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Genetic variations modulate gene expression at the transcriptionnal or post-transcriptionnal level and they may therefore alter an individual's phenotype. Measuring the differential allelic expression at the locus of heterozygotes in an individual, a phenomenon called Allele Specific Expression (ASE) can be used to detect variants having a cis-regulating effect on gene expression. With the massive DNA and RNA seuqencing methods available, it is now possible to study this allelic expression bias of a whole genome.

In cattle, this type of a study has only been performed on Holstein. In a study that was recently published in Scientific Reports, Dominique Rocha and his colleagues from the Animal Genetics and Integrative Biology Unit (GABI UMR 1313, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas) analyzed the ASE at the genome scale using 19 samples of animal muscle from Limousine cattle. The scientists sequenced the complete genomes and transcriptomes of these animals and identified 5 658 Single Nucleotide Polymorphisms (SNP) showing a biais of allele expression in 13% of the genes expressed. They also noted a biais for allele expression in the AOX1, PALLD and CAST genes. They also found 2 107 "SNP ASE" located in the regions associated with traits linked to meat quality. In order to identify the regulating causing variants that explain ASE, the scientists saught SNP that modify the linkage sites for transcription factors or microRNA targetting sites. They also identified an SNP in the 3'UTR region of the PRNP gene which could be a modifying causal variation. In this study they showed that ASE is frequent in muscle samples.

UMR Génétique Animale et Biologie Intégrative

G2B Team
Contact : dominique.rocha@inra.fr