Nucleosome positioning by sequence, state of the art and apparent finale.
All major suggestions about the nucleosome positioning sequence pattern(s) are overviewed. Two basic binary periodical patterns are well established: in purine/pyrimidine alphabet - YRRRRRYYYYYR and in strong/weak alphabet -SWWWWWSSSSSW. Their merger in four-letter alphabet sequence coincides with first ever complete matrix of nucleosome DNA bendability derived from very large database of nucleosome DNA sequences. Its simplified linear form is CGGAAATTTCCG. Several independent ways of derivation of the same pattern are described. It appears that the pattern represents an ultimate solution of long-standing problem of nucleosome positioning, and provides simple means for nucleosome mapping on sequences with single-base resolution.
Trifonov
Edward N
EN
Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel. trifonov@research.haifa.ac.il
D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D042002:Chromatin Assembly and Disassembly / Q000235:genetics; D006657:Histones / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism*; D011485:Protein Binding; D016415:Sequence Alignment
D006657:Histones; D009707:Nucleosomes