Weak Signal Carried by Chromatin DNA Sequences: Zooming In and Sobering Surprises

Abstract

The 35 year long story of the chromatin signal (code) started with discovery of a very weak 10-11 base sequence periodicity of AA and TT dinucleotides, detected by distance analysis (equivalent of autocorrelation in time series). It soon became clear that this is counter-phase oscillation of AA and TT, or rather of RR and YY - by a version of multiple alignment ("synchronous detection" in signal processing). The campaign incrementally agonized through reconstruction of signal from its parts, N-gram Shannon extension and strong nucleosomes (SNs) with visible sequence periodicity to (RRRRRYYYYY)n pattern, and culminated in this form, with small changes suggested by consensuses from strong nucleosomes. 10-11 base YR dinucleotide periodicity (first suggested by Zhurkin) is a part of the above consensus. The periodically repeating YR elements form long tracks of hundreds to thousands base-pairs indicating that the chromatin consists of columnar structures, rather than of solitary nucleosomes. In particular, the classical SV40 minichromosome appears to form one continuous column.