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Evidence for turnover of functional noncoding DNA in mammalian genome evolution.

Smith, Nick G.C. and Brandström, Mikael and Ellegren, Hans (2004) Evidence for turnover of functional noncoding DNA in mammalian genome evolution. Genomics, 84 (5). pp. 806-813.

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Abstract

The vast majority of the mammalian genome does not code for proteins, and a fundamental question in genomics is: What proportion of the noncoding mammalian genome is functional? Most attempts to address this issue use sequence comparisons between highly diverged mammals such as human and mouse to identify conservation due to negative selection. But such comparisons will underestimate the true proportion of functional noncoding DNA if there is turnover, if patterns of negative selection change over time. Here we test whether the inferred level of negative selection differs between different pairwise species comparisons. Using a multiple alignment of more than a megabase of contiguous sequence from eight mammalian species, we find a strong negative relationship between inferred levels of negative selection and pairwise divergence using 21 pairwise comparisons. This result suggests that there is a high rate of turnover of functional noncoding elements in the mammalian genome, so measures of functional constraint based on human–mouse comparisons may seriously underestimate the true value.

Item Type: Article
Journal or Publication Title: Genomics
Subjects: Q Science > QA Mathematics
Departments:
ID Code: 9535
Deposited By: Mrs Yaling Zhang
Deposited On: 16 Jun 2008 08:47
Refereed?: Yes
Published?: Published
Last Modified: 26 Jul 2012 18:38
Identification Number:
URI: http://eprints.lancs.ac.uk/id/eprint/9535

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