title: Revisiting operons: an analysis of the landscape of transcriptional units in E. coli.
abstract: BACKGROUND
  Bacterial operons are considerably more complex than what were thought. At least their components are dynamically rather than statically defined as previously assumed. Here we present a computational study of the landscape of the transcriptional units (TUs) of E. coli K12, revealed by the available genomic and transcriptomic data, providing new understanding about the complexity of TUs as a whole encoded in the genome of E. coli K12.
  
  
  CONCLUSIONS
  Our main findings include that (i) different TUs may overlap with each other by sharing common genes, giving rise to clusters of overlapped TUs (TUCs) along the genomic sequence; (ii) the intergenic regions in front of the first gene of each TU tend to have more conserved sequence motifs than those of the other genes inside the TU, suggesting that TUs each have their own promoters; (iii) the terminators associated with the 3' ends of TUCs tend to be Rho-independent terminators, substantially more often than terminators of TUs that end inside a TUC; and (iv) the functional relatedness of adjacent gene pairs in individual TUs is higher than those in TUCs, suggesting that individual TUs are more basic functional units than TUCs.
authors.affiliation: Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. xizeng.mao@gmail.com.|Present address: MD Anderson Cancer Center, Houston, TX, 77054, USA. xizeng.mao@gmail.com.
authors.forename: Xizeng
authors.initials: X
authors.lastname: Mao
authors.affiliation: Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. qin.ma@sdstate.edu.|BioEnergy Research Center (BESC), Athens, GA, USA. qin.ma@sdstate.edu.|Present address: Department of Plant Science, South Dakota State University, Brookings, SD, 57006, USA. qin.ma@sdstate.edu.|Present address: BioSNTR, Brookings, SD, USA. qin.ma@sdstate.edu.
authors.forename: Qin
authors.initials: Q
authors.lastname: Ma
authors.affiliation: School of Mathematics, Shandong University, Jinan, Shandong, China. bingqiangsdu@gmail.com.
authors.forename: Bingqiang
authors.initials: B
authors.lastname: Liu
authors.affiliation: Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. chenxin@uga.edu.|College of Computer Sciences and Technology, Changchun, Jilin, China. chenxin@uga.edu.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. jluzhhy@gmail.com.|Present address: Systems Biology and Biomedical Informatics (SBBI) Laboratory University of Nebraska-Lincoln 122B/122C Avery Hall, 1144 T St, Lincoln, NE, 68588-0115, USA. jluzhhy@gmail.com.
authors.forename: Hanyuan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. xyn@bmb.uga.edu.|BioEnergy Research Center (BESC), Athens, GA, USA. xyn@bmb.uga.edu.|College of Computer Sciences and Technology, Changchun, Jilin, China. xyn@bmb.uga.edu.|School of Public Health, Jilin University, Changchun, Jilin, China. xyn@bmb.uga.edu.
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
mesh_terms: D001665:Binding Sites; D017124:Conserved Sequence / Q000235:genetics; D048168:Escherichia coli K12 / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism; D005798:Genes, Bacterial; D059372:Nucleotide Motifs / Q000235:genetics; D009876:Operon / Q000235:genetics*; D011401:Promoter Regions, Genetic; D018085:Regulon / Q000235:genetics; D013728:Terminator Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D029968:Escherichia coli Proteins; C534627:Rho protein, E coli; D014157:Transcription Factors