Russian version English version
Volume 8   Issue 2   Year 2013
Panyukov V.V., Kiselev S.S., Shavkunov K.S., Masulis I.S., Ozoline O.N.

Mixed Promoter Islands as Genomic Regions with Specific Structural and Functional Properties

Mathematical Biology & Bioinformatics. 2013;8(2):432-448.

doi: 10.17537/2013.8.432.


  1. Shavkunov KS, Masulis IS, Tutukina MN, Deev AA, Ozoline ON. Gains and unexpected lessons in genome-scale promoter mapping. Nucl. Acids Res. 2009;37:4419-4431. doi: 10.1093/nar/gkp490
  2. Huerta AM, Collado-Vides J. Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J. Mol. Biol. 2003;333:261-278. doi: 10.1016/j.jmb.2003.07.017
  3. Tutukina MN, Shavkunov KS, Masulis IS, Ozoline ON. Intragenic promoter-like sites in the genome of Escherichia coli. Discovery and functional implication. J. Bioinform. Comput. Biol. 2007;5:549-560. doi: 10.1142/S0219720007002801
  4. Tutukina MN, Shavkunov KS, Masulis IS, Ozoline ON. Antisense transcription within the hns locus of Escherichia coli. Molecular Biology. 2010;44:439-447. doi: 10.1134/S002689331003012X
  5. Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E. Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS ONE. 2009;4. Article e7526. doi: 10.1371/journal.pone.0007526
  6. Dornenburg JE, DeVita AM, Palumbo MJ, Wade JT. Widespread antisense transcription in Escherichia coli. mBio. 2010;1. Article e00024-10.
  7. Salgado H, Peralta M, Gama-Castro S, Santos-Zavaleta A, Muniz-Rascado LJ, Garcia-Sotelo JS, Weiss V, Solano-Lira H, Martinez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernandez S, Alquicira-Hernandez K, Lopez-Fuentes A, Porron-Sotelo L, Huerta AM, Bonavides-Martinez C, Balderas-Martinez Y, Pannier L, Olvera M, Labastida A, Jimenez-Jacinto V, Vega-Alvarado L, del Moral-Chavez V, Hernandez-Alvarez A, Morett E, Collado-Vides J. RegulonDB (version 8.0): omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucl. Acids Res. 2013:D203-D213. http://regulondb.ccg.unam (accessed 03 September 2013).
  8. Shavkunov KS, Tutukina MN, Masulis IS, Ozoline ON. Promoter islands: the novel elements in bacterial genomes. J. Biomol. Struct. Dynam. 2011;28:1128-1129.
  9. Panyukov VV, Ozoline ON. Promoters of Escherichia coli versus promoter islands: function and structure comparison. PLoS ONE. 2013;8. Article e62601. doi: 10.1371/journal.pone.0062601
  10. Reppas NB, Wade JT, Church GM, Struhl K. The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol. Cell. 2006;24:747-757. doi: 10.1016/j.molcel.2006.10.030
  11. Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, Palsson BO. Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J. Bacteriol. 2005;178:6166-6174. doi: 10.1128/JB.187.17.6166-6174.2005
  12. Panyukov VV, Nazipova NN, Ozoline ON. Software package as a tool to study the spatial conformation of bacterial genome sites. Mathematical Biology and Bioinformatics. 2011;6:t36-t52. doi: 10.17537/2011.6.t36
  13. Kahramanoglou C, Seshasayee ASN, Prieto AI, Ibberson D, Schmidt S, Zimmermann J, Benes V, Fraser GM, Luscombe NM. Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucl. Acids Res. 2011;39:2073-2091. doi: 10.1093/nar/gkq934
  14. Grainger DC, Hurd D, Goldberg MD, Busby SJW. Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucl. Acids Res. 2006;34:4642-4652. doi: 10.1093/nar/gkl542
  15. Grainger DC, Aiba H, Hurd D, Browning DF, Busby SJW. Transcription factor distribution in Escherichia coli: studies with FNR protein. Nucl. Acids Res. 2007;35:269-278. doi: 10.1093/nar/gkl1023
  16. Prieto AI, Kahramanoglou C, Ali RM, Fraser GM, Seshasayee ASN, Luscombe NM. Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. Nucl. Acids Res. 2012;40:3524-3537. doi: 10.1093/nar/gkr1236
  17. Cho BK, Knight EM, Barrett CL, Palsson BO. Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res. 2008;18:900-910. doi: 10.1101/gr.070276.107
  18. Lawrence JG, Ochman H. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA. 1998;95:9413-9417. doi: 10.1073/pnas.95.16.9413
  19. Nakamura Y, Itoh T, Matsuda H, Gojobori T. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nature Genetics. 2004;36:760-766. doi: 10.1038/ng1381
  20. Price MN, Dehal PS, Arkin AP. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol. 2008;9. Article R4.
  21. Kiselev SS, Ozoline ON. Structure-specific modules as indicators of promoter DNA in bacterial genomes. Mathematical Biology and Bioinformatics. 2011;6:t1-t13. doi: 10.17537/2011.6.t1
  22. Huang Q, Cheng X, Cheung MK, Kiselev SS, Ozoline ON, Kwan HS. High-density transcriptional initiation signals underline genomic islands in bacteria. PLoS ONE. 2012;7. Article e33759. doi: 10.1371/journal.pone.0033759
  23. Langille MG, Brinkman FS. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics. 2009;25:664-665. doi: 10.1093/bioinformatics/btp030
  24. Vlahovicek K, Kajan L, Pongor S. DNA analysis servers:,, and IS. Nucl. Acids Res. 2003;31:3686-3687. (accessed 03 September 2013). doi: 10.1093/nar/gkg559
  25. Friedel M, Nikolajewa S, Suehnel J, Wilhelm T. DiProDB: a database for dinucleotide properties. Nucl. Acids Res. 2009;37:D37-D40. (accessed 03 September 2013). doi: 10.1093/nar/gkn597
  26. Sponer J, Gabb HA, Leszczynski J, Hobza P. Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study. Biophys. J. 1997;73:76-87. doi: 10.1016/S0006-3495(97)78049-4
  27. Oshima T, Ishikawa S, Kurokawa K, Aiba H, Ogasawara N. Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res. 2006;13:141-153. doi: 10.1093/dnares/dsl009
  28. Lucchini S, Rowley G, Goldberg MD, Hurd D, Harrison M, Hinton JCD. H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog. 2006;2. Article e81. doi: 10.1371/journal.ppat.0020081
  29. Dorman CJ. H-NS, the genome sentinel. Nat. Rev. Microbiol. 2007;5:157-161. doi: 10.1038/nrmicro1598
  30. Munch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D. Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics. 2005;21:4187-4189. doi: 10.1093/bioinformatics/bti635
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2013.8.432
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
Supplementary data Translation into English
Math. Biol. Bioinf.
doi: 10.17537/2013.8.t12

Full text (eng., pdf)


  Copyright IMPB RAS © 2005-2024