Investigation of Latent Periodicity Phenomenon in the Genomes of Eukaryotic Organisms

M. B. Chaley ; V. A. Kutyrkin ; E. I. Teplukhina ; G. E. Tyulbasheva ; N. N. Nazipova

Matematičeskaâ biologiâ i bioinformatika, Tome 8 (2013) no. 2, pp. 480-501.

Résumé

Analysis of the data from the first release of HeteroGenome database, collecting the revealed regions of latent periodicity in the genomes of a number of eukaryotic organisms, is presented. Tandem repeats with different conservation of a pattern copies, including the highly diverged repeats, were identified in the genomes of S. cerevisiae, A. thaliana, C. elegans and D. melanogaster. The data were obtained with the help of original spectral-statistical approach to searching for the reliable regions of latent periodicity in DNA sequences. Introduction of the two-level structure for the data presentation (At the first, nonredundant level the regions of latent periodicity is generally viewed, at the second level only the fragments of conservative periodic structure are considered.) allowed to estimate a share of genome coverage by the regions of latent periodicity which counts $\sim10\%$ of a whole genome length. The estimate is deduced according to the data of the first level. An analysis of quantitative and qualitative content (corresponding to the divergence levels) of the latent periodicity regions over all the chromosomes of the considered organisms revealed the characteristic types of periodicity in a genome of each organism. The histograms showing density distribution of the latent periodicity regions along every chromosome in the analyzed genomes were built. A repertoire of period lengths were revealed in the genomes. Moreover, HeteroGenome base offers some additional possibilities for its’ data analysis and is freely available at URL: http://www.jcbi.ru/lp_baze/.

Bibliographie

[1] Richard G. F., Kerrest A., Dujon B., “Comparative genomics and molecular dynamics of DNA repeats in eukaryotes”, Microbiol. Mol. Biol. Rev., 72 (2008), 686–727 | DOI

[2] Kelkar Y. D., Strubczewski N., Hile S. E., Chiaromonte F., Eckert K. A., Makova K. D., “What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats”, Genome Biol. Evol., 2 (2010), 620–635 | DOI

[3] Ellegren H., “Microsatellites: simple sequences with complex evolution”, Nat. Rev. Genet., 5 (2004), 435–445 | DOI

[4] Welch J. W., Maloney D. H., Fogel S., “Unequal crossing-over and gene conversion at the amplified CUP1 locus of yeast”, Mol. Gen. Genet., 222 (1990), 304–310 | DOI

[5] Tyler-Smith C., Willard H. F., “Mammalian chromosome structure”, Curr. Opin. Genet. Dev., 3 (1993), 390–397 | DOI

[6] Hewett D. R., Handt O., Hobson L., Mangelsdorf M., Eyre H. J., Baker E., Sutherland G. R., Schuffenhauer S., Mao J. I., Richards R. I., “FRA10B structure reveals common elements in repeat expansion and chromosomal fragile site genesis”, Mol. Cell., 1 (1998), 773–781 | DOI

[7] Yu S., Mangelsdorf M., Hewett D., Hobson L., Baker E., Eyre H. J., Lapsys N., Le Paslier D., Doggett N. A., Sutherland G. R., Richards R. I., “Human chromosomal fragile site FRA16B is an amplified AT-rich minisatellite repeat”, Cell, 88 (1997), 367–374 | DOI

[8] Fu Y. H., Kuhl D. P., Pizzuti A., Pieretti M., Sutcliffe J. S., Richards S., Verkerk A. J., Holden J. J., Fenwick R. G. Jr, Warren S. T., et al., “Variation of the CGG repeat at the fragile X site results in genetic instability: resolution of the Sherman paradox”, Cell, 67 (1991), 1047–1058 | DOI

[9] Liquori C. L., Ricker K., Moseley M. L., Jacobsen J. F., Kress W., Naylor S. L., Day J. W., Ranum L. P., “Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9”, Science, 293 (2001), 864–867 | DOI

[10] Matsuura T., Fang P., Pearson C. E., Jayakar P., Ashizawa T., Roa B. B., Nelson D. L., Interruptions in the expanded ATTCT repeat of spinocerebellar ataxia type 10: repeat purity as a disease modifier?, Am. J. Hum. Genet., 78 (2006), 125–129 | DOI

[11] Lalioti M. D., Scott H. S., Buresi C., Rossier C., Bottani A., Morris M. A., Malafosse A., Antonarakis S. E., “Dodecamer repeat expansion in cystatin B gene in progressive myoclonus epilepsy”, Nature, 386 (1997), 847–851 | DOI

[12] Martin P., Makepeace K., Hill S. A., Hood D. W., Moxon E. R., “Microsatellite instability regulates transcription factor binding and gene expression”, Proc. Natl. Acad. Sci. USA, 102 (2005), 3800–3804 | DOI

[13] Benson G., “Tandem repeats finder: a program to analyze DNA sequences”, Nucleic Acids Res., 27 (1999), 573–580 | DOI

[14] Reneker J., Shyu C. R., Zeng P., Polacco J. C., Gassmann W., “ACMES: fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval”, Nucleic Acids Res., 32 (2004), W649–W653 | DOI

[15] Roset R., Subirana J. A., Messeguer X., “MREPATT: detection and analysis of exact consecutive repeats in genomic sequences”, Bioinformatics, 19 (2003), 2475–2476 | DOI

[16] Parisi V., Fonzo V. D., Aluffi-Pentini F., “STRING: finding tandem repeats in DNA sequences”, Bioinformatics, 19 (2003), 1733–1738 | DOI

[17] Kolpakov R., Kucherov G., “Mreps: efficient and flexible detection of tandem repeats in DNA”, Nucleic Acids Res., 31 (2003), 3672–3678 | DOI

[18] Wexler Y., Yakhini Z., Kashi Y., Geiger D., “Finding approximate tandem repeats in genomic sequences”, J. Comput. Biol., 12 (2005), 928–942 | DOI

[19] Boeva V., Regnier M., Papatsenko D., Makeev V., “Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression”, Bioinformatics, 22 (2006), 676–684 | DOI

[20] Mudunuri S. B., Nagarajaram H. A., “IMEx: imperfect microsatellite extractor”, Bioinformatics, 23 (2007), 1181–1187 | DOI

[21] Pellegrini M., Renda M. E., Vecchio A., “TRStalker: an efficient heuristic for finding fuzzy tandem repeats”, Bioinformatics, 26 (2010), i358–i366 | DOI

[22] Sokol D., Benson G., Tojeira J., “Tandem repeats over the edit distance”, Bioinformatics, 23 (2007), e30–e35 | DOI

[23] Sokol D., Atagun F., “TRedD — A database for tandem repeats over the edit distance”, Database, 2010, baq003

[24] Gelfand Y., Rodriguez A., Benson G., “TRDB — the Tandem Repeats Database”, Nucleic Acids Res., 35 (2007), 80–87 | DOI

[25] Boby T., Patch A., Aves S., “TRbase: a database relating tandem repeats to disease genes for the human genome”, Bioinformatics, 21 (2005), 860–921 | DOI

[26] Chaley M. B., Nazipova N. N., Kutyrkin V. A., “Statistical methods for detecting latent periodicity patterns in biological sequences: the case of small-size samples”, Pattern Recogn. Image Anal., 19 (2009), 358–367 | DOI

[27] Chalei M. B., Nazipova N. N., Kutyrkin V. A., “Sovmestnoe ispolzovanie razlichnykh kriteriev proverki odnorodnosti dlya vyyavleniya skrytoi periodichnosti v biologicheskikh posledovatelnostyakh”, Mat. biol. i bioinform., 2:1 (2007), 20–35 (data obrascheniya: 28.07.2013) http://www.matbio.org/downloads/Chaley2007(2_20).pdf

[28] Chaley M., Kutyrkin V., “Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences”, Math. Biosci., 211 (2008), 186–204 | DOI | MR | Zbl

[29] Fields S., Johnston M., Cell biology. Whither model organism research?, Science, 307 (2005), 1885–1886 | DOI

[30] “International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome”, Nature, 409 (2001), 860–921 | DOI