A Caenorhabditis motif compendium for studying transcriptional gene regulation.

BMC Genomics
Christoph Dieterich, Ralf J Sommer

Abstract

Controlling gene expression is fundamental to biological complexity. The nematode Caenorhabditis elegans is an important model for studying principles of gene regulation in multi-cellular organisms. A comprehensive parts list of putative regulatory motifs was yet missing for this model system. In this study, we compile a set of putative regulatory motifs by combining evidence from conservation and expression data. We present an unbiased comparative approach to a regulatory motif compendium for Caenorhabditis species. This involves the assembly of a new nematode genome, whole genome alignments and assessment of conserved k-mers counts. Candidate motifs are selected from a set of 9,500 randomly picked genes by three different motif discovery strategies. Motif candidates have to pass a conservation enrichment filter. Motif degeneracy and length are optimized. Retained motif descriptions are evaluated by expression data using a non-parametric test, which assesses expression changes due to the presence/absence of individual motifs. Finally, we also provide condition-specific motif ensembles by conditional tree analysis. The nematode genomes align surprisingly well despite high neutral substitution rates. Our pipeline delivers motif ...Continue Reading

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Citations

Jan 25, 2008·BMC Genomics·Christoph Dieterich, Ralf J Sommer
Aug 19, 2008·Developmental Biology·Vikas Ghai, Jeb Gaudet
Jun 24, 2020·PLoS Neglected Tropical Diseases·Alexandra GroteElodie Ghedin

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