Conserved noncoding sequence (CNS) Bioinformatics

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The University of California at Berkeley has been awarded a grant to provide the public an accurate database of conserved noncoding sequences (CNSs) in the grass family of flowering plants. CNSs are sequences that are highly conserved over evolutionary time, but that do not encode proteins. The function of many CNSs involves regulation of gene action. Because rice, a grass, has been sequenced and maize (corn) has a great deal of useful genomic sequence available, CNSs may be identified by comparison between the two. Because of the great evolutionary distance between rice and maize, the CNSs so discovered are expected to exist in most all of the other 10,000 grass species. These include economically important crop plants whose genomes have not and will not be sequenced. A CNS database facilitates research on all grass species by providing useful pan-grass PCR binding sites, these being particularly useful for genetic mapping and obtaining important and useful gene regions from wild grass species. It is also important to learn more about the functions that explain why these CNS sequences have been conserved over the last 50 million years. Among the broader impacts of this project is collaboration with Berkeley High School designed to help close the achievement gaps between students of different socio-economic groups. This project includes a summer research experience program for high school students who have done well in advanced placement biology.