 | E-GEOD-42721 | ArrayExpress