title: Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana.
abstract: BACKGROUND
  The understanding of the mechanisms of transcriptional regulation remains a challenge for molecular biologists in the post-genome era. It is hypothesized that the regulatory regions of genes expressed in the same tissue or cell type share a similar structure. Though several studies have analyzed the promoters of genes expressed in specific metazoan tissues or cells, little research has been done in plants. Hence finding specific patterns of motifs to explain the promoter architecture of co-expressed genes in plants could shed light on their transcription mechanism.
  
  
  RESULTS
  We identified novel patterns of sets of motifs in promoters of genes co-expressed in four different plant structures (PSs) and in the entire plant in Arabidopsis thaliana. Sets of genes expressed in four PSs (flower, seed, root, shoot) and housekeeping genes expressed in the entire plant were taken from a database of co-expressed genes in A. thaliana. PS-specific motifs were predicted using three motif-discovery algorithms, 8 of which are novel, to the best of our knowledge. A support vector machine was trained using the average upstream distance of the identified motifs from the translation start site on both strands of binding sites. The correctly classified promoters per PS were used to construct specific patterns of sets of motifs to describe the promoter architecture of those co-expressed genes. The discovered PS-specific patterns were tested in the entire A. thaliana genome, correctly identifying 77.8%, 81.2%, 70.8% and 53.7% genes expressed in petal differentiation, synergid cells, root hair and trichome, as well as 88.4% housekeeping genes.
  
  
  CONCLUSIONS
  We present five patterns of sets of motifs which describe the promoter architecture of co-expressed genes in five PSs with the ability to predict them from the entire A. thaliana genome. Based on these findings, we conclude that the positioning and orientation of transcription factor binding sites at specific distances from the translation start site is a reliable measure to differentiate promoters of genes expressed in different A. thaliana structures from background genomic promoters. Our method can be used to predict novel motifs and decipher a similar promoter architecture for genes co-expressed in A. thaliana under different conditions.
authors.forename: Yosvany
authors.initials: Y
authors.lastname: López
authors.forename: Ashwini
authors.initials: A
authors.lastname: Patil
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakai
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D019295:Computational Biology; D018506:Gene Expression Regulation, Plant; D020043:Genes, Essential / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D023281:Genomics; D059372:Nucleotide Motifs; D018514:Plant Structures / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*