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United States Department of Agriculture

Agricultural Research Service

Title: Comprehensive Search of Bovine Micrornas Expressed in Immune and Gut Tissues by Deep Sequencing

Authors
item Sonstegard, Tad
item Matukumalli, Lakshmi - GEORGE MASON UNIVERSITY
item Coutinho, Luiz - UNIVERSITY OF SAO PAULO
item Liu, Ge
item Gasbarre, Louis
item Smith, Timothy

Submitted to: International Conference on Animal Genetics
Publication Type: Abstract Only
Publication Acceptance Date: April 6, 2006
Publication Date: August 17, 2006
Citation: Sonstegard, T.S., Matukumalli, L.K., Coutinho, L.L., Liu, G., Gasbarre, L.C., Smith, T.P. 2006. Comprehensive search of bovine micrornas expressed in immune and gut tissues by deep sequencing [abstract]. International Conference on Animal Genetics. pp. C354.

Technical Abstract: MicroRNAs (miRs) are small RNA transcripts (~22 nt long) that modulate gene expression by interfering with protein synthesis and/or targeting mRNA for degradation. Only 332 miRs have been described for humans, while estimates based on prediction algorithms identify approximately 800 microRNA stem loop loci from human genome sequence. Because of the paucity of information on bovine miRs, we initiated characterization of the miR portion of the transcriptome. Our intial effort was focused on gut and immune-related tissues considering the potential role of miRs in regulating cellular proliferation, differentiation and immune response. Small RNA derived from bovine thymus, abomasal and mesenteric lymph nodes, spleen, bone marrow, Peyer’s patches, fundic abomasum, and small intestine was isolated by gel-based size fractionation. Samples were pooled to increase the potential diversity of miRs prior to ligation of 5’ and 3’ RNA adaptors and cDNA synthesis. This cDNA was cloned and sequenced by Massively Parallel Signature Sequencing (MPSS) to generate approximately 1 million sequence tags ranging from 17 to 20 nt in length. A total of 3,001 distinct tags were identified and these tags could be clustered into 1,692 sequences. Subsequent filtering against rRNA, tRNA and snoRNA (Small Nucleolar RNA) sequences and alignment to the bovine genome assembly yielded 1,252 tags potentially corresponding to miRs. Comparison of these 1,252 tags against miRBase resulted in the identification of 178 putative bovine miRs with 130 of these having very significant matches to known vertebrate miRs. The tags that matched miRBase were 83% and 68% of the total tag counts, respectively. The remainder of the sequence tags are being analyzed as potential novel miRs. These results indicate a moderate diversity of miR expression in adult cattle tissues and suggest that less intensive sequencing of different tissues at multiple developmental stages will be optimal for miR discovery and expression profiling.

Last Modified: 4/24/2014
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