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Updated: Feb 6, 2026
Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
Published on: April 29, 2010
Dynamic changes in ORC localization and replication fork progression during tissue differentiation
Brian L Hua1,2,3, George W Bell1, Helena Kashevsky1
1Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.
Background:
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. Studies in Drosophila polytene cells, however, raised the possibility that impeding replication fork progression also plays a major role.
Results:
We 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.
Conclusions:
These 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.
Insights
Replication repression in Drosophila is not solely due to lack of origins. Impeding DNA replication fork progression, rather than origin inhibition, controls replication in regions lacking the Origin Recognition Complex (ORC).
Area of Science:
- Molecular Biology
- Genetics
- Cell Biology
Background:
- Genomic regions with repressed DNA replication are typically thought to be controlled by inhibiting replication origin activation.
- However, studies in Drosophila polytene cells suggest that impeding replication fork progression may also play a significant role.
Purpose of the Study:
- To investigate the mechanisms of replication repression in Drosophila polytene cells, focusing on tissue-specific underreplicated regions (URs).
- To determine the role of Origin Recognition Complex (ORC) binding and replication fork progression in controlling DNA replication.
Main Methods:
- Localization of the Origin Recognition Complex (ORC) in the larval fat body and salivary gland of Drosophila.
- Comparison of ORC binding patterns between different tissues and cell types (polytene vs. diploid).
- Analysis of underreplicated (UR) regions in relation to ORC binding sites and replication fork dynamics.
Main Results:
- ORC binding sites exhibit significant tissue specificity in Drosophila polytene cells.
- Common genomic domains lacking ORC and origins were identified in both salivary gland and fat body tissues.
- Replication occurred in ORC-deficient domains in some polytene tissues, indicating that ORC absence alone does not repress replication.
- Replication of ORC-deficient regions is dependent on the inhibition of replication forks originating outside these regions.
Conclusions:
- Inhibition of replication fork progression is a key mechanism for blocking replication in genomic regions that constitutively lack ORC.
- Replication fork progression can be regulated in both tissue-specific and genomic region-specific manners.
- Altered control of replication forks during differentiation is a critical factor to consider when evaluating sources of genome instability.
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