Morphology of polytene chromosomes in JIL-1 and Su(var)3-9 double mutant backgrounds. Polytene chromosome preparations from third instar larvae were labeled with Hoechst or with propidium iodide to visualize the chromatin. (A) Polytene chromosome preparations from wild-type (wt) male and female larvae and from male and female homozygous JIL-1z2 larvae (z2/z2). Note the misalignment and intermixing of interband and banded regions and the extensive coiling and folding of the chromosome arms in JIL-1z2/JIL-1z2 mutant chromosomes. The male X chromosome (X) is particularly affected and no remnants of banded regions are discernable. (B) Polytene chromosomes from male and female JIL-1z2 Su(var)3-91/JIL-1z2 (z2/z2, 3-91), JIL-1z2 Su(var)3-92/JIL-1z2 (z2/z2, 3-92), and JIL-1z2 Su(var)3-91/JIL-1z2 Su(var)3-92 (z2, 3-91/z2, 3-92) larvae. (C) Polytene chromosomes from male and female JIL-1z2 Su(var)3-906/JIL-1z2 (z2/z2, 3-906) and JIL-1z2 Su(var)3-906/JIL-1z2 Su(var)3-906 (z2, 3-906/z2, 3-906) larvae. Note the marked improvement of polytene chromosome morphology of both male and female autosomes in B and C. The chromosome arms were to a large extent unfolded with reduced ectopic contacts and a clearly discernible banding pattern that in some cases attained near wild-type morphology. In contrast, there was no discernible improvement in the morphology of the male X chromosome. (D) High magnification examples of regions of polytene chromosomes from JIL-1z2 Su(var)3-91/JIL-1z2 (z2/z2, 3-91) and JIL-1z2 Su(var)3-906/JIL-1z2 Su(var)3-906 (z2, 3-906/z2, 3-906) larvae with near wild-type morphology of band and interband regions.