NUCLEOSOME DNA-SEQUENCE PATTERN REVEALED BY MULTIPLE ALIGNMENT OF EXPERIMENTALLY MAPPED SEQUENCES

Five different algorithms have been applied for detecting DNA sequence pattern hidden in 204 DNA sequences collected from the literature whi ch are experimentally found to be involved in nucleosome formation. Ea ch algorithm was used to perform a multiple alignment of the nucleosom e DNA sequences within the window 145 nt, the size of a nucleosome cor e DNA. From these alignments five pairs of AA and TT dinucleotide posi tional frequency distributions have been computed. The frequency profi les calculated by different algorithms are rather different due to sub stantial noise. They, however, share several important features. Both AA and TT dinucleotide positional frequencies display periodicity with the period of 10.3(+/-0.2) bases. TT dinucleotides appear to be distr ibuted symmetrically relative to AA dinucleotides of the same DNA stra nd, with the center of symmetry at the midpoint of the nucleosome core DNA. The phase shift between the AA and TT patterns is about 6 bp. Su perposition of the five pairs of the AA (TT) positional frequency prof iles has produced the refined pattern, with the above features well pr onounced. An interesting novel feature of the pattern is an absence of central peaks in the periodical AA and TT distributions. This may ind icate that the central section of nucleosome DNA, 15 bp around the dya d axis of the nucleosome, is not bent. Positional distributions of oth er dinucleotides were not found in this study to be as informative as the ones for AA and TT. (C) 1996 Academic Press Limited