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United States Department of Agriculture

Agricultural Research Service

Title: In Silico Prediction of Regulatory Elements by Phylogenetic Footprinting.

Authors
item Liu, Ge
item Yang, Jianqu - CASE WESTERN
item Matukumalli, Lakshmi - GEORGE MASON UNIVERSITY
item Sonstegard, Tad
item Van Tassell, Curtis
item Hanson, Richard - CASE WESTERN

Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: April 26, 2006
Publication Date: April 26, 2006
Citation: Liu, G., Yang, J., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P., Hanson, R.W. 2006. In silico prediction of regulatory elements by phylogenetic footprinting. [abstract] BARC Poster Day. Beltsville, MD. pp. 32.

Technical Abstract: Comparative genomics provides a powerful approach for the systematic discovery of functional elements, by identifying highly conserved sequences due to evolutionary constraints. Besides protein-coding, these functional elements are likely to function as regulatory elements, RNA genes and structural motifs. However, it has been difficult to recognize these short degenerated functional elements in a systematic fashion. Most of these elements remain unidentified, such as cis DNA elements in promoters acting as transcription factor binding sites (TFBS) and microRNA target sites in 3’ UTR. We designed a systematic approach combining position-weight matrixes and phylogenetic footprinting to systematically identify functional elements in bovine promoters and 3’ UTRs by cross-species comparison of several mammals. To verify our approach, we analyzed some well-studied promoters and the initial analysis yielded most previously known TFBS and several new candidate sites. We began to test these new sites by experimental validation and the preliminary results are promising. We are in the process of evaluating and customizing existing matrixes and algorithms in order to apply them to individual pathways and the whole genome. This study will provide a comprehensive catalog of functional elements in bovine promoters and 3’ UTRs and may provide the first insights into the fundamental understanding of genome-wide regulation and variation in the bovine gene expression.

Last Modified: 10/24/2014
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