DNA Sequence Characteristics and Phylogenetics of Putative Imprinted Genes on Bovine Chromosome 29

Abstract

Cattle are important livestock species with huge genetic resource for food security, agriculture and livelihoods. Over 60% of its genes are homologous to all mammalian species which creates a molecular basis for conducting comparative genomic analysis. Genomic imprinting has been implicated in a variety of biological functions and so identification of new or verification of known imprinted genes in livestock species is of high agricultural and biomedical importance. Fourteen (14) putative imprinted genes on bovine chromosome 29 (Bta 29) as well as the human (Hg 11) and mouse (Mm 7) orthologs were computationally characterized with respect to the CpG islands (CGI), transcription factor binding elements and sequence motif. Phylogenetic analysis was conducted across the three species for each of the genes identified to have promoter CGI. Promoter CGI were identified in ASCL2, TSSC4, CDKN1C, KCNQ1, PHLDA2 and NAP1L4. The promoter CGI were enriched with CpG containing transcription factor binding sites. Generally, it was observed that cattle was more closely related to human than mouse and that natural selection was the force driving the evolutionary change between the three species. Protein kinase motifs involved in phosphorylation were identified in the amino-acid sequences of ASCL2, TSSC4, PHLDA2 and NAP1L4. Our results suggest the post-translation regulation of imprinting and that the predicted promoter CGI can be assayed to determine molecular function, gene expression and DNA methylation status of the bovine putative imprinted genes.

Tissue Expression Profiles of 5 Putative Imprinted Genes in Bovine Chromosome 29

“…This is consistent with the associated molecular functions of the respective genes [17]. The presence of the protein kinases (cAMP, PKC, CK2) involved in glycogen regulation, muscle development and cellular regulation earlier reported by Bamidele et al [3] to be found in TSSC4, PHLDA2 and NAP1L4, could also explain the up-regulation of the respective gene transcripts in the muscle tissue system. This is in contrast to that observed in KCNQ1 and CDKN1C wherein no protein kinases were earlier found and whose transcripts were only upregulated in the nervous and secretory tissue systems respectively.…”

“…have also been reported to be actively involved in the complex regulatory system [21]- [23]. Two of these regulators (SOX and CK2) have been reportedly identified in NAP1L4 gene [3] which according to Busca and Balotti [22], play a significant role in the regulation of melanogenesis. Several studies in human and mice have reported that the inhibition of the CK2 is specifically linked to variations in skin pigmentations [24] [25].…”

“…In addition to the unique expression patterns of imprinted genes, their relative abundance and mRNA levels have been reported to be of significance to genomic imprinting [2]. In a previous study conducted on the sequence characteristics of some putative imprinted genes on bovine chromosome 29, Bamidele et al [3] had identified 5 genes for further experimental analysis. These genes were TSSC4, CDKN1C, KCNQ1, PHLDA and NAP1L4.…”