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Genomics

Decoding the regulatory genome

Nature Reviews Genetics volume 8, pages 908–909 (2007)Cite this article

Existing methods for predicting regulatory elements are limited to specific species or to particular types of element and expression data — this is because they rely on underlying assumptions about the relationship between elements and expression patterns. Elemento and colleagues developed a method — FIRE (Finding Informative Regulatory Elements) — that dispenses with such assumptions, instead directly quantifying the relationship between gene expression levels and potential regulatory motifs using information theory

The authors tested their approach on gene clusters derived from existing Saccharomyces cerevisiae microarray data, using FIRE to identify short sequence motifs that are highly informative about gene expression. FIRE predicted 17 DNA motifs from promoter regions and 6 RNA motifs from 3′ UTRs; 14 of these matched known yeast regulatory elements, indicating that the approach works well. Further validation came from conservation of the predicted motifs in a closely related yeast species, and from the fact that the target genes of a particular motif generally have related functions.

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ORIGINAL RESEARCH PAPER

  1. Elemento, O., Slonim, N. & Tavazoie, S. A universal framework for regulatory element discovery across all genomes and data types. Mol. Cell 28, 337–350 (2007)

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  1. Louisa Flintoft
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Flintoft, L. Decoding the regulatory genome. Nat Rev Genet 8, 908–909 (2007). https://doi.org/10.1038/nrg2281

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  • DOI: https://doi.org/10.1038/nrg2281

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