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Mapping Cancer Cells’ Starting Lines

Graphic shows a strand of DNA with two different replication sites opening up so DNA can be copied. Above that graphic is shown a large peak of cytosine-guanine nucleotides that are methylated, and these sites are near the location where DNA replication begins.
High transcription rates reduce the frequency of replication initiation events in two human cancer cell lines, MCF7 and K562.

Many of the defective regulatory pathways that lead to aberrant proliferation in cancer converge on DNA replication. So replication regulatory pathways could be targeted to more specifically kill cancer cells.  Unfortunately such targeting would require knowing where and when DNA replication starts in the cancer genome.  In yeast, the locations of replication initiation sites on chromatin have been extensively mapped, but in human cancer cells only a handful of these sites have been identified.

Mirit Aladjem, Ph.D.,—collaborating with Yves Pommier, M.D., Ph.D,  in CCR’s Laboratory of Molecular Pharmacology, with Paul Meltzer, M.D.,in CCR’s Genetics Branch, and with James Doroshow, M.D., in NCI’s Division of Cancer Treatment and Diagnosis—has used genome-wide massively parallel sequencing to map these needed replication initiation events. She has created a database of all the replication initiation sites within non-repetitive DNA in two human cell lines.  Aladjem and her colleagues next compared this database with another NCI database profiling the transcription levels of all genes in the same cells ( ). When the team then analyzed these two databases, they discovered that genomic regions transcribed at moderate levels were generally associated with a high frequency of initiation events. And in genomic regions with high rates of transcription, very few replication initiation events were detected. While replication initiation events were absent from these transcription start sites, they were highly enriched in adjacent, downstream sequences. Aladjem reported these findings in the November issue of Genome Research.

Aladjem and her collaborators also looked at epigenetic influences and found that methylation of adjacent cytosine-guanine (CpG) sequences strongly increased the frequency of replication initiation events, whereas histone modifications did not have much effect on these start sites. By contrast, the likelihood of transcription decreases with an increase in CpG methylation, again showing an inverse relationship between replication and transcription.  So the Aladjem team suspect that high levels of transcription interfere with formation of pre-replication protein complexes.

This first whole-genome depository of human replication origin sequences in cancer cells provides the needed information on the sites where replication begins.  It can now help scientists to better understand the mechanics and regulation of DNA replication and possibly use this information to target the networks involved.

Martin MM, Ryan M, Kim R, Zakas AL, Fu H, Lin CM, Reinhold WC, Davis SR, Bilke S, Liu H, Doroshow JH, Reimers MA, Valenzuela MS, Pommier Y, Meltzer PS, Aladjem MI. Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res. 21:1822-1832. 2011.

Reviewed by Donna Kerrigan