Figure 1

Strand-seq involves sequencing of template strands only. Newly formed DNA strands containing BrdU (dashed lines) in parental cells (left panels), are removed in daughter cells after cell division, hence only the original template-strand DNA is sequenced (solid lines, right panels). One template is derived from the Watson (W) strand (shown in orange), and the other template is derived from the Crick (C) strand (shown in blue); centromeres are shown in green. (a) Identification of template strands by Strand-seq. Daughter cells inherit two template strands because there is a maternal (m) and paternal (p) copy of each chromosome (chromosome 1 shown). Chromatids segregate either with both Watson strands inherited into one daughter and both Crick strands in the other (top panel), or with one Watson and one Crick strand in each daughter cell (bottom panel). Sequence read density is plotted onto ideograms (gray bars) representing the template state of each chromosome; the template-strand 'dose’ is inferred from W and C read counts (scale bar shown at bottom of ideograms). (b) Sister chromatid exchange (SCE) results in changes to templates on chromosomes. An SCE event (red outline) has reads aligning to different template strands on either side of it. These events are reciprocal between daughter cells, and will always be seen as a change from a WC state to either a CC or WW state. (c) Translocations and inversions are identified by Strand-seq. Translocations will align in the direction of the template strand of the chromosome to which they translocated, but still map to their original chromosome location. For example, for the Philadelphia translocation between chr9 and chr22, sequence reads from the translocated portion of chr22 will still map to chr22, but will have the template inheritance pattern of chr9 (chr9 fragments shown as solid boxes, chr22 fragments shown as open boxes).