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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 27, 2018 |
| Title |
Impact of conditional uterine deletion of Esr1, Foxa2 or Foxo1 on DES-induced gene expression |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Neonatal exposure to diethylstilbestrol (DES) results in abnormal reproductive tract morphology, female infertility and uterine cancer in mice. This exposure also causes altered gene expression in the female reproductive tract that persists into adulthood. To further explore on a genome-wide basis how neonatal estrogen exposure results in permanent epigenetic changes, we performed RNA-seq and ChIP-seq analyses of DES-treated and control mice. CD-1 mice were treated on postnatal days (PND) 1-5 with DES (2 µg/pup/day) or corn oil as a control; uterine tissues were collected on PND5. RNA-seq analysis resulted in 4,498 differentially expressed genes (>1.5 fold difference; RPKM >1; FDR <0.05). ChIP-seq was performed on uterine samples using H3K4me3, H3K27me3, H3K27acetyl and H3K4me1 as the precipitating antibodies. The most significant findings at the TSS were increased H3K4me3 at up-regulated genes (22%), increased H3K27ac at up-regulated genes (55%) and differential H3K27ac at down-regulated genes (33%). The most striking finding was differential association of H3K27ac at presumed enhancer regions; 3,012 out of 4498 altered genes (67%) had a differential H3K27ac peak associated with them and 2,962 out of 4,498 (66%) had differential H3K4me1. These differences were generally coordinated with gene expression with increased gene expression having more H3K27ac associated although a small subset of genes showed the opposite. To further investigate the mechanism of differential H3K27ac binding in enhancer regions near estrogen regulated genes, we overlapped these enhancers to Esr1 ChIP seq data; a large percentage of them overlap with Esr1 peaks (39%). We also performed motif analysis where ERE was enriched in the differential H3K27ac peaks. We further investigated Esr1’s role in differential H3K27ac enhancer binding by using a conditional uterine deletion of Esr1 by crossing Esr1 floxed mice with PgR-cre and then treating with vehicle or DES and collecting uteri on day 5. We performed a microarray and pattern analysis and determined there were 4,073 out of 4,617 altered genes (88%) protected by conditional uterine deletion of Esr1. We also performed H3K27ac ChIP seq on these samples and found a large number of these protected genes have a differential H3K27ac enhancer. Several Fox genes were up-regulated following DES treatment and Fox binding motifs were found to be enriched in both H3K27ac and H3K4me1 differential enhancer peaks. To further study the impact of Foxa2 or Foxo1, we conditionally deleted each of these using PgR-cre. There were far fewer genes impacted by deletion of either Foxa2 or Foxo1 suggesting these Fox genes are not responsible for DES induced gene expression and these two lines were not followed further. Taken together, these data suggest estrogen regulates gene expression in the neonatal mouse uterus by H3K27ac association at Esr1 binding sites near estrogen regulated genes. Changes in the epigenome during the time of treatment may contribute to the permanent alterations in gene expression observed in aged DES treated mice.
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| Overall design |
Each group has 4 biological replicates - day 5 control Esr1 WT, day5 control Esr1 cKO, day 5 DES Esr1 WT, day 5 DES Esr1 cKO, day 5 Foxa2 WT, day 5 Foxa2 cKO, day 5 Foxo1 WT, day 5 Foxo1 cKO
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| Contributor(s) |
Jefferson WN, Wang T, Kinyamu H, Padilla-Banks E, Suen A, Williams CJ |
| Citation(s) |
29648668 |
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| Submission date |
Mar 27, 2017 |
| Last update date |
Jun 26, 2018 |
| Contact name |
Wendy Jefferson |
| E-mail(s) |
jeffers1@niehs.nih.gov
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| Organization name |
NIEHS
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| Street address |
111 TW alexander Drive
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| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platforms (1) |
| GPL4134 |
Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Feature Number version) |
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| Samples (32)
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| This SubSeries is part of SuperSeries: |
| GSE104402 |
ERα Dependent Alterations in the Epigenetic Landscape of the Mouse Uterus Following Neonatal Estrogen Exposure |
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| Relations |
| BioProject |
PRJNA380628 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE97073_RAW.tar |
77.4 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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