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BioMed Research International
Volume 2015 (2015), Article ID 821596, 7 pages
http://dx.doi.org/10.1155/2015/821596
Research Article

Nucleosome Organization around Pseudogenes in the Human Genome

Guoqing Liu,1,2 Fen Feng,2 Xiujuan Zhao,1,2 and Lu Cai1,2

1The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
2School of Mathematics, Physics, and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou 014010, China

Received 9 September 2014; Accepted 17 December 2014

Academic Editor: Elena Papaleo

Copyright © 2015 Guoqing Liu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. Maestre, T. Tchénio, O. Dhellin, and T. Heidmann, “mRNA retroposition in human cells: processed pseudogene formation,” The EMBO Journal, vol. 14, no. 24, pp. 6333–6338, 1995. View at Google Scholar · View at Scopus
  2. E. S. Balakirev and F. J. Ayala, “Pseudogenes: are they “junk” or functional DNA?” Annual Review of Genetics, vol. 37, pp. 123–151, 2003. View at Publisher · View at Google Scholar · View at Scopus
  3. C. Esnault, J. Maestre, and T. Heidmann, “Human LINE retrotransposons generate processed pseudogenes,” Nature Genetics, vol. 24, no. 4, pp. 363–367, 2000. View at Publisher · View at Google Scholar · View at Scopus
  4. H. H. Kazazian Jr., “Mobile elements: drivers of genome evolution,” Science, vol. 303, no. 5664, pp. 1626–1632, 2004. View at Publisher · View at Google Scholar · View at Scopus
  5. P. M. Harrison, N. Echols, and M. B. Gerstein, “Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome,” Nucleic Acids Research, vol. 29, no. 3, pp. 818–830, 2001. View at Publisher · View at Google Scholar · View at Scopus
  6. Z. Zhang, P. M. Harrison, Y. Liu, and M. Gerstein, “Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome,” Genome Research, vol. 13, no. 12, pp. 2541–2558, 2003. View at Publisher · View at Google Scholar · View at Scopus
  7. S. A. Korneev, J.-H. Park, and M. O'Shea, “Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene,” The Journal of Neuroscience, vol. 19, no. 18, pp. 7711–7720, 1999. View at Google Scholar · View at Scopus
  8. S. A. Korneev, V. Straub, I. Kemenes et al., “Timed and targeted differential regulation of nitric oxide synthase (NOS) and anti-NOS genes by reward conditioning leading to long-term memory formation,” The Journal of Neuroscience, vol. 25, no. 5, pp. 1188–1192, 2005. View at Publisher · View at Google Scholar · View at Scopus
  9. S. Hirotsune, N. Yoshida, A. Chen et al., “An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene,” Nature, vol. 423, no. 6935, pp. 91–96, 2003. View at Publisher · View at Google Scholar · View at Scopus
  10. L. Poliseno, L. Salmena, J. Zhang, B. Carver, W. J. Haveman, and P. P. Pandolfi, “A coding-independent function of gene and pseudogene mRNAs regulates tumour biology,” Nature, vol. 465, no. 7301, pp. 1033–1038, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. Y. J. Han, S. F. Ma, G. Yourek, Y.-D. Park, and J. G. N. Garcia, “A transcribed pseudogene of MYLK promotes cell proliferation,” The FASEB Journal, vol. 25, no. 7, pp. 2305–2312, 2011. View at Publisher · View at Google Scholar · View at Scopus
  12. O. H. Tam, A. A. Aravin, P. Stein et al., “Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes,” Nature, vol. 453, pp. 534–538, 2008. View at Google Scholar
  13. T. Watanabe, Y. Totoki, A. Toyoda et al., “Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes,” Nature, vol. 453, no. 7194, pp. 539–543, 2008. View at Publisher · View at Google Scholar · View at Scopus
  14. X. Guo, Z. Zhang, M. B. Gerstein, and D. Zheng, “Small RNAs originated from pseudogenes: cis- or trans-acting?” PLoS Computational Biology, vol. 5, no. 7, Article ID e1000449, 2009. View at Publisher · View at Google Scholar · View at Scopus
  15. Y.-Z. Wen, L.-L. Zheng, J.-Y. Liao et al., “Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 20, pp. 8345–8350, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. T. Hayakawa, T. Angata, A. L. Lewis, T. S. Mikkelsen, N. M. Varki, and A. Varki, “A human-specific gene in microglia,” Science, vol. 309, no. 5741, p. 1693, 2005. View at Publisher · View at Google Scholar · View at Scopus
  17. T. Benatar and M. J. H. Ratcliffe, “Polymorphism of the functional immunoglobulin variable region genes in the chicken by exchange of sequence with donor pseudogenes,” European Journal of Immunology, vol. 23, no. 10, pp. 2448–2453, 1993. View at Publisher · View at Google Scholar · View at Scopus
  18. T. J. Richmond and C. A. Davey, “The structure of DNA in the nucleosome core,” Nature, vol. 423, no. 6936, pp. 145–150, 2003. View at Publisher · View at Google Scholar · View at Scopus
  19. D. E. Schones, K. Cui, S. Cuddapah et al., “Dynamic regulation of nucleosome positioning in the human genome,” Cell, vol. 132, no. 5, pp. 887–898, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. T. N. Mavrich, I. P. Ioshikhes, B. J. Venters et al., “A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome,” Genome Research, vol. 18, no. 7, pp. 1073–1083, 2008. View at Publisher · View at Google Scholar · View at Scopus
  21. Y. Zhang, Z. Moqtaderi, B. P. Rattner et al., “Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo,” Nature Structural and Molecular Biology, vol. 16, no. 8, pp. 847–852, 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. D. Zheng, A. Frankish, R. Baertsch et al., “Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution,” Genome Research, vol. 17, no. 6, pp. 839–851, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. P. M. Harrison, D. Zheng, Z. Zhang, N. Carriero, and M. Gerstein, “Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability,” Nucleic Acids Research, vol. 33, no. 8, pp. 2374–2383, 2005. View at Publisher · View at Google Scholar · View at Scopus
  24. R. E. Dickerson, “Definitions and nomenclature of nucleic acid structure parameters,” Journal of Biomolecular Structure & Dynamics, vol. 6, no. 4, pp. 627–634, 1989. View at Publisher · View at Google Scholar · View at Scopus
  25. A. V. Morozov, K. Fortney, D. A. Gaykalova, V. M. Studitsky, J. Widom, and E. D. Siggia, “Using DNA mechanics to predict in vitro nucleosome positions and formation energies,” Nucleic Acids Research, vol. 37, no. 14, pp. 4707–4722, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. J.-Y. Wang and G. Liu, “Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning,” Chromosome Research, vol. 20, no. 7, pp. 889–902, 2012. View at Publisher · View at Google Scholar · View at Scopus
  27. Z. Zhang, P. Harrison, and M. Gerstein, “Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome,” Genome Research, vol. 12, no. 10, pp. 1466–1482, 2002. View at Publisher · View at Google Scholar · View at Scopus
  28. S. Washietl, R. Machné, and N. Goldman, “Evolutionary footprints of nucleosome positions in yeast,” Trends in Genetics, vol. 24, no. 12, pp. 583–587, 2008. View at Publisher · View at Google Scholar · View at Scopus
  29. D. Tillo and T. R. Hughes, “G+C content dominates intrinsic nucleosome occupancy,” BMC Bioinformatics, vol. 10, article 442, 2009. View at Publisher · View at Google Scholar · View at Scopus