Distribution of STAT92E in polytene chromosomes depends on H1. Polytene chromosomes of salivary gland cells from L3 larvae were analyzed by indirect immunofluorescence (IF) staining with antibodies against H1 (red) and STAT92E (green). DNA was stained with DAPI (blue). Scale bars represent 10 μm. (A) Top, genome-wide localization of H1 and STAT92E in polytene chromosomes. Localization patterns of H1 and STAT92E extensively overlap in the euchromatic arms and the chromocenter of polytene chromosomes. DNA was stained with DAPI (blue). Bottom, higher magnification view of co-localization of H1 and STAT92E in polytene chromosome arms. Merged split image illustrates that STAT and H1 exhibit nearly identical localization patterns, which correlate with polytene bands. (B) Genome-wide localization of STAT92E in wild type, H1-depleted, Su(var)3-9/Su(var)3-9 and HP1-depleted polytene chromosomes. In H1-depleted salivary glands, the polytene chromosome structure is disrupted, and STAT92E staining is strongly reduced to barely above background. Neither Su(var)3-9 mutation nor HP1 depletion substantially affects STAT92E localization. (C) The occupancy of H1 and STAT92E at regulatory regions of euchromatic (tubulin) and heterochromatic (light, concertina) genes and transposable element ZAM. The occupancy was measured by qChIP in control and H1 RNAi alleles. The ordinate indicates the amounts of specific polymerase chain reaction (PCR) products in ChIP DNA samples relative to input DNA. All qChIP experiments were performed in triplicate. Error bars, standard deviation. (D) Genome-wide localization of H1 in STAT92E-depleted and hopTum-l mutant polytene chromosomes. The localization pattern of H1 is not affected and is similar to that in wild type chromosomes (compare to A).