Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.

PloS One
Xu WangAndrew G Clark

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 exhaust...Continue Reading

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Citations

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Methods Mentioned

BETA
Illumina sequencing
PCR
Assay

Software Mentioned

binom
R
BLAST
Pyrosequencing Assay Design
ELAND
Solexa
Pyrosequencing
CodonCode
Illumina Genome Analyzer
CodonCode Aligner

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