Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain

Abstract

Imprinted genes display differential allelic expression in a manner that depends on the sex of the transmitting parent. The degree of imprinting is often tissue-specific and/or developmental stage-specific, and may be altered in some diseases including cancer. Here we applied Illumina/Solexa sequencing of the transcriptomes of reciprocal F1 mouse neonatal brains and identified 26 genes with parent-of-origin dependent differential allelic expression. Allele-specific Pyrosequencing verified 17 of them, including three novel imprinted genes. The known and novel imprinted genes all are found in proximity to previously reported differentially methylated regions (DMRs). Ten genes known to be imprinted in placenta had sufficient expression levels to attain a read depth that provided statistical power to detect imprinting, and yet all were consistent with non-imprinting in our transcript count data for neonatal brain. Three closely linked and reciprocally imprinted gene pairs were also discovered, and their pattern of expression suggests transcriptional interference. Despite the coverage of more than 5000 genes, this scan only identified three novel imprinted refseq genes in neonatal brain, suggesting that this tissue is nearly exhaustively characterized. This approach has the potential to yield an complete catalog of imprinted genes after application to multiple tissues and developmental stages, shedding light on the mechanism, bioinformatic prediction, and evolution of imprinted genes and diseases associated with genomic imprinting.

SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data

“…If these DMRs control the imprinting of one or more genes, these regions are called imprinting control regions (ICRs). It is known that many of these ICRs PAGE 11 OF 14 Nucleic Acids Research, 2014, Vol. 42, No.…”

“…The samples were sequenced according to the protocol described in the paper of De Meyer et al (29) with some additional modifications: (i) After DNA fragmentation, the methylated fragments PAGE 3 OF 14 Nucleic Acids Research, 2014, Vol. 42, No.…”

“…Although imprinting is a well-investigated topic and several studies already provided evidence (e.g. compu-tational predictions based on DNA sequence characteristics or detection of monoallelic expression) of some regions with monoallelic DNA-methylation (2,3,(10)(11)(12)(13)(14)(15)(16), only a few imprinted regions are well characterized in humans, like, for example, the IGF2/H19 region. Furthermore, monoallelic methylation has recently been recognized as very common at non-imprinted loci affecting autosomal genes, regulating, for example, the production of specific antibodies and receptors in the immune system as well as the selection of olfactory receptors (17,18).…”

Using next-generation RNA sequencing to identify imprinted genes

“…To search for novel imprinted genes genome-wide in an unbiased way, we and others have applied next-generation RNA sequencing (RNA-seq) and quantitatively measured the allele-specific expression in RNA samples from reciprocal crosses of inbred mouse strains. This was accomplished by directly counting the number reference/alternative allelecontaining reads at polymorphic SNP positions in the parental genome (Babak et al, 2008;Wang et al, 2008Wang et al, , 2011Gregg et al, 2010a, b;DeVeale et al, 2012;Okae et al, 2012). This approach has been successful in identifying a number of additional imprinted genes in mice.…”

Imprinting meets genomics: new insights and new challenges

“…Genomics approaches to identify imprinted genes are also being applied in mammalian systems [14][15][16]. This research faces many of the same challenges as in plants and offers additional useful insight.…”