Figure 6: Nucleosomes are positioned downstream of DREAM promoter binding sites.

(a) Structural model of DREAM–DNA association constructed from the LIN54 DBD-CHR13 crystal structure from our study and the previously determined structure of the E2F4-DP2 DBD heterodimer bound to a CDE-like DNA sequence (1CF7.pdb). The LIN54 DBD binds the minor groove, while E2F4-DP2 DBDs bind the major groove. In this model built with four nucleotides separating the CHR and CDE elements, the DBDs bind to opposite sides of the helix. (b) Average read density profiles of E2F4 (orange) and nucleosomes (blue) 1,000 bp upstream and downstream of the TSS of 155 late cell cycle genes bound by the DREAM complex and containing a TTYRAA CHR motif (bold line) and 900 late cell cycle genes not bound by the DREAM complex and not containing a TTYRAA CHR motif (dashed line). The read density profile of nucleosomes and E2F4 surrounding 3,804 housekeeping genes (light dashed line) and 1,732 genes with low expression (dotted line) are included as references. The semi-transparent shade around the mean represents the standard error of the mean across the regions. The positions of the CHR (TTYRAA) and CDE (SGCGCGS) near the TSS of DREAM-bound late cell cycle genes are shown. Box plots indicate the median position (black bar), the 25th–75th percentile (box) and the 2.5th and 97.5th percentile (extended whiskers). (c) Read density profiles of nucleosomes surrounding the TSS of two late cell cycle genes bound by DREAM and containing a TTYRAA CHR: CDK1 (encodes CDK1) and CCNB2 (encodes Cyclin B2). A housekeeping gene, POLR2A (encodes RNA Pol II), is shown for comparison. Triangles indicate approximate locations of well-positioned nucleosomes. Asterisks indicate approximate locations of a CHR motif. (d) Schematic representation of the DREAM complex assembled on a promoter containing both CDE and CHR sites with a nucleosome nearby in the body of the gene.