Yak TNFα gene: Sequence analysis reveals high amino acid identity with cattle but variations in potential binding sites for transcription factors

Abstract

The present study reports the sequence characterization of TNFα gene in Indian yak (Bos grunniens). A total of 2786
nucleotides long sequence data were generated by primer walking method covering complete TNFα gene and 5’ upstream
basal promoter region. Predicted coding DNA sequence (CDS) of yak TNFα gene revealed only 4 nucleotide changes
compared to that of cattle however, without altering amino acid sequence. Similarly, predicted CDS of yak had a very
high sequence similarity with other ruminants like buffalo (99%), goat (96.2%) and sheep (95.9%). Phylogenetic analysis
of conceptualized amino acid sequences of TNFα gene of various species revealed the clustering of yak sequence with
other ruminants under a major group distinct from the non-ruminants species. A total of 14 putative transcription factor
binding sites were predicted within 818 nucleotides long 5’upstream region of yak TNFα gene. Interestingly, 2 potential
binding sites for transcription factors Elk-1 and v-Myb were present in yak and indicine cattle but absent in taurine
cattle due to an A-G transition within promoter at 526 nucleotides upstream to start codon. Variations within 5’ upstream
sequence need to be explored further for their functional and regulatory roles in altering expression level of TNFα gene
in these species.