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Physiol. Genomics 29: 35-43, 2007. First published November 14, 2006; doi:10.1152/physiolgenomics.00081.2006 Free Article
1094-8341/07 $8.00
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Received 4 May 2006; accepted in final form 8 November 2006.
Physiological Genomics 29:35-43 (2007)
1094-8341/07 $8.00 © 2007 American Physiological Society

Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues

Luiz L. Coutinho2,*, Lakshmi K. Matukumalli1,3,*, Tad S. Sonstegard1, Curtis P. Van Tassell1, Louis C. Gasbarre1, Anthony V. Capuco1 and Timothy P. L. Smith4

1 United States Department of Agriculture, Agricultural Research Center, Beltsville Area Research Center, Beltsville, Maryland
2 University of Sao Paulo-ESALQ, Piracicaba, SP, Brazil
3 Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia
4 United States Department of Agriculture, Agricultural Research Center, U.S. Meat Animal Research Center, Clay Center, Nebraska

MicroRNAs are small ~22 nucleotide-long noncoding RNAs capable of controlling gene expression by inhibiting translation. Alignment of human microRNA stem-loop sequences (mir) against a recent draft sequence assembly of the bovine genome resulted in identification of 334 predicted bovine mir. We sequenced five tissue-specific cDNA libraries derived from the small RNA fractions of bovine embryo, thymus, small intestine, and lymph node to validate these predictions and identify new mir. This strategy combined with comparative sequence analysis identified 129 sequences that corresponded to mature microRNAs (miR). A total of 107 sequences aligned to known human mir, and 100 of these matched expressed miR. The other seven sequences represented novel miR expressed from the complementary strand of previously characterized human mir. The 22 sequences without matches displayed characteristic mir secondary structures when folded in silico, and 10 of these retained sequence conservation with other vertebrate species. Expression analysis based on sequence identity counts revealed that some miR were preferentially expressed in certain tissues, while bta-miR-26a and bta-miR-103 were prevalent in all tissues examined. These results support the premise that species differences in regulation of gene expression by miR occur primarily at the level of expression and processing.

small RNA; microRNA; embryo; immune




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[Abstract] [Full Text] [PDF]


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