Heterochromatin protein 1 (HP1) modulates replication timing of Drosophila heterochromatin

The replication of a genomic region during S-phase can be highly dynamic between cell types that differ in transcriptome and epigenome. Replication timing has been positively correlated with several histone modifications that occur at active genes, while repressive histone modifications mark late replicating regions. This raises the question if chromatin modulates the initiating events of replication. To gain insights into this question we have studied the function of heterochromatin protein 1 (HP1), a reader of to the repressive histone lysine 9 methylation of H3, in genome-wide organization of replication. Cells with reduced levels of HP1 show an advanced replication timing of centromeric repeats in agreement with the model that repressive chromatin mediates the very late replication of large clusters of constitutive heterochromatin. Surprisingly however regions with high levels of interspersed repeats on the chromosomal arms in particular on chromosome 4 and in pericentromeric regions of chromosome 2 behave differently. Here loss of HP1 results in delayed replication timing. The fact that these regions are bound by HP1 suggests a direct effect. Thus while HP1 mediates very late replication of centromeric DNA it is also required for early replication of autosomal regions with high levels of repeats. This observation of opposing functions of HP1 suggests a model where repeat inactivation on autosomes is required for proper activation of origins of replication that fire early, while HP1 mediated repression at constitutive heterochromatin is required to ensure replication of centromeric repeats at the end of S phase. Keywords: RNAi, chip-chip, replication timing RNA was isolated from Kc cells after knockdown of HP1 using RNAi (5 replicates) and hybridized to gene expression arrays. RNA was isolated from Kc cells after knockdown of HP1 using RNAi (2 replicates) and hybridised to tiling arrays. Early and late replicating DNA was isolated from Kc cells after knockdown of HP1 using RNAi (2 replicates) and hybridized to tiling arrays. ChIP-chip was perfomred for H3K27me3 and H3K9me2 in Kc (2 replicates) cells.