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Series GSE119882 Query DataSets for GSE119882
Status Public on Feb 28, 2019
Title Imprinted gene expression at the Dlk1-Dio3 cluster is controlled by both maternal and paternal IG-DMRs in a tissue-specific fashion.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Imprinting at the Dlk1-Dio3 cluster is controlled by the IG-DMR, an imprinting control region differentially methylated between maternal and paternal chromosomes. The maternal IG-DMR is essential for imprinting control, functioning as a cis enhancer element. Meanwhile, DNA methylation at the paternal IG-DMR is thought to prevent enhancer activity. To explore whether suppression of enhancer activity at the methylated IG-DMR requires the transcriptional repressor TRIM28, we analyzed Trim28chatwo embryos and performed epistatic experiments with IG-DMR deletion mutants. We found that while TRIM28 regulates the enhancer properties of the paternal IG-DMR, it also controls imprinting through other mechanisms. Additionally, we found that the paternal IG-DMR, previously deemed dispensable for imprinting, is required in certain tissues, demonstrating that imprinting is regulated in a tissue-specific manner. Using ChRO-seq to analyze nascent transcription, we show that different tissues have a distinctive regulatory landscape at the Dlk1-Dio3 cluster, providing insight into potential mechanisms of tissue-specific imprinting control. ChRO-seq identified 30 novel transcribed regulatory elements, including a candidate regulatory region that depends on the paternal IG-DMR. Together, our findings challenge the model that Dlk1-Dio3 imprinting is regulated through a single mechanism and demonstrate that different tissues use distinct strategies for imprinting control.
 
Overall design Duplicates of PRO-seq in E14.5 liver and yolk sac samples obtained from mating C57BL/6J females with males of a mixed genetic background (C57BL/6J and CAST/EiJ). Males in this cross were selected to exclusively carry CAST/EiJ polymophisms at the Dlk1/Gtl2 locus on chromosome 12
 
Contributor(s) Alexander KA, Garcia-Garcia MJ
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Submission date Sep 12, 2018
Last update date Mar 25, 2019
Contact name Katherine Ann Alexander
E-mail(s) katalex115@gmail.com
Phone 503-702-5140
Organization name University of Pennsylvania
Street address 3400 Civic Center Blvd.
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (4)
GSM3386268 Liver Rep1
GSM3386269 Liver Rep2
GSM3386270 Yolk Sac Rep1
Relations
BioProject PRJNA490551
SRA SRP161618

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Supplementary file Size Download File type/resource
GSE119882_RAW.tar 550.1 Mb (http)(custom) TAR (of BED, BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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