PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
Tóm tắt
Periodic spacing of short adenine or thymine runs phased with DNA helical period of ~10.5 bp is associated with intrinsic DNA curvature and deformability, which play important roles in DNA-protein interactions and in the organization of chromosomes in both eukaryotes and prokaryotes. Local differences in DNA sequence periodicity have been linked to differences in gene expression in some organisms. Despite the significance of these periodic patterns, there are virtually no publicly accessible tools for their analysis. We present novel tools suitable for assessments of DNA curvature-related sequence periodicity in nucleotide sequences at the genome scale. Utility of the present software is demonstrated on a comparison of sequence periodicities in the genomes of Haemophilus influenzae, Methanocaldococcus jannaschii, Saccharomyces cerevisiae, and Arabidopsis thaliana. The software can be accessed through a web interface and the programs are also available for download. The present software is suitable for comparing DNA curvature-related sequence periodicity among different genomes as well as for analysis of intrachromosomal heterogeneity of the sequence periodicity. It provides a quick and convenient way to detect anomalous regions of chromosomes that could have unusual structural and functional properties and/or distinct evolutionary history.
Tài liệu tham khảo
Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JP, Widom J: A genomic code for nucleosome positioning. Nature. 2006, 442: 772-778. 10.1038/nature04979.
Trifonov EN, Sussman JL: The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc Natl Acad Sci USA. 1980, 77: 3816-3820. 10.1073/pnas.77.7.3816.
Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B: The role of DNA shape in protein-DNA recognition. Nature. 2009, 461: 1248-1253. 10.1038/nature08473.
Mrázek J: Comparative analysis of sequence periodicity among prokaryotic genomes points to differences in nucleoid structure and a relationship to gene expression. J Bacteriol. 2010, 192: 3763-3772. 10.1128/JB.00149-10.
Tolstorukov MY, Virnik KM, Adhya S, Zhurkin VB: A-tract clusters may facilitate DNA packaging in bacterial nucleoid. Nucleic Acids Res. 2005, 33: 3907-3918. 10.1093/nar/gki699.
Herzel H, Weiss O, Trifonov EN: Sequence periodicity in complete genomes of archaea suggests positive supercoiling. J Biomol Struct Dyn. 1998, 16: 341-345.
Schieg P, Herzel H: Periodicities of 10-11 bp as indicators of the supercoiled state of genomic DNA. J Mol Biol. 2004, 343: 891-901. 10.1016/j.jmb.2004.08.068.
Kozobay-Avraham L, Hosid S, Bolshoy A: Involvement of DNA curvature in intergenic regions of prokaryotes. Nucleic Acids Res. 2006, 34: 2316-2327. 10.1093/nar/gkl230.
Bolshoy A, Nevo E: Ecologic genomics of DNA: upstream bending in prokaryotic promoters. Genome Res. 2000, 10: 1185-1193. 10.1101/gr.10.8.1185.
Worning P, Jensen LJ, Nelson KE, Brunak S, Ussery DW: Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima. Nucleic Acids Res. 2000, 28: 706-709. 10.1093/nar/28.3.706.
Fire A, Alcazar R, Tan F: Unusual DNA structures associated with germline genetic activity in Caenorhabditis elegans. Genetics. 2006, 173: 1259-1273. 10.1534/genetics.106.057364.
Willenbrock H, Ussery DW: Prediction of highly expressed genes in microbes based on chromatin accessibility. BMC Mol Biol. 2007, 8: 11-10.1186/1471-2199-8-11.
Kiyama R, Trifonov EN: What positions nucleosomes?--A model. FEBS Lett. 2002, 523: 7-11. 10.1016/S0014-5793(02)02937-X.
Ulanovsky LE, Trifonov EN: Estimation of wedge components in curved DNA. Nature. 1987, 326: 720-722. 10.1038/326720a0.
Herzel H, Weiss O, Trifonov EN: 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding. Bioinformatics. 1999, 15: 187-193. 10.1093/bioinformatics/15.3.187.
Mrázek J: Phylogenetic signals in DNA composition: limitations and prospects. Mol Biol Evol. 2009, 26: 1163-1169. 10.1093/molbev/msp032.
Mrázek J, Guo X, Shah A: Simple sequence repeats in prokaryotic genomes. Proc Natl Acad Sci USA. 2007, 104: 8472-8477. 10.1073/pnas.0702412104.
Jacq C, Alt-Morbe J, Andre B, Arnold W, Bahr A, Ballesta JP, Bargues M, Baron L, Becker A, Biteau N, et al: The nucleotide sequence of Saccharomyces cerevisiae chromosome IV. Nature. 1997, 387: 75-78.
Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, et al: Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996, 273: 1058-1073. 10.1126/science.273.5278.1058.
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al: Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995, 269: 496-512. 10.1126/science.7542800.
Theologis A, Ecker JR, Palm CJ, Federspiel NA, Kaul S, White O, Alonso J, Altafi H, Araujo R, Bowman CL, et al: Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature. 2000, 408: 816-820. 10.1038/35048500.
Gu SG, Fire A: Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning. Chromosoma. 2010, 119: 73-87. 10.1007/s00412-009-0235-3.