Intron retention in Cathelicidin-4 in river buffalo

Abstract

Abstract Background The function of cathelicidins-4 (CATH4) is not limited to microbial killing, but extends to other aspects of immunity and tissue repair. The presence of different CATH4 variants including intron retention affects the immunity system. Intron retention, in buffalo, is not fully studied. In this study, we investigated CATH4 mRNA in river buffalo and their variants, which can be used in the future for selecting buffalo resistant to diseases. Results and conclusion Analysis of CATH4 mRNA in river buffalo (Egyptian breed) revealed the presence of a novel variant (1073 bp) which includes unspliced part of intron 3 (469 bp) in addition to previously reported unspliced complete intron 1 (103) and intron 2 (137 bp). Identification of intron retention was conducted by comparing the amplified unspliced cDNA and DNA sequences. Analysis of the 3 retained intronic regions revealed the presence of the 4 splice signals, needed for splicing which include the 5′ (GT) and 3′ (AG) intron splice sites, the branch point, and the polypyrimidine tract. However, in the intron-retained sequence, the polypyrimidine tract was weak. It contained 6 and 4 non-continuous uridine stretch in introns 1 and 2, respectively, (intron 3 was partial) which may have caused introns retention. In addition, analysis of the unspliced sequence showed three unique exonic SNPS located close to the splice sites (1 to 22 nucleotides) and five SNPs in retained intronic regions located near the splice sites (18 to 246 nucleotides away from exon/intron boundaries) which may be related to the retention of the three introns.

Keywords

• Egyptian buffalo
• Cathelicidine-4
• CATH4 splice sites
• cDNA
• SNPs