Microarray Analysis of DNA Replication Timing

  • Neerja Karnani
  • Christopher M. Taylor
  • Anindya Dutta
Part of the Methods in Molecular Biology™ book series (MIMB, volume 556)


Although all of the DNA in an eukaryotic cell replicates during the S-phase of cell cycle, there is a significant difference in the actual time in S-phase when a given chromosomal segment replicates. Methods are described here for generation of high-resolution temporal maps of DNA replication in synchronized human cells. This method does not require amplification of DNA before microarray hybridization and so avoids errors introduced during PCR. A major advantage of using this procedure is that it facilitates finer dissection of replication time in S-phase. Also, it helps delineate chromosomal regions that undergo biallelic or asynchronous replication, which otherwise are difficult to detect at a genome-wide scale by existing methods. The continuous TR50 (time of completion of 50% replication) maps of replication across chromosomal segments identify regions that undergo acute transitions in replication timing. These transition zones can play a significant role in identifying insulators that separate chromosomal domains with different chromatin modifications.

Key words

Replication timing BrdU labeling tiling arrays TR50 


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Neerja Karnani
    • 1
  • Christopher M. Taylor
    • 2
  • Anindya Dutta
    • 1
  1. 1.Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleUSA
  2. 2.Department of Biochemistry and Molecular Genetics, and Department of Computer ScienceUniversity of VirginiaCharlottesvilleUSA

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