CHD1 (chromodomain, helicase, DNA-binding domain) is a conserved member of the SWI2 family of chromatin remodeling factors. While not an essential gene, Chd1 is important for male and female fertility and wing development. CHD1 stoichiometrically co-localizes with elongating RNA Polymerase II (Pol II) on polytene chromosomes from salivary glands of third instar larvae, suggesting that CHD1 may be important to allow or facilitate the passage of Pol II through chromatin. However, CHD1 is not required for persistence of elongating Pol II on polytenes. Instead, we observed that CHD1 is important for genome-wide deposition of H3.3, a histone variant enriched at transcriptionally active genes, suggesting that CHD1 may be important for the deposition of new or recycled nucleosomes in the wake of Pol II. These findings are consistent with studies of the Chd1 remodeler in mammalian cell lines and yeast. To investigate the function of CHD1 across active genes in a metazoan, we have used both native and cross-linked chromatin immunoprecipitation (ChIP) to investigate changes in nucleosome composition across the transcriptionally active CrebA gene in salivary glands of third instar larvae. The use of salivary glands allows us to correlate our ChIP results with our low-resolution immuno-staining of polytene chromosomes. Consistent with prior immuno-staining results, we observe that CHD1 is enriched at CrebA relative to the transcriptionally inactive white gene, and the remodeler is not required for transcription of CrebA in salivary glands. Using both native and cross-linked ChIP, we investigate changes in H3/H3.3, H3K36me3, H3K56Ac and H3K9me2 across the CrebA gene in salivary glands lacking CHD1.