Bioinformatics, Vol 15, 187-193, Copyright © 1999 by Oxford University Press
H Herzel, O Weiss and EN Trifonov
MOTIVATION: Completely sequenced genomes allow for detection and analysis
of the relatively weak periodicities of 10-11 basepairs (bp). Two sources
contribute to such signals: correlations in the corresponding protein
sequences due to the amphipatic character of alpha-helices and the folding
of DNA (nucleosomal patterns, DNA supercoiling). Since the topological
state of genomic DNA is of importance for its replication, recombination
and transcription, there is an immediate interest to obtain information
about the supercoiled state from sequence periodicities. RESULTS: We show
that correlations within proteins affect mainly the oscillations at
distances below 35 bp. The long-ranging correlations up to 100 bp reflect
primarily DNA folding. For the yeast genome these oscillations are
consistent in detail with the chromatin structure. For eubacteria and
archaea the periods deviate significantly from the 10.55 bp value for free
DNA. These deviations suggest that while a period of 11 bp in bacteria
reflects negative supercoiling, the significantly different period of
thermophilic archaea close to 10 bp corresponds to positive supercoiling of
thermophilic archaeal genomes. AVAILABILITY: Protein sets and C programs
for the calculation of correlation functions are available on request from
the authors (see http://itb.biologie.hu- berlin.de).
ARTICLES
10-11 bp periodicities in complete genomes reflect protein structure and DNA folding
Institute for Theoretical Biology, Humboldt University, Invalidenstr. 43, D-10115 Berlin, Germany. h.herzel@biologie.hu-berlin.de
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