Chromatin structure marks cell-type and gender specific replication of the Drosophila genome

Duplication of eukaryotic genomes during S phase is coordinated in space and time. In order to identify zones of initiation and cell-type as well as gender-specific plasticity of DNA replication, we profiled replication timing, histone acetylation and transcription throughout the Drosophila genome. We observed two waves of replication initiation with many distinct zones firing in early and multiple, less defined peaks at the end of S phase, suggesting that initiation becomes more promiscuous at the end of S phase. A comparison of different cell types revealed widespread plasticity of replication timing on autosomes. Most occur in large regions but only half coincide with local differences in transcription. In contrast to confined autosomal differences, a global shift in replication timing occurs throughout the single male X chromosome. Unlike in females, the dosage compensated X chromosome replicates almost exclusively early. This difference occurs at sites which are not transcriptionally hyperactivated, but show increased acetylation of lysine 16 of histone H4. This suggests a transcription-independent, yet chromosome-wide process related to chromatin. Importantly, H4K16ac is also enriched at initiation zones as well as early replicating regions on autosomes during S phase. Together, our data reveal novel organizational principles of DNA replication of the Drosophila genome and imply chromatin structure as a determinant of replication timing locally and chromosome-wide. Keywords: cell type comparison, chip-chip, replication timing RNA was isolated from Kc and Cl8 cells (5 replicates each) and hybridized to gene expression arrays. RNA was isolated from kc ane Cl8 cells (2 replciates each) and hybridised to tiling arrays. Early and late replicating DNA was isolated from Kc (5 replicates), Cl8 (2 replicates) and S2 (2 replicates) cells and hybridized to tiling arrays. Replicating DNA from four S phase fractions ( 2 replicates each) was isolated from Kc cells and hybridized to tiling arrays, with genomic DNA (2 replicates) from Kc cells as a control. Nascent DNA was isolated from Kc cells and hybridized to tiling arrays, with genomic DNA as a control (3 replicates each). ChIP-chip was perfomred for RNA Polymerase II in Kc (2 replicates) and Cl8 (3 replicates) cells. ChIP-chip was performed for H4K16ac in Kc (3 replicates) and Cl8 (4 replicates) cells. ChIP-chip for H4K16ac was performed in early and late S phase Kc cells (2 replicates each).