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).