Nucleosome RNA sequence pattern revealed by multiple alignment of experimentally mapped sequences

Ilya Ioshikhes, Alex Bolshoy, Konstantin Derenshteyn, Mark Borodovsky, Edward N. Trifonov

Research output: Contribution to journalArticlepeer-review

Abstract

Five different algorithms have been applied for detecting DNA sequence pattern hidden in 204 DNA sequences collected from the literature which are experimentally found to be involved in nucleosome formation. Each algorithm was used to perform a multiple alignment of the nucleosome DNA sequences within the window 145 nt, the size of a nucleosome core DNA. From these alignments five pairs of AA and TT dinucleotide positional frequency distributions have been computed. The frequency profiles calculated by different algorithms are rather different due to substantial 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 distributed symmetrically relative to AA dinucleotides of the same DNA strand, 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. Superposition of the five pairs of the AA (TT) positional frequency profiles has produced the refined pattern, with the above features well pronounced. An interesting novel feature of the pattern is an absence of central peaks in the periodical AA and TT distributions. This may indicate that the central section of nucleosome DNA, 15 bp around the dyad axis of the nucleosome, is not bent. Positional distributions of other dinucleotides were not found in this study to be as informative as the ones for AA and TT.

Original languageEnglish
Pages (from-to)129-139
Number of pages11
JournalJournal of Molecular Biology
Volume262
Issue number2
DOIs
StatePublished - 20 Sep 1996
Externally publishedYes

Bibliographical note

Funding Information:
The authors are thankful to E. Kolker who kindly provided the original program for spectral analysis, Dr E. Shpigelman for helpful discussions and to Dr A. Neuwald for providing the Gibbs sampling program and helpful comments on its use. The work was carried out with support of Ministry of Absorption, Ministry of Science and Technology of Israel, L. Bein Scholarship (to I.I.), NIH grant GM-47853, and by the WIS Genome Committee.

Keywords

  • Algorithm
  • Database
  • Multiple alignment
  • Nucleosome pattern
  • Nucleosome positioning

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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