Regulatory Mechanisms That Prevent Re-initiation of DNA Replication Can Be Locally Modulated at Origins by Nearby Sequence Elements

Eukaryotic cells must inhibit re-initiation of dna replication at each of the thousands of origins in their genome because re-initiation can generate genomic alterations with extraordinary frequency. to minimize the probability of re-initiation from so many origins,cells use a battery of regulatory mechanisms that reduce the activity of replication initiation proteins. given the global nature of these mechanisms,it has been presumed that all origins are inhibited identically. however,origins re-initiate with diverse efficiencies when these mechanisms are disabled,and this diversity cannot be explained by differences in the efficiency or timing of origin initiation during normal s phase replication. this observation raises the possibility of an additional layer of replication control that can differentially regulate re-initiation at distinct origins. we have identified novel genetic elements that are necessary for preferential re-initiation of two origins and sufficient to confer preferential re-initiation on heterologous origins when the control of re-initiation is partially deregulated. the elements do not enhance the s phase timing or efficiency of adjacent origins and thus are specifically acting as re-initiation promoters (rips). we have mapped the two rips to ~60 bp at rich sequences that act in a distance- and sequence-dependent manner. during the induction of re-replication,mcm2-7 reassociates both with origins that preferentially re-initiate and origins that do not,suggesting that the rip elements can overcome a block to re-initiation imposed after mcm2-7 associates with origins. our findings identify a local level of control in the block to re-initiation. this local control creates a complex genomic landscape of re-replication potential that is revealed when global mechanisms preventing re-replication are compromised. hence,if re-replication does contribute to genomic alterations,as has been speculated for cancer cells,some regions of the genome may be more susceptible to these alterations than others. © 2014 richardson,li.