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This article is part of the supplement: Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

Open Access Proceedings

Evidence for intron length conservation in a set of mammalian genes associated with embryonic development

Cathal Seoighe* and Paul K Korir

Author Affiliations

National University of Ireland, Galway, University Road, Galway, Republic of Ireland

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BMC Bioinformatics 2011, 12(Suppl 9):S16  doi:10.1186/1471-2105-12-S9-S16

Published: 5 October 2011

Abstract

Background

We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples of genes that showed the most extreme conservation of total intron content in mammals.

Results

Gene sets annotated as being involved in pattern specification in the early embryo or containing the homeobox DNA-binding domain, were significantly enriched among genes with highly conserved intron content. We used ancestral sequences reconstructed with probabilistic models that account for insertion and deletion mutations to distinguish insertion and deletion events on lineages leading to human and mouse from their last common ancestor. Using a randomization procedure, we show that genes containing the homeobox domain show less change in intron content than expected, given the number of insertion and deletion events within their introns.

Conclusions

Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.