Submitted to: Physiological Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 9, 2006
Publication Date: January 1, 2007
Citation: Coutinho, L.L., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P., Gasbarre, L.C., Capuco, A.V., Smith, T.P. 2007. Discovery and profiling of bovine micrornas from immune related and embryonic tissues. Physiological Genomics. 29(1):35-43.
Interpretive Summary: Gene expression is regulated at many different levels. Regulation of protein synthesis and mRNA degradation by microRNA binding to target mRNAs is a relatively new mechanism found to be important for control of gene expression in numerous biological processes affecting cellular proliferation and differentiation. This study is the first report for cattle that identifies microRNAs involved with processes affecting animal health and development. The tissues of focus included embryo, thymus, small intestine, abomasal and mesenteric lymph nodes. Another important finding of this survey was that even though bovine microRNA sequences are strictly conserved across mammalian species, the expression of these regulatory transcripts differs when comparing similar tissues from other species. The cloning and sequencing of bovine microRNAs is the first step in understanding the role these molecules play in regulating gene networks important for immune response and early development.
MicroRNAs are small ~22 nucleotide-long non-coding RNAs capable of controlling gene expression by inhibiting translation or targeting messenger RNA for degradation. Alignment of human microRNA stem loop sequences (mir) against a recent assembly of the bovine genome draft sequence resulted in identification of 221 predicted bovine mirs. We constructed and sequenced cDNA libraries made from small RNA fractions of bovine embryo, thymus, small intestine, abomasum, and mesenteric lymph nodes, in order to validate these predictions and identify new mirs. This strategy resulted in identification of 129 putative mature microRNAs (miRs). Of these, 100 aligned to known human mirs while an additional seven novel miRs aligned to the complementary arm. The remaining 22 putative miRs did not match, but displayed characteristic mir secondary structures and 10 of these showed phylogenetic conservation among other vertebrate species. Further characterization based on sequence identity counts identified miRs that were preferentially expressed in embryo, small intestine or immune related tissues. The prevalence of bta-miR-26a in all tissues surveyed and discovery of miRs from the complementary strand of known human mirs indicated that important insights into miR regulation can be gained through comparative studies between species.