Sequence Analysis and Tissue Expression of the Putative Bovine Imprinted ASCL2 Gene

Achaete-scute like-2 (ASCL2) gene is a maternally expressed gene encoding a lineage-specific transcription factor essential for neurectoderm and trophectoderm development and implicated in pre-natal and post-natal development in mammals. To better understand its functional role in cattle using comparative genomics, we performed in-silico sequence analysis to identify motifs of the bovine orthologs in human and mouse as well as tissue expression analysis in adult cattle. We identified three site-specific motifs (cAMP and cGMP dependent protein kinase phosphorylation, casein kinase II phosphorylation and Protein Kinase C phosphorylation) in both cattle and humans within the highly conserved bHLH domain. Sequence comparison in cattle, human and mouse identified 657 polymorphic sites in the genomic sequences with a nucleotide diversity (Pi) of 0.23, 0.32 and 0.33 for the pair-wise comparisons between cattle/human, cattle/mouse and human/mouse respectively. A pairwise comparison of the coding sequence of cattle and human revealed a significant deviation from the neutral expectation (d_N/d_S <1, Fisher’s Exact Test, p < 0.05). This suggests that negative selection may be responsible for directional amino acid changes and similarities found between cattle and human. Two non-synonymous SNPs were found within 1kb of the cloned cDNA. Our study also shows the expression of the bovine ASCL2 mRNA in 8 adult tissues (muscle, heart, liver, kidney, skin, brain, spinal cord and lymph node). The conservation of the three motifs in cattle and human may provide a better understanding of the mechanism of epigenetic regulation of the bovine ASCL2 gene.