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

Abstract：

: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 analysis did not reveal any novel imprinted genes, but detected extended parental allele-specific transcripts in several known imprinted domains: maternal allele-specific transcripts downstream of Grb10 and downstream of Meg3, Rtl1as and Rian in the Dlk1-Dio3 cluster, an imprinted domain implicated in development and pluripotency. We detected paternal allele-specific transcripts 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. The 5' end points of the imprinted transcript extensions 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 imprinted genes. Based on the imprinting signature of MEFs, these cells provide valid models for understanding the biochemical aspects of genomic imprinting.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Tran DA,Bai AY,Singh P,Wu X,Szabó PE

doi

10.1093/nar/gkt1042

subject

Has Abstract

pub_date

2014-02-01 00:00:00

pages

1772-83

issue

3

eissn

0305-1048

issn

1362-4962

pii

gkt1042

journal_volume

42

pub_type

杂志文章

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