This article is part of the supplement: Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics
Evidence for intron length conservation in a set of mammalian genes associated with embryonic development
National University of Ireland, Galway, University Road, Galway, Republic of Ireland
BMC Bioinformatics 2011, 12(Suppl 9):S16 doi:10.1186/1471-2105-12-S9-S16Published: 5 October 2011
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.
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.
Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.