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Nucleic Acids Research Advance Access originally published online on May 1, 2008
Nucleic Acids Research 2008 36(10):3484-3493; doi:10.1093/nar/gkn155
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Nucleic Acids Research, 2008, Vol. 36, No. 10 3484-3493
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs

Aristotelis Tsirigos and Isidore Rigoutsos*

Bioinformatics and Pattern Discovery Group, IBM Thomas J. Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA

*To whom correspondence should be addressed. Tel: +(914) 945 1384; Fax: +(914) 945 4217; Email: rigoutso{at}us.ibm.com

Received February 18, 2008. Accepted March 19, 2008.

We identified the most frequent, variable-length DNA sequence motifs in the human and mouse genomes and sub-selected those with multiple recurrences in the intergenic and intronic regions and at least one additional exonic instance in the corresponding genome. We discovered that these motifs have virtually no overlap with intronic sequences that are conserved between human and mouse, and thus are genome-specific. Moreover, we found that these motifs span a substantial fraction of previously uncharacterized human and mouse intronic space. Surprisingly, we found that these genome-specific motifs are over-represented in the introns of genes belonging to the same biological processes and molecular functions in both the human and mouse genomes even though the underlying sequences are not conserved between the two genomes. In fact, the processes and functions that are linked to these genome-specific sequence-motifs are distinct from the processes and functions which are associated with intronic regions that are conserved between human and mouse. The findings show that intronic regions from different genomes are linked to the same processes and functions in the absence of underlying sequence conservation. We highlight the ramifications of this observation with a concrete example that involves the microsatellite instability gene MLH1.


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