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A new way to visualize DNA’s base succession: the Caenorhabditis elegans chromosome landscapes

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Abstract

In the eukaryotic genomes, the genetic diseases are generally associated with the tandem repeats. These repeats seem to appear frequently. In this paper, we are describing a wavelet transform technique which provides a new way to represent the DNA succession bases as a DNA progression images. These images offer DNA landscapes, visualizing and following up periodicities through genomes. We investigated in a structural coding technique the Pnuc. Then, we illustrated, with time–frequency representation, the existence and the superposition of the periodicities in some biological features, their locations and the different ways in which they appear. The representations generated showed that one periodicity can sometimes be alone, but generally, it is incorporated to others. These periodicities associations create, in the Caenorhabditis elegans chromosome, a precise structural image of biological features, such as CeRep, Helitrons, repeats and satellites.

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References

  1. Altenburger W, Hörz W, Zachau HG (1976) Nuclease cleavage of chromatin at 100-nucleotide pair intervals. Nature 264(5586):517–522

    Article  CAS  PubMed  Google Scholar 

  2. Anastassiou D (2001) Genomic signal processing. Signal Process Mag IEEE 18(4):8–20

    Article  Google Scholar 

  3. Arneodo A, Vaillant C, Audit B, Argoul F, d’Aubenton-Carafa Y, Thermes C (2011) Multi-scale coding of genomic information: from DNA sequence to genome structure and function. Phys Rep 498(2):45–188

    Article  CAS  Google Scholar 

  4. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27(2):573

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Berger JA, Mitra SK, Carli M, Neri A (2002) A new approaches to genome sequence analysis based on digital signal processing. University of California, Oakland

    Google Scholar 

  6. Berger JA, Mitra SK, Astola J (2003) Power spectrum analysis for DNA sequences. In: Signal processing and its applications. In: Proceedings. Seventh international symposium on, July, vol 2. IEEE, pp 29–32

  7. Boeva V, Regnier M, Papatsenko D, Makeev V (2006) Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinformatics 22(6):676–684

    Article  CAS  PubMed  Google Scholar 

  8. Caenorhabditis elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282(2012):2018

  9. Cangiano G, La Volpe A (1993) Repetitive DNA sequences located in the terminal portion of the Caenorhabditis elegans chromosomes. Nucleic Acids Res 21(5):1133–1139

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Cristea PD (2001) Genetic signals: an emerging concept. In: Proceedings of the international workshop on system, signals and image processing IWSSIP 2001, Bucharest, Romania

  11. Cristea PD (2003) Large scale features in DNA genomic signals. Signal Process 83(4):871–888

    Article  Google Scholar 

  12. Daubechies I (1992) Ten lectures on wavelets. In: CBMS-NSF regional conference series in applied mathematics, Lectures delivered at the CBMS conference on wavelets, University of Lowell, MA, June 1990, vol 1. Society for Industrial and Applied Mathematics (SIAM), Philadelphia

  13. Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445

    Article  CAS  PubMed  Google Scholar 

  14. Feschotte C, Zhang X, Wessler SR (2002) Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons. http://forest.mtu.edu/faculty/joshi/publish/pdf/MobDNA2002pre.pdf

  15. Fukushima A, Ikemura T, Kinouchi M, Oshima T, Kudo Y, Mori H, Kanaya S (2002) Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis. Gene 300(1):203–211

    Article  CAS  PubMed  Google Scholar 

  16. Gemayel R, Vinces MD, Legendre M, Verstrepen KJ (2010) Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu Rev Genet 44:445–477

    Article  CAS  PubMed  Google Scholar 

  17. Jorda J, Kajava AV (2009) T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm. Bioinformatics 25(20):2632–2638

    Article  CAS  PubMed  Google Scholar 

  18. Kluwe L (2013) Chapter ‘Application of microsatellite marker analysis’. In: Ulucan K (ed) Applications of molecular genetics in personalized medicine. Omics Group eBooks, USA, pp 3–8

  19. Kolpakov R, Bana G, Kucherov G (2003) mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 31(13):3672–3678

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Krishnan A, Tang F (2004) Exhaustive whole-genome tandem repeats search. Bioinformatics 20(16):2702–2710

    Article  CAS  PubMed  Google Scholar 

  21. Heisenberg W (1949) The physical principles of the quantum theory. Courier Dover, Mineola

    Google Scholar 

  22. http://www.edu.upmc.fr/sdv/masselot_05001/polymorphisme/microsatellites.html. Accessed on 11 Mar 2015

  23. http://www.uwyo.edu/dbmcd/molmark/lect08/lect8.html. Accessed on 11 Mar 2015

  24. LeBlanc MD, Aspeslagh G, Buggia NP, Dyer BD (2000) An annotated catalog of inverted repeats of Caenorhabditis elegans chromosomes III and X, with observations concerning odd/even biases and conserved motifs. Genome Res 10(9):1381–1392

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Lecture 8. Population genetics VI: Introduction to microsatellites: from theory to lab. practice

  26. Lim KG, Kwoh CK, Hsu LY, Wirawan A (2013) Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance. Brief Bioinform 14(1):67–81

    Article  PubMed  Google Scholar 

  27. Lowary PT, Widom J (1997) Nucleosome packaging and nucleosome positioning of genomic DNA. Proc Natl Acad Sci 94(4):1183–1188

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Mallat S (1999) A wavelet tour of signal processing. Access Online via Elsevier

  29. Merkel A, Gemmell N (2008) Detecting short tandem repeats from genome data: opening the software black box. Brief Bioinform 9(5):355–366

    Article  CAS  PubMed  Google Scholar 

  30. Messaoudi I, Oueslati AE, Lachiri Z (2011) Caractérisation des génomes bactériens par la représentation en jeu de Chaos et étude fréquentielle des textures par Transformée de Fourier à deux dimensions, Revue électronique Sciences et Technologies de l’Automatique, 27

  31. Messaoudi I, Oueslati AE, Lachiri Z (2013) Detection of the 6.5- base periodicity in the C. elegans introns based on the frequency chaos game signal and the complex Morlet wavelet analysis. Int J Sci Eng Technol IJSET 2:1247–1251

  32. Mudunuri SB, Nagarajaram HA (2007) IMEx: imperfect microsatellite extractor. Bioinformatics 23(10):1181–1187

    Article  CAS  PubMed  Google Scholar 

  33. Newland DE (1998) Time-frequency and time-scale signal analysis by harmonic wavelets. Signal analysis and prediction. Birkhäuser, Boston, pp 3–26

    Google Scholar 

  34. Oppenheim AV, Schafer RW, Buck JR (1999) Discrete-time signal processing, vol 5. Prentice Hall, Upper Saddle River

    Google Scholar 

  35. Oueslati AE, Lachiri Z, Ellouze N (2007) Spectral analysis of DNA sequence: the Exon’s location method. In Digital signal processing, 2007 15th international conference on, July. IEEE, pp 115–118

  36. Oueslati AE, Ellouze N, Lachiri Z (2007) 3D spectrum analysis of DNA sequence: application to Caenorhabditis elegans genome. In: Bioinformatics and bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE international conference on, October. IEEE, pp 864–871

  37. Oueslati AE, Lachiri Z, Ellouze N (2011) Detecting particular features in C. elegans genomes using synchronous analysis based on wavelet transform. Int J Bioinform Res Appl 7(2):183–201

  38. Oueslati AE, Messaoudi I, Lachiri Z, Ellouze N (2012) Spectral analysis of global behaviour of C. elegans chromosomes. INTECH, pp 205–228

  39. Parisi V, De Fonzo V, Aluffi-Pentini F (2003) STRING: finding tandem repeats in DNA sequences. Bioinformatics 19(14):1733–1738

    Article  CAS  PubMed  Google Scholar 

  40. Richard GF, Kerrest A, Dujon B (2008) Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 72(4):686–727

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  41. Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, Moore IK, Widom J (2006) A genomic code for nucleosome positioning. Nature 442(7104):772–778

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  42. Shapiro JA, Sternberg R (2005) Why repetitive DNA is essential to genome function. Biol Rev 80(2):227–250

    Article  PubMed  Google Scholar 

  43. Sharma PC, Grover A, Kahl G (2007) Mining microsatellites in eukaryotic genomes. Trends Biotechnol 25(11):490–498

    Article  CAS  PubMed  Google Scholar 

  44. Sokol D, Benson G, Tojeira J (2007) Tandem repeats over the edit distance. Bioinformatics 23(2):e30–e35

    Article  CAS  PubMed  Google Scholar 

  45. Sussillo D, Kundaje A, Anastassiou D (2004) Spectrogram analysis of genomes. EURASIP J Appl Signal Process 2004(1):29–42

    Article  Google Scholar 

  46. Strassman JE, Barefield K, Solis CR, Hughes CR, Queller DC (1997) Trinucleotide microsatellite loci for a social wasp, Poliste. Mol Ecol 6:97–100

    Article  Google Scholar 

  47. Trifonov EN (1998) 3-, 10.5-, 200-and 400-base periodicities in genome sequences. Phys A Stat Mech Appl 249(1):511–516

    Article  CAS  Google Scholar 

  48. Vaidyanathan PP, Yoon BJ (2004) The role of signal-processing concepts in genomics and proteomics. J Franklin Inst 341(1):111–135

    Article  Google Scholar 

  49. Wexler Y, Yakhini Z, Kashi Y, Geiger D (2005) Finding approximate tandem repeats in genomic sequences. J Comput Biol 12(7):928–942

    Article  CAS  PubMed  Google Scholar 

  50. Wirawan A, Kwoh CK, Hsu LY, Koh TH (2010) INVERTER: integrated variable number tandem repeat finder. In: Chan JH, Ong Y-S, Cho S-B (eds) Computational systems-biology and bioinformatics. Springer, Berlin, pp 151–164

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Authors and Affiliations

  1. Laboratoire Signal, Image et Technologies de l’information, Département de Génie Electrique, Ecole Nationale d’Ingénieurs de Tunis, BP 37, Campus Universitaire, Le Belvédère, 1002, Tunis Cedex, Tunisia

    Afef Elloumi Oueslati, Imen Messaoudi & Noureddine Ellouze

  2. Département de Génie Physique et Instrumentation, Institut National des Sciences Appliquées et de Technologie, BP 676, Centre Urbain, 1080, Tunis Cedex, Tunisia

    Zied Lachiri

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  1. Afef Elloumi Oueslati
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  2. Imen Messaoudi
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  3. Zied Lachiri
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  4. Noureddine Ellouze
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Correspondence to Afef Elloumi Oueslati.

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Oueslati, A.E., Messaoudi, I., Lachiri, Z. et al. A new way to visualize DNA’s base succession: the Caenorhabditis elegans chromosome landscapes. Med Biol Eng Comput 53, 1165–1176 (2015). https://doi.org/10.1007/s11517-015-1304-9

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  • DOI: https://doi.org/10.1007/s11517-015-1304-9

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