dc.contributor.authorYang, Peng
dc.contributor.authorWu, Min
dc.contributor.authorGuo, Jing
dc.contributor.authorKwoh, Chee Keong
dc.contributor.authorPrzytycka, Teresa M.
dc.contributor.authorZheng, Jie
dc.date.accessioned2014-05-19T03:11:12Z
dc.date.available2014-05-19T03:11:12Z
dc.date.copyright2014en_US
dc.date.issued2014
dc.identifier.citationYang, P., Wu, M., Guo, J., Kwoh, C. K., Przytycka, T. M., & Zheng, J. (2014). LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms. BMC Bioinformatics, 15:48.en_US
dc.identifier.issn1471-2105en_US
dc.identifier.urihttp://hdl.handle.net/10220/19368
dc.description.abstractBackground: As a fundamental genomic element, meiotic recombination hotspot plays important roles in life sciences. Thus uncovering its regulatory mechanisms has broad impact on biomedical research. Despite the recent identification of the zinc finger protein PRDM9 and its 13-mer binding motif as major regulators for meiotic recombination hotspots, other regulators remain to be discovered. Existing methods for finding DNA sequence motifs of recombination hotspots often rely on the enrichment of co-localizations between hotspots and short DNA patterns, which ignore the cross-individual variation of recombination rates and sequence polymorphisms in the population. Our objective in this paper is to capture signals encoded in genetic variations for the discovery of recombination-associated DNA motifs. Results: Recently, an algorithm called "LDsplit" has been designed to detect the association between single nucleotide polymorphisms (SNPs) and proximal meiotic recombination hotspots. The association is measured by the difference of population recombination rates at a hotspot between two alleles of a candidate SNP. Here we present an open source software tool of LDsplit, with integrative data visualization for recombination hotspots and their proximal SNPs. Applying LDsplit on SNPs inside an established 7-mer motif bound by PRDM9 we observed that SNP alleles preserving the original motif tend to have higher recombination rates than the opposite alleles that disrupt the motif. Running on SNP windows around hotspots each containing an occurrence of the 7-mer motif, LDsplit is able to guide the established motif finding algorithm of MEME to recover the 7-mer motif. In contrast, without LDsplit the 7-mer motif could not be identified. Conclusions: LDsplit is a software tool for the discovery of cis-regulatory DNA sequence motifs stimulating meiotic recombination hotspots by screening and narrowing down to hotspot associated SNPs. It is the first computational method that utilizes the genetic variation of recombination hotspots among individuals, opening a new avenue for motif finding. Tested on an established motif and simulated datasets, LDsplit shows promise to discover novel DNA motifs for meiotic recombination hotspots.en_US
dc.language.isoenen_US
dc.relation.ispartofseriesBMC bioinformaticsen_US
dc.rights© 2014 Yang et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.en_US
dc.subjectDRNTU::Engineering::Computer science and engineering
dc.titleLDsplit : screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphismsen_US
dc.typeJournal Article
dc.contributor.schoolSchool of Computer Engineeringen_US
dc.identifier.doihttp://dx.doi.org/10.1186/1471-2105-15-48
dc.description.versionPublished versionen_US


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