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IN BRIEF

Bigfoot Genes and Plant Response to Environmental Change

neckardt{at}aspb.org

Functional DNA sequence changes at a lower rate over evolutionary time and therefore is more highly conserved than sequence without function. In comparing homoeologous chromosomal regions having diverged from a common ancestor, a high degree of sequence similarity in noncoding regions is assumed to provide a measure of noncoding DNA function, where function is inferred from conservation. Conserved noncoding sequences (CNSs) have been studied extensively in mammals, and putative functions include matrix attachment regions, transcription factor (TF) binding sites, gene enhancers, and chromosome-level regulatory regions. The most recent tetraploidy event in Arabidopsis left numerous homoeologous regions. Freeling et al. (pages 1441–1457) conducted an alignment of homoeolgous pairs that generated 15,000 intragenomic CNSs. Analysis of this database identified 254 genes, called Bigfoot genes, located in CNS-rich chromosomal regions. Known TF binding motifs, such as the G-box, were found to be overrepresented in the CNSs, and the Bigfoot genes were found to be overrepresented for genes encoding TFs that respond to environmental signals. This suggests that Bigfoot genes may have a particular function in plant adaptation to environmental change.

Footnotes

www.plantcell.org/cgi/doi/10.1105/tpc.107.190511

Related articles in Plant Cell:

G-Boxes, Bigfoot Genes, and Environmental Response: Characterization of Intragenomic Conserved Noncoding Sequences in Arabidopsis

Michael Freeling, Lakshmi Rapaka, Eric Lyons, Brent Pedersen, and Brian C. Thomas
Plant Cell 2007 19: 1441-1457. [Abstract] [Full Text]  

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