Progesterone-induced changes in nucleosome positioning in exons and flanking regions. (A) General profile of nucleosome density in exons and flanking sequences in control and hormone-stimulated T47D cells. Chromatin from permeabilized cells treated with MNase was isolated, mononucleosome-associated DNA deep-sequenced and the number of reads covering each nucleotide represented, after normalization by genomic DNA reads, relative to the 3′ splice site of exons. Profiles of nucleosome densities in R5020-included (B) and R5020-skipped (C) exons and their flanking exons and introns in control and hormone-stimulated T47D cells. (D,E) Profiles of nucleosome densities as in B,C, corresponding to regulated alternative exons located in genes that do not display changes in expression upon hormone stimulation. (F–I) Profiles of nucleosome densities as in B,C for alternative exons that experience a change in inclusion or skipping higher than twofold or with a ΔPSI of ≥0.25, as indicated.
