Description

The five subtracks in this annotation correspond to five different time points relative to the start of the DNA synthesis phase (S-phase) of the cell cycle.

Display Conventions and Configuration

Regions that are replicated during the given time interval are shown in green. Varying shades of green are used to distinguish one subtrack from another. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide.

Methods

The experimental strategy adopted to map this profile involved isolation of replication products from HeLa cells synchronized at the G1-S boundary by thymidine-aphidicolin double block. Cells released from the block were labeled with BrdU at every two-hour interval of the 10 hours of S-phase and DNA was isolated from them. The heavy-light(H/L) DNA representing the pool of DNA replicated during each two-hour labeling period was separated from the unlabeled DNA by double cesium chloride density gradient centrifugation. The purified heavy-light DNA was then hybridized to a high-density genome-tiling Affymetrix array comprised of all unique probes within the ENCODE regions.

The raw data generated by the microarray experiments was processed by computing the enrichment of signal in a particular part of the S-phase relative to the entirety of the S-phase (10 hours). High confidence regions (P-value = 1E-04) of replication were mapped by applying the Wilcoxon Rank Sum test in a sliding window of size 10 kb using the standard Affymetrix data analysis tools and the April 2003 (hg15) version of the human genome assembly. These coordinates were then mapped to the July 2003 (hg17) assembly by UCSC using the liftOver tool.

Verification

The submitted data are from two biological experimental sets. Regions of significant enrichment were included from both of the biological replicates.

Credits

Data generation and analysis for this track were performed by the DNA replication group in the Dutta Lab at the University of Virginia: Neerja Karnani, Christopher Taylor, Hakkyun Kim, Louis Lim, Ankit Malhotra, Gabe Robins and Anindya Dutta.

Neerja Karnani and Christopher Taylor prepared the data for presentation in the UCSC Genome Browser.

References

Jeon, Y., Bekiranov, S., Karnani, N., Kapranov, P., Ghosh, S., MacAlpine, D., Lee, C., Hwang, D.S., Gingeras, T.R. and Dutta, A. Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A 102(18), 6419-24 (2005).