Genome-scale profiling of histone H3.3 replacement patterns in Drosophila S2 cells

Histones of higher eukaryotes are assembled into chromatin primarily during DNA replication, but at other times the histone H3.3 variant replaces canonical H3. We introduce a novel strategy for profiling epigenetic patterns based on H3.3 replacement, using microarrays covering about one third of the Drosophila melanogaster genome at 100-bp resolution. Striking patterns of H3.3 replacement were found over active genes and transposons. H3.3 replacement occurs prominently at sites of abundant RNA polymerase II and methylated H3 lysine-4 throughout the genome, and is enhanced on the dosage-compensated male X chromosome. Active genes are depleted of histones at promoters and are enriched in H3.3 from upstream to downstream of transcription units. Based on these findings, we propose that deposition and inheritance of actively modified H3.3 in regulatory regions maintains transcriptionally active chromatin. Keywords: Chromatin affinity-purification on microarray Chromatin affinity profiling of histones H3 and H3.3 on Drosophila cDNA and tiling arrays