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Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Nucleosome Positioning by Sequence, State of the Art

All major suggestions about the nucleosome-positioning sequence pattern(s) are overviewed. In binary presentation two basic periodical patterns are well established: in purine/pyrimidine alphabet - YRRRRRYYYYYR (1,2) and in strong/weak alphabet ?SWWWWWSSSSSW (3). There are only four different four-letter alphabet patterns that satisfy both binary forms. One of them coincides with first ever complete matrix of nucleosome DNA bendability (in simple consensus form CGGAAATTTCCG) derived (4) from very large database of nucleosome DNA sequences (5). Three other formally possible patterns may or may not correspond to physical reality. Mapping of the nucleosomes by matching to the full-length nucleosome DNA size bendability matrix suggests the single-base mapping accuracy.

References and Footnotes
  1. V. B. Zhurkin. FEBS Letters 158, 293-297 (1983).
  2. F. Salih, B. Salih, E. N. Trifonov. J. Biomol. Str. Dyn. 26, 273-282 (2008).
  3. H.-R. Chung, M. Vingron. J. Molec. Biol. (2008), doi: 10. 1016/j.jmb.2008.11.049 (in press).
  4. I. Gabdank, D. Barash, E. N. Trifonov. J. Biomol. Str. Dyn. 26, 403-412 (2009).
  5. S. M. Johnson, F. J. Tan, H. L. McCullough, D. P. Riordan, A. Z. Fire. Genome Research 16, 1505-1516 (2006).

Edward N. Trifonov1,2

1Genome Diversity Center
Institute of Evolution
University of Haifa
Mount Carmel, Haifa 31905, Israel
2Division of Functional Genomics and Proteomics
Faculty of Science
Masaryk University
Kamenice 5, Brno CZ-62500, Czech Republic

trifonov@research.haifa.ac.il