Abstract
BackgroundGenomic regions repressed for DNA replication, resulting in either delayed replication in S phase or underreplication in polyploid cells, are thought to be controlled by inhibition of replication origin activation. Studies in Drosophila polytene cells, however, raised the possibility that impeding replication fork progression also plays a major role.ResultsWe exploited genomic regions underreplicated (URs) with tissue specificity in Drosophila polytene cells to analyze mechanisms of replication repression. By localizing the Origin Recognition Complex (ORC) in the genome of the larval fat body and comparing this to ORC binding in the salivary gland, we found that sites of ORC binding show extensive tissue specificity. In contrast, there are common domains nearly devoid of ORC in the salivary gland and fat body that also have reduced density of ORC binding sites in diploid cells. Strikingly, domains lacking ORC can still be replicated in some polytene tissues, showing absence of ORC and origins is insufficient to repress replication. Analysis of the width and location of the URs with respect to ORC position indicates that whether or not a genomic region lacking ORC is replicated is controlled by whether replication forks formed outside the region are inhibited.ConclusionsThese studies demonstrate that inhibition of replication fork progression can block replication across genomic regions that constitutively lack ORC. Replication fork progression can be inhibited in both tissue-specific and genome region-specific ways. Consequently, when evaluating sources of genome instability it is important to consider altered control of replication forks in response to differentiation.
Highlights
Genomic regions repressed for DNA replication, resulting in either delayed replication in S phase or underreplication in polyploid cells, are thought to be controlled by inhibition of replication origin activation
Tissue-specific programming of replication Prior to investigating mechanisms of underreplication we extended our previous analysis of the developmental regulation of differential DNA replication by examining two adult tissues and by changing our statistical method for determining genomic regions with altered gene copy number
The Malpighian tubules function as the kidney and are an unusual tissue in Drosophila, because of their persistence from the larval through the adult stage where they attain an average ploidy of 168C (Additional file 1: Figure S1)
Summary
Genomic regions repressed for DNA replication, resulting in either delayed replication in S phase or underreplication in polyploid cells, are thought to be controlled by inhibition of replication origin activation. The genome is organized into large replication timing domains that correspond to regions of higher-order chromatin structure defined by interaction maps [2]. As embryonic stem cells differentiate, replication timing domains consolidate into larger units, and 20% of the mouse genome changes its time of replication [3]. These changes are associated with altered gene expression within a replication timing domain, evidence for causality has not yet been established. The time in S phase when domains replicate has been proposed to be controlled at the level of replication
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