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A Caenorhabditis motif compendium for studying transcriptional gene regulation

BACKGROUND: 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 s...

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Detalles Bibliográficos
Autores principales: Dieterich, Christoph, Sommer, Ralf J
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248174/
https://www.ncbi.nlm.nih.gov/pubmed/18215260
http://dx.doi.org/10.1186/1471-2164-9-30
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author Dieterich, Christoph
Sommer, Ralf J
author_facet Dieterich, Christoph
Sommer, Ralf J
author_sort Dieterich, Christoph
collection PubMed
description BACKGROUND: 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. DESCRIPTION: 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. CONCLUSION: The nematode genomes align surprisingly well despite high neutral substitution rates. Our pipeline delivers motif sets by three alternative strategies. Each set contains less than 400 motifs, which are significantly conserved and correlated with 214 out of 270 tested gene expression conditions. This motif compendium is an entry point to comprehensive studies on nematode gene regulation. The website: http://corg.eb.tuebingen.mpg.de/CMC has extensive query capabilities, supplements this article and supports the experimental list.
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spelling pubmed-22481742008-02-20 A Caenorhabditis motif compendium for studying transcriptional gene regulation Dieterich, Christoph Sommer, Ralf J BMC Genomics Database BACKGROUND: 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. DESCRIPTION: 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. CONCLUSION: The nematode genomes align surprisingly well despite high neutral substitution rates. Our pipeline delivers motif sets by three alternative strategies. Each set contains less than 400 motifs, which are significantly conserved and correlated with 214 out of 270 tested gene expression conditions. This motif compendium is an entry point to comprehensive studies on nematode gene regulation. The website: http://corg.eb.tuebingen.mpg.de/CMC has extensive query capabilities, supplements this article and supports the experimental list. BioMed Central 2008-01-23 /pmc/articles/PMC2248174/ /pubmed/18215260 http://dx.doi.org/10.1186/1471-2164-9-30 Text en Copyright © 2008 Dieterich and Sommer; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Dieterich, Christoph
Sommer, Ralf J
A Caenorhabditis motif compendium for studying transcriptional gene regulation
title A Caenorhabditis motif compendium for studying transcriptional gene regulation
title_full A Caenorhabditis motif compendium for studying transcriptional gene regulation
title_fullStr A Caenorhabditis motif compendium for studying transcriptional gene regulation
title_full_unstemmed A Caenorhabditis motif compendium for studying transcriptional gene regulation
title_short A Caenorhabditis motif compendium for studying transcriptional gene regulation
title_sort caenorhabditis motif compendium for studying transcriptional gene regulation
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248174/
https://www.ncbi.nlm.nih.gov/pubmed/18215260
http://dx.doi.org/10.1186/1471-2164-9-30
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