Tuesday, June 21, 2011

Paper: "High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain", extracts

Science 6 August 2010:
vol. 329 no. 5992 pp. 643-648

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain
Christopher Gregg, Jiangwen Zhang, Brandon Weissbourd, Shujun Luo, Gary P. Schroth, David Haig, Catherine Dulac

This paper shows that in mice there are 8 times more genes that are imprinted than it was previously known and that imprinting is more of a continuum of differential expression between parental alleles than strict monoallelic expression as previously defined.

Extracts:

-Currently, fewer than 100 imprinted genes have been identified.

-Parent-specific biases emerged as a continuum from the data set, which suggested that imprinting may manifest as relative allele-specific expression bias, rather than strict monoallelic transcription, or that allelic bias is cell-type specific and is partially masked by cellular heterogeneity in brain samples.

-Imprinted genes and genes with imprinted features were identified by the presence of one or more SNP sites exhibiting a significant paternal or maternal expression bias, as described above. This approach enabled us to identify 1308 candidate imprinted loci, among which were 824 genes annotated in the University of California Santa Cruz genome database (UCSC) and 484 putative noncoding RNAs (ncRNAs) annotated in the functional RNA database (fRNAdb) (4.1% of the 11,545 ncRNAs assessed).

-Sixty-one percent of genes identified in the E15 brain were maternally expressed genes (MEGs), which revealed a significant maternal bias in the developing brain [paternally expressed genes (PEGs), 215; MEGs, 338; P < 0.0001; hi2 analysis). In contrast, a paternal bias was observed in both the adult pre optic area POA (PEGs, 172; MEGs, 84; P < 0.0001; hi2 analysis) and the adult medial prefrontal cortex mPFC (PEGs, 109; MEGs, 44; P < 0.0001; hi2 analysis), such that ~70% of genes identified in the adult brain were PEGs.



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