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Insights into the Link between the Organization of DNA Replication and the Mutational Landscape
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Genes 2019, 10(4), 269;

Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
Authors to whom correspondence should be addressed.
These authors contributed equally.
Received: 14 February 2019 / Revised: 25 March 2019 / Accepted: 29 March 2019 / Published: 2 April 2019
(This article belongs to the Special Issue DNA Replication Timing: Where, When, How and Why?)
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Centromeres serve a critical function in preserving genome integrity across sequential cell divisions, by mediating symmetric chromosome segregation. The repetitive, heterochromatic nature of centromeres is thought to be inhibitory to DNA replication, but has also led to their underrepresentation in human reference genome assemblies. Consequently, centromeres have been excluded from genomic replication timing analyses, leaving their time of replication unresolved. However, the most recent human reference genome, hg38, included models of centromere sequences. To establish the experimental requirements for achieving replication timing profiles for centromeres, we sequenced G1- and S-phase cells from five human cell lines, and aligned the sequence reads to hg38. We were able to infer DNA replication timing profiles for the centromeres in each of the five cell lines, which showed that centromere replication occurs in mid-to-late S phase. Furthermore, we found that replication timing was more variable between cell lines in the centromere regions than expected, given the distribution of variation in replication timing genome-wide. These results suggest the potential of these, and future, sequence models to enable high-resolution studies of replication in centromeres and other heterochromatic regions. View Full-Text
Keywords: DNA replication timing; centromeres; heterochromatin; next-generation sequencing DNA replication timing; centromeres; heterochromatin; next-generation sequencing

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Massey, D.J.; Kim, D.; Brooks, K.E.; Smolka, M.B.; Koren, A. Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing. Genes 2019, 10, 269.

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