Nucleic Acids Research Advance Access originally published online on February 10, 2009
Nucleic Acids Research 2009 37(6):2003-2013; doi:10.1093/nar/gkp077
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Nucleic Acids Research, 2009, Vol. 37, No. 6 2003-2013
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Molecular Biology |
Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites
1Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA and 2Department of Biological Sciences, KAIST, Daejeon 305-701, South Korea
*To whom correspondence should be addressed. Tel: +1 225-578-7692; Fax: +1 225-578-2597; Email: jkim{at}lsu.edu
Received August 13, 2008. Revised January 19, 2009. Accepted January 27, 2009.
We have developed a new bioinformatics approach called ECMFinder (Evolutionary Conserved Motif Finder). This program searches for a given DNA motif within the entire genome of one species and uses the gene association information of a potential transcription factor-binding site (TFBS) to screen the homologous regions of a second and third species. If multiple species have this potential TFBS in homologous positions, this program recognizes the identified TFBS as an evolutionary conserved motif (ECM). This program outputs a list of ECMs, which can be uploaded as a Custom Track in the UCSC genome browser and can be visualized along with other available data. The feasibility of this approach was tested by searching the genomes of three mammals (human, mouse and cow) with the DNA-binding motifs of YY1 and CTCF. This program successfully identified many clustered YY1- and CTCF-binding sites that are conserved among these species but were previously undetected. In particular, this program identified CTCF-binding sites that are located close to the Dlk1, Magel2 and Cdkn1c imprinted genes. Individual ChIP experiments confirmed the in vivo binding of the YY1 and CTCF proteins to most of these newly discovered binding sites, demonstrating the feasibility and usefulness of ECMFinder.