Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading
- Heather K MacAlpine1,
- Raluca Gordan2,
- Sara K Powell1,
- Alexander J. Hartemink2 and
- David M MacAlpine1,3
- * Corresponding author; email: david.macalpine{at}duke.edu
Abstract
The origin recognition complex (ORC) is an essential DNA replication initiation factor conserved in all eukaryotes. In S. cerevisiae ORC binds to specific DNA elements; however, in higher eukaryotes, ORC exhibits little sequence specificity in vitro or in vivo. We investigated the genome-wide distribution of ORC in Drosophila and found that ORC localizes to specific chromosomal locations in the absence of any discernible simple motif. Open chromatin appears to be the underlying factor that is deterministic for ORC binding. ORC-associated sequences are enriched for the histone variant, H3.3, often at transcription start sites, and depleted for bulk nucleosomes. Although no clear sequence motif emerged from the ORC binding sites, we were able to use machine learning approaches to accurately discriminate between ORC-associated sequences and ORC-free sequences based solely on primary sequence. The complex sequence features that define ORC binding sites are highly correlated with nucleosome positioning signals and likely represent a preferred nucleosomal landscape for ORC association. The density of ORC binding along the chromosome is reflected in the time at which a sequence replicates, with early replicating sequences having a high density of ORC binding. Finally, we found a high concordance between sites of ORC binding and cohesin loading, suggesting that in addition to DNA replication, ORC may be required for the loading of cohesin on DNA in Drosophila
Footnotes
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- Received July 11, 2009.
- Accepted November 23, 2009.
- Copyright © 2009, Cold Spring Harbor Laboratory Press
