Figure 1.

Assignment of paired-end reads to chimeric fragment classes. (A) Simplified representations of four cross-linked protein–DNA complexes. Restriction fragments (curved arrows) are connected via protein-mediated cross-links (circles). The four possible re-ligations between the different restriction fragment ends (α, β, γ and δ) are shown as colored lines. Four different structures of complexes are indicated, with one of the two fragments being gradually rotated by 90°. (B) In this representation, the two restriction fragments from (A) are arranged sequentially on the genomic sequence and the four possible re-ligations are represented as arcs colored accordingly. To the right, the four corresponding biotinylated re-ligation products and chimeric fragments are shown. Chimeric fragments are sequenced from one side on the forward strand (small arrows pointing to the right) and from the other side on the reverse strand (small arrows pointing to the left). Mapping of paired-end reads to the reference sequence results in four different relative orientations of reads, each corresponding to one of the four chimeric fragment classes. See Supplementary Figure S1 for a more detailed schematic representation.