title: Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana.
abstract: BACKGROUND
  Simple sequence repeats or microsatellites have been found abundantly in many genomes. However, the significance of distribution preference has not been completely understood. Completion of the Arabidopsis genome sequencing allows us to better understand and characterize microsatellites.
  
  
  RESULTS
  Microsatellite distribution was more abundant in 5'-flanking regions of genes compared with that expected in the whole genome, with an over-representation of AG and AAG repeats; there were clear differences from distributions in 3'-flanks and coding fractions, where triplet frequencies evidently corresponded to codon usage. We identified 1140 full-length genes that contained at least one locus of AG or AAG repeats in their upstream sequences, and whose functional characteristics were significantly associated with the repeats. This observation indicates that selective pressure markedly differed in the three transcribed regions, with positive selection of AG and AAG repeats in 5'-flanks close to those genes whose products are preferentially involved in transcription.
authors.affiliation: Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China.
authors.forename: Lida
authors.initials: L
authors.lastname: Zhang
authors.forename: Dejun
authors.initials: D
authors.lastname: Yuan
authors.forename: Shunwu
authors.initials: S
authors.lastname: Yu
authors.forename: Zhugang
authors.initials: Z
authors.lastname: Li
authors.forename: Youfang
authors.initials: Y
authors.lastname: Cao
authors.forename: Zhiqi
authors.initials: Z
authors.lastname: Miao
authors.forename: Hongmei
authors.initials: H
authors.lastname: Qian
authors.forename: Kexuan
authors.initials: K
authors.lastname: Tang
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D018744:DNA, Plant / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D018745:Genome, Plant; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018744:DNA, Plant