Altered nuclease sensitivity at regulatory chromatin sites of Hmgn1−/−n2−/− MEFs. (A–C) Quantitative analysis of DNase I sensitivity at promoters and enhancers of three selected genes. The extent of DNase I digestion at regions overlapping either H3K4me1 or H3K4me3 (pink or blue in genome browser), quantified by PCR amplification. Loss of HMGNs affected regions overlapping with H3K4me1 more significantly than regions overlapping H3K4me3. Numbers in parentheses indicate the scales of the y-axes. (D) Loss of HMGN does not affect the kinetics of MNase digestion. (E) Deep sequencing of nucleosome positions reveals enhanced occupancy of unstable nucleosomes at the TSS of Hmgn1−/−n2−/− MEFs. Arrows point to the presence of a nucleosome detectable at the TSS in limited, but not extensive digests.
