Discovery of Stress Responsive DNA Regulatory Motifs in Arabidopsis 英文参考文献.docVIP

DiscoveryofStressResponsiveDNARegulatoryMotifsin Arabidopsis Shisong Ma1* , Shawn Bachan1 , Matthew Porto1 , Hans J. Bohnert2 , Michael Snyder3 , Savithramma P. Dinesh-Kumar1* 1 Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California Davis, Davis, California, United States of America, 2 Departements of Plant Biology and Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America, 3 Department of Genetics, Stanford University, Stanford, California, United States of America Abstract The discovery of DNA regulatory motifs in the sequenced genomes using computational methods remains challenging. Here, we present MotifIndexer - a comprehensive strategy fordenovo identification of DNA regulatory motifs at a genome level. Using word-counting methods, we indexed the existence of every 8-mer oligo composed of bases A, C, G, T, r, y, s, w, m, k, n or 12-mer oligo composed of A, C, G, T, n, in the promoters of all predicted genes ofArabidopsisthaliana genome and of selected stress-induced co-expressed genes. From this analysis, we identified number of over-represented motifs. Among these, major critical motifs were identified using a position filter. We used a model based on uniform distribution and the z-scores derived from this model to describe position bias. Interestingly, many motifs showed position bias towards the transcription start site. We extended this model to show biased distribution of motifs in the genomes of bothA.thaliana and rice. We also used MotifIndexer to identify conserved motifs in co-expressed gene groups from two Arabidopsis species, A.thaliana andA.lyrata. This new comparative genomics method does not depend on alignments of homologous gene promoter sequences. Citation: Ma S, Bachan S, Porto M, Bohnert HJ