GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
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
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Sep 12, 2018
Last update date Mar 25, 2019
Contact name Katherine Ann Alexander
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
BioProject PRJNA490551
SRA SRP161618

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap