Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

Yeast Nucleosomes Mapped with High Resolution by Paired-end Sequencing Exhibit Strong Positioning Patterns

Despite intense efforts, recently summarized in a series of publications (1-14), understanding nucleosome positioning continues to be challenging. Recent advances in massively parallel shotgun sequencing techniques allowed detecting nucleosome positions across the genomes of yeast (15, 16), nematode (17) and human (18). Millions of DNA fragments derived in the course of micrococcal nuclease cleavage were partially sequenced at the 5’ end. As a result, the ‘properly’ trimmed nucleosome core particles have been mixed up with the over-digested or incompletely trimmed nucleosomes. To resolve this ambiguity, we used the paired-end sequencing technique and obtained ~15 million paired reads that are uniquely mapped to the yeast genome (19). The lengths of DNA fragments obtained in this way span the interval from 120 bp (over-digested core particles) to 180 bp (poorly trimmed nucleosomes), with the highest occurrence at 150 bp. The data for 147-152 bp-long fragments (~5 million) were compared with the two published datasets, one with the same length interval, 147-152 bp (~72,000) (16), and the other with the estimated length 147 bp (~50,000) (20).

The high-resolution nucleosomes in our new dataset are depleted in the promoter regions and positioned regularly downstream of gene starts, consistent with the earlier studies (16, 20). This regularity was further supported by the start-to-start distance correlation function having periodicity of 160-170-bp, close to the yeast nucleosome repeat ~165 bp. A detailed analysis of this distance correlation rendered a clear 10-bp periodicity, more pronounced than in the two published datasets (16, 20). Moreover, a stronger variation of occurrence of the AT-containing fragments (21) was found in the paired-end nucleosomes (19). This new dataset is being used to analyze the occurrence of the DNA dimers, trimers and tetramers in various positions in the nucleosome core particles, and to further develop our scheme for prediction of the nucleosome positioning (9).

  1. A. Travers, E. Hiriart, M. Churcher, M. Caserta, and E. Di Mauro, J Biomol Struct Dyn 27, 713-724 (2010).
  2. F. Xu, and W. K. Olson, J Biomol Struct Dyn 27, 725-739 (2010).
  3. E. N. Trifonov, J Biomol Struct Dyn 27, 741-746 (2010).
  4. P. De Santis, S. Morosetti, and A. Scipioni, J Biomol Struct Dyn 27, 747-764 (2010).
  5. G. A. Babbitt, M. Y. Tolstorukov, and Y. Kim, J Biomol Struct Dyn 27, 765-780 (2010).
  6. D. J. Clark, J Biomol Struct Dyn 27, 781-793 (2010).
  7. S. M. Johnson, J Biomol Struct Dyn 27, 795-802 (2010).
  8. G. Arya, A. Maitra, and S. A. Grigoryev, J Biomol Struct Dyn 27, 803-820 (2010).
  9. F. Cui and V. B. Zhurkin, J Biomol Struct Dyn 27, 821-841 (2010).
  10. D. Wang, N. B. Ulyanov, and V. B. Zhurkin, J Biomol Struct Dyn 27, 843-859 (2010).
  11. S. M. West, R. Rohs, R. S. Mann, and B. Honig, J Biomol Struct Dyn 27, 861-866 (2010).
  12. Y. V. Sereda and T. C. Bishop. 14. J Biomol Struct Dyn 27, 867-887 (2010).
  13. I. Gabdank, D. Barash and E. N. Trifonov, J Biomol Struct Dyn 26, 403-411 (2009).
  14. I. Gabdank, D. Barash, and E. N. Trifonov, J Biomol Struct Dyn 28, 107-121 (2010).
  15. I. Albert, T. N. Mavrich, L. P. Tomsho, J. Qi, S. J. Zanton, S. C. Schuster and B. F. Pugh. Nature 446, 572-576 (2007).
  16. T. N. Mavrich, I. P. Ioshikhes, B. J. Venters, C. Jiang, L. P. Tomsho, J. Qi, S. C. Schuster, I. Albert and B. F. Pugh. Genome Res 18, 1073-1083 (2008).
  17. A. Valouev, J. Ichikawa, T. Tonthat, J. Stuart, S. Ranade, H. Peckham, K. Zeng, J. A. Malek, G. Costa, K. McKernan, A. Sidow, A. Fire and S. M. Johnson. Genome Res 18, 1051-1063 (2008).
  18. D. E. Schones, K. Cui, S. Cuddapah, T-Y. Roh, A. Barski, Z. Wang, G. Wei and K. Zhao. Cell 132, 887-898 (2008).
  19. H. A. Cole, B. H. Howard and D. J. Clark. Submitted for publication (2011).
  20. Y. Field, N. Kaplan, Y. Fondufe-Mittendorf, I. K. Moore, E. Sharon, Y. Lubling, J. Widom and E. Segal. PLoS Comp Biol 4, e1000216 (2008).
  21. S. C. Satchwell, H. R. Drew and A. A. Travers. J Mol Biol 191, 659-675 (1986).

Feng Cui1*
Hope A. Cole2
David J. Clark2
and Victor B. Zhurkin1

1Laboratory of Cell Biology, NCI, NIH
2Program in Genomics of Differentiation, NICHD, NIH Bethesda, MD 20892

*Phone: 301 402 6551
Fax: 301 402 4724