Genome-wide maps of chromatin state in rat IUGR islets at 2 time points
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE147992 | GEO | 2020/07/15
REPOSITORIES: GEO
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Project description:Intrauterine growth restriction (IUGR) increases the risk of developing type 2 diabetes in adulthood. A rat model of IUGR induced by bilateral uterine artery ligation at day 18 of gestation, which reduces the blood supply and critical substrates to the fetus, was used to assess the alterations of genome-wide DNA methylation in IUGR islets. At 2 weeks of age, pancreatic islets were isolated and genomic DNA were extracted for TruSeq-HELP tagging assay. Cytosine methylation was compared in the study.
2022-01-12 | GSE151684 | GEO
Project description:Intrauterine growth restriction is a common complication of pregnancy. We induce IUGR in rats by bilateral uterine artery ligation at e18 of a 23 day gestation. This mimics placental insufficiency. This array experiment compares gene expression changes in isolated pancreatic islets from e19, 24 hours post-surgery , or sham operated animals. RNA from isolated pancreatic islets from e19 fetuses, pooled from an entire litter. There are 4 control (sham) operated litters and 4 IUGR litters.
2013-07-10 | E-GEOD-48655 | biostudies-arrayexpress
Project description:Intrauterine growth restriction (IUGR) increases the risk of developing type 2 diabetes during adulthood. At day 18 of gestation, we used bilatual uterine artery ligation (BUAL) to restrict nutrient supply to developing rat fetuses to produce IUGR pups. At 2 and 10 weeks of age pancreatic islets were isolated and total RNA extracted using Trizol. Samples with RNA integrity numbers greater than 7 were used to generate libraries
2018-09-11 | GSE104017 | GEO
Project description:Intrauterine growth restriction is a common complication of pregnancy. We induce IUGR in rats by bilateral uterine artery ligation at e18 of a 23 day gestation. This mimics placental insufficiency. This array experiment compares gene expression changes in isolated pancreatic islets from e19, 24 hours post-surgery , or sham operated animals.
2013-07-10 | GSE48655 | GEO
Project description: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).
2010-06-24 | E-GEOD-16839 | biostudies-arrayexpress
Project description:IUGR is a common complication of pregnancy. We have created a rat model of IUGR which mimics placental insufficiency. Surgery is performed at embryonic day 18 and dams are allowed to deleiver spontaneously. At postnatal day 14, we isolate pancreatic islets and have compared their gene expression with that of control (sham) surgery animals. Two-condition experiment, control vs IUGR pancreatic islets. Biological replicates: 4 control replicates, 4 IUGR replicates.
2013-07-13 | E-GEOD-48822 | biostudies-arrayexpress
Project description: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.
2010-03-09 | GSE16839 | GEO
Project description:IUGR is a common complication of pregnancy. We have created a rat model of IUGR which mimics placental insufficiency. Surgery is performed at embryonic day 18 and dams are allowed to deleiver spontaneously. At postnatal day 14, we isolate pancreatic islets and have compared their gene expression with that of control (sham) surgery animals.
2013-07-13 | GSE48822 | GEO
Project description:Impaired muscle growth as a result of IUGR is a major contributor to lifelong reductions in muscle mass (sarcopenia) and metabolic disease risk. We use an ovine model of chronic placental insufficiency which restricts nutrient supply from mother to fetus and results in intrauterine growth restriction. In our model of placental insufficiency and IUGR, fetal hindlimb muscles weigh less than normally-grown control fetuses and have smaller myofiber diameters. Given the frequent correlation between functional changes and transcriptional changes, we investigated the effect of chronic placental insufficiency and IUGR on fetal skeletal muscle gene expression. We found that gene expression in the skeletal muscle is significantly altered by chronic placental insufficiency. In gene ontology analysis, we found that genes involved in cell cycle regulation were most significantly affected, with downregulation of several cyclins. These observations may in part account for decreased muscle weight relative to brain weight observed in the late gestation IUGR fetus.
2014-12-31 | GSE64578 | GEO
Project description:Intrauterine growth restriction (IUGR) represents a major obstetric challenge with perinatal complications and a risk factor of developing disease in adult life. Placental insufficiency is one of the common features accompanying IUGR. The aim of this study was to evaluate global placental gene expression profile in IUGR compared to normal pregnancies. Placental samples were collected by eight IUGR pregnancies with placental insufficiency ascertained by Doppler and eight healthy controls. A 30K Human Genome Survey Microarray v.2.0 (Applied Biosystems) was used to evaluate global gene expression profile. Principal component analysis showed good separation in terms of gene expression patterns between the groups. Pathway analysis with Bonferroni correction for multiple testing showed significant (p<0.05) up-regulation of inflammation mediated by chemokine and cytokine signalling pathway in the IUGR placentas. Genes involved in metabolism of glucocorticoids (HSD11B1 and DHRS2) were found differentially expressed. We found no imprinted genes to be differentially expressed and only one gene involved in epigenetic modifications (MBD3) to be down-regulated in the IUGR placentas, indicating that IUGR due to placental insufficiency is not associated to placental imprinting. Subgroup analysis between pure IUGR and IUGR with preeclampsia placentas showed only 27 differentially expressed genes suggesting common pathophysiology. Eight placental samples from normal human placenta compared to eight human placental samples from patients with intrauterine growth restrictions due to placental insufficiency
2008-08-01 | E-GEOD-12216 | biostudies-arrayexpress