title: Conserved noncoding sequences in the grasses.
abstract: As orthologous genes from related species diverge over time, some sequences are conserved in noncoding regions. In mammals, large phylogenetic footprints, or conserved noncoding sequences (CNSs), are known to be common features of genes. Here we present the first large-scale analysis of plant genes for CNSs. We used maize and rice, maximally diverged members of the grass family of monocots. Using a local sequence alignment set to deliver only significant alignments, we found one or more CNSs in the noncoding regions of the majority of genes studied. Grass genes have dramatically fewer and much smaller CNSs than mammalian genes. Twenty-seven percent of grass gene comparisons revealed no CNSs. Genes functioning in upstream regulatory roles, such as transcription factors, are greatly enriched for CNSs relative to genes encoding enzymes or structural proteins. Further, we show that a CNS cluster in an intron of the knotted1 homeobox gene serves as a site of negative regulation. We showthat CNSs in the adh1 gene do not correlate with known cis-acting sites. We discuss the potential meanings of CNSs and their value as analytical tools and evolutionary characters. We advance the idea that many CNSs function to lock-in gene regulatory decisions.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA.
authors.forename: Dan Choffnes
authors.initials: DC
authors.lastname: Inada
authors.forename: Ali
authors.initials: A
authors.lastname: Bashir
authors.forename: Chunghau
authors.initials: C
authors.lastname: Lee
authors.forename: Brian C
authors.initials: BC
authors.lastname: Thomas
authors.forename: Cynthia
authors.initials: C
authors.lastname: Ko
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Goff
authors.forename: Michael
authors.initials: M
authors.lastname: Freeling
mesh_terms: D024506:5' Flanking Region / Q000235:genetics; D000818:Animals; D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D005809:Genes, Regulator / Q000235:genetics; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D007438:Introns / Q000235:genetics; D005810:Multigene Family / Q000235:genetics; D034521:Nuclear Matrix-Associated Proteins / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D020506:Untranslated Regions / Q000235:genetics*; D003313:Zea mays / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D018398:Homeodomain Proteins; C095848:Kn1 protein, plant; D034521:Nuclear Matrix-Associated Proteins; D010940:Plant Proteins; D020506:Untranslated Regions