Transcriptomics

Dataset Information

241

Characterization of the Imprinting Signature of Mouse Embryo Fibroblasts by RNA Deep Sequencing


ABSTRACT: Mouse embryo fibroblasts (MEFs) closely resemble mouse embryos and are convenient sources for biochemical studies when cell number may be limiting from mouse embryos. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we characterized them using strand- and allele-specific RNA deep sequencing. We used Sequenom allelotyping in embryo and adult organs to verify parental allele-specific expression patterns. We found correct parental allele-specific transcription of 32 known ubiquitously imprinted genes in MEFs. Our analysis did not reveal any novel imprinted genes in MEFs, but detected extended parental allele-specific transcription in several known imprinted domains: maternal allele-specific transcription downstream of Grb10 and downstream of Meg3, Rtl1as and Rian in the Dlk1-Dio3 cluster, an imprinted domain implicated in development. We detected paternal allele-specific transcription downstream of Nespas, Peg3, Peg12 and Snurf/Snrpn. These imprinted transcript extensions were not unique to MEFs, but were also present in other somatic cells. Their 5’ end points did not carry opposing chromatin marks or parental allele-specific DNA methylation, suggesting that their parental allele-specific transcription is under the control of the extended genes. Based on the imprinting signature of MEFs, they provide valid models for understanding the biochemical aspects of genomic imprinting. Strand-specific and parental allele-specific RNA-seq was done in female mouse embryo fibroblasts.

ORGANISM(S): Mus musculus  

SUBMITTER: Piroska E Szabo   Xiwei Wu  Diana Tran 

PROVIDER: E-GEOD-49538 | ArrayExpress | 2013-11-18

SECONDARY ACCESSION(S): GSE49538SRP028516PRJNA214195

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Characterization of the imprinting signature of mouse embryo fibroblasts by RNA deep sequencing.

Tran Diana A DA   Bai Angela Y AY   Singh Purnima P   Wu Xiwei X   Szabó Piroska E PE  

Nucleic Acids Research 20131111 3


Mouse embryo fibroblasts (MEFs) are convenient sources for biochemical studies when cell number in mouse embryos is limiting. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we performed strand- and allele-specific RNA deep sequencing. We used sequenom allelotyping in embryo and adult organs to verify parental allele-specific expression. Thirty-two known ubiquitously imprinted genes displayed correct parental allele-specific transcripts in MEFs. Our analys  ...[more]

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