International Mammalian Genome Society

logo18th International Mouse Genome Conference

17-22 October 2004, Seattle, USA


ORAL PRESENTATION

TUESDAY OCTOBER 19

2.30pm – 2.45pm

ESTABLISHING THE FUNCTIONAL POTENTIAL OF CONSERVED NON-CODING SEQUENCES

Grice EA1, Emison E1, Portnoy ME2, Rochelle E1, Comparative Sequencing Program NISC2, Green ED2, Chakravarti A1, McCallion AS1

1 McKusick-Nathans Institute of Genetics Medicine, Johns Hopkins University, Baltimore, United States, 2 National Human Genome Research Institute, National Institutes of Health, Bethesda, United States

Mutations in regulatory sequences influence tissue specificity, timing and/or level of the corresponding gene product.  Despite the predicted role of regulatory mutations in human genetic disease, their nature and identity remain largely unknown. Sequence conservation among distantly related species is proposed to be an indicator of sequence functionality.  Sequence analysis of putative regulatory elements at known disease genes may reveal variants that are significantly associated with disease.  However, it provides little direct evidence of causation. Consequently, functional non-coding sequences and the variants that compromise them must be interrogated in model organisms like the mouse.  We have combined the use of computational tools, in vitro pre-screens and human genetic data to preliminarily interrogate conserved sequences.  We are employing the mouse to further examine the functional potential of critical subsets of non-coding conserved sequences.  The RET gene is ideal for the development of such strategies - as coding sequence mutations are known and non-coding mutations are predicted among a known disease population (Hirschsprung disease: HSCR). We recently completed comparative analysis of ~350 Kb of genomic sequence from 13 vertebrates, identifying multi-species conserved sequences (MCSs) at RET.   We will report the analysis of >30 such non-coding MCSs, demonstrating that >85% can function as enhancers/suppressors in vitro. We also report the identification of a HSCR-associated variant in an MCS in RET intron 1 and will discuss its functional impact. Our long-term objective is to develop rapid screens to uncover the nature, identity and phenotypic impact of regulatory mutations in critical developmental / disease genes.

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