Figure 2. Polytene Bands are TADs.

(A) Normalized Hi-C heatmap (15 kb bins) of a 3 Mb region of polytene chromosome 2L. In the left panel, areas bounded by black boxes represent locations of polytene bands for which reliable DNA sequence coordinates are available (Belyaeva et al., 2012; Vatolina et al., 2011). In the right panel, areas bounded by black boxes represent TADs.

(B) Photographic image (bottom) of the region of polytene chromosome 2L from (A) and the same region of Bridges’s chromosome map (top). Arrows indicate bands represented by black boxes in (A). The DNA sequence coordinates of other bands in this region are not known and therefore cannot be compared with the Hi-C data. Adapted from (Lefevre, 1976).

(C) Mean directionality index (DI) of polytene bands (upper panel; n = 61) and heatmap of the directionality index of each band along its length (lower panel). Bands were normalized to the same length and 50 kb of flanking DNA is shown next to each normalized band.

(D) Heatmap of the agreement between polytene bands (n = 61) and TADs. Each band is represented by a row. Bands were normalized to the same length and 50 kb of flanking DNA is shown next to each normalized band. Orange segments overlap with polytene TADs, black segments overlap with regions between TADs.

(E) Fraction of band boundaries (n = 122) at the distance indicated on the abscissa from the closest TAD boundary (calculated in 20 kb windows).

See also Figures S3, S4, and S5 and Table S1.