Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions
Figure 5
Nucleosome oscillations around CTCF and Pol2 ChIP-seq peaks reveal DNA sequence modulation.
A) Red and green lines - experimental nucleosomes in ESCs around Pol2 sites using MNase-seq data from [28] and [73], correspondingly. Black and blue lines - average nucleosome occupancies around Pol2 ChIP-seq peaks predicted from the DNA sequence without competition with Pol2, at different core histone concentrations: KNCP*c0(NCP) = 1.4·10−6 and KNCP*c0(NCP) = 1.5 respectively. B) Heat map of the nucleosome density [73] for all individual genomic regions used in the calculation of the average profile in panel A. C) Raw energy of nucleosome formation averaged for the same genomic regions as in A using the method of Kaplan et al [13] (black line), and the difference between the raw energy and its fit with the 90th power polynomial regression, followed by the Fourier transformation. Changing the power of the polynomial regression in the range >50 did not affect the calculated NRL. D) Theoretical nucleosome occupancies in ESCs around CTCF sites predicted from sequence as in (A), black line: KNCP*c0(NCP) = 1.4·10−6, blue line: KNCP*c0(NCP) = 1.5. E) Red line - experimental nucleosome occupancies in ESCs around CTCF sites. Black line - theoretical nucleosome occupancies predicted from DNA sequence including competition with CTCF. hmax = 40 bp; V = 40 bp KNCP*c0(NCP) = 0.2; KCTCF*c0(CTCF) = 0.5. F) The probability to find a strong Trifonov's nucleosome determined by the (R5Y5)11 pattern, as a function of the distance from CTCF.