Specific heptamers show different patterns of nucleosome occupancy between cell lines and also between cell lines and <i>in vitro</i> chromatin.

<p>Mapped nucleosome midpoints centered over heptamer sequences revealed several different patterns of nucleosome positioning. (A) AT-rich heptamers that exclude nucleosomes both <i>in vivo</i> and <i>in vitro</i> showed “depleted” patterns centered on the sequence, such as the poly-A kmer AAAAAAA. (B) “Covered” motifs such as CAACGAC showed increased occupancy in all datasets. (C) “Noisy” motifs such as GATCACC showed no discernible pattern of nucleosome occupancy centered on the heptamer. (D) The homopolymeric motif CCCCCCC was depleted of nucleosomes in the <i>in vitro</i> dataset only (arrow marks <i>in vivo</i> occupancies, arrowhead indicates <i>in vitro</i> chromatin). (E) Long range ordering could be seen in the +/- 2000bp surrounding poly-C heptamers. Visibly phased nucleosomes marked with asterisks. (F) In contrast to the CCCCCC motif in (D), the AACAACA motif was more covered in the <i>in vitro</i> dataset than in the cell lines (arrowhead marks <i>in vitro</i> chromatin, arrow marks <i>in vivo</i>). (G-H) Some motifs showed cell line-specific occupancy of heptamers. Whereas AATAATA was more covered in the eye cell line (yellow line marked by arrowhead in G) than other cell lines or <i>in vitro</i> chromatin, CAACAGC was more covered in the leg cell line (H, arrowhead and purple line vs arrow other lines indicated by arrow), and CGAACGA was less covered in the haltere cell line (I, green line indicated by arrowhead vs other lines indicated by arrow).