Mouse preimplantation imprinting [RNA-seq]

In mammals, chromatin marks at imprinted genes are asymmetrically inherited from each parent to control gene expression. Many genomic imprints are determined by differentially methylated regions (DMRs), but these have not been comprehensively mapped physically or functionally in mouse preimplantation embryos. We here address this by integrating transcriptomic and epigenomic approaches. Transcriptome analysis of blastocysts from genetically distinguishable crosses identified 106 genes with previously unknown parent-of-origin-specific allelic bias (nBsX genes), and 71 novel imprinted genes with parent-of-origin-specific expression with an allelic ratio of 70:30 or greater (nBiX genes). Uniparental expression of tested nBsX and nBiX transcripts disappeared soon after implantation. Overall design: Allele-specific RNA-sequencing (SMART-Seq2) on E3.5 embryos obtained without in vitro culture from reciprocal Mus musculus musculus C57BL/6 (B6) x Mus musculus castaneus (cast) natural mating. 3 and 5 embryos were analysed from the B6 x cast (forward cross) and the cast x B6 (reverse cross) matings, respectively.