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 basepairs 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.