Allelic gene expression imbalance of bovine IGF2, LEP and CCL2 genes in liver, kidney and pituitary

Abstract

Allelic expression imbalance (AEI) is an important genetic factor being the cause of differences in phenotypic traits that can be heritable. Studying AEI can be useful in searching for factors that modulate gene expression and help to understand molecular mechanisms underlying phenotypic changes. Although it was commonly recognized in many species and we know many genes show allelic expression imbalance, this phenomena was not studied on a larger scale in cattle. Using the pyrosequencing method we analyzed a set of 29 bovine genes in order to find those that have preferential allelic expression. The study was conducted in three tissues: liver, pituitary and kindey. Out of the studied group of genes 3 of them—LEP (leptin), IGF2 (insulin-like growth factor 2), CCL2 (chemokine C–C motif ligand 2) showed allelic expression imbalance.Electronic supplementary materialThe online version of this article (doi:10.1007/s11033-012-2161-3) contains supplementary material, which is available to authorized users.

RNA-Seq Analyses Identify Frequent Allele Specific Expression and No Evidence of Genomic Imprinting in Specific Embryonic Tissues of Chicken

“…More than 50% and 30% of genes show ASE patterns in humans and mice, respectively 1 – 6 . In agricultural animals, ASE genes have been found related to economically important traits 7 – 9 . Particularly, ASE SNPs have been observed in response to Marek’s disease (MD) virus in chickens 10 , 11 , and selection using those ASE SNPs reduced MD incidence after one generation of selection 12 .…”

Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF

“…Any bias resulting from variations in nucleotide incorporation during pyrosequencing reaction was normalized for each gene by dividing the allelic ratio of cDNA and gDNA samples by the mean allelic ratio from gDNA. The bi-directional character of ASE was neutralized by dividing the higher percentage by the lower, as described by Olbromski et al ( 2013 ). Next, the allelic transcript ratios were log 10 -transformed and the mean allelic expression between cDNA and gDNA for each breed and tissue was compared by two-tailed t test with unequal variances (Forton et al 2007 ; Murani et al 2009 ).…”

Investigation of allele-specific expression of genes involved in adipogenesis and lipid metabolism suggests complex regulatory mechanisms of PPARGC1A expression in porcine fat tissues

“…Any bias resulting from variations in nucleotide incorporation during pyrosequencing reaction was normalized by dividing the allelic ratio of cDNA and gDNA samples by a mean allelic ratio derived from gDNA for each gene tested [ 45 , 46 ]. Individual samples were defined as imbalanced when the allelic proportion (mean of two measurements) exceeded a 60:40 threshold [ 46 ], i.e. allelic transcript ratios were > 1.5 for one-directional and < 0.667 or > 1.5 for bi-directional ASE.…”

“…The deviation of mean allelic expression between cDNA and gDNA for each breed was tested by two-tailed t test with unequal variances using log 10 -transformed allelic transcript ratios [ 19 , 45 ]. For PPARGC1A , the bi-directional character of ASE was neutralized by dividing the higher percentage by the lower as previously described [ 46 ].…”