Libraries of Restriction Fragments that Contain Replication Initiation Sites (Bubbles)

Bubble-Seq prepares libraries of restriction fragments that contained replication initiation sites (bubbles) in vivo (Mesner et al., 2013). In this method, DNA from origin libraries is biotinylated by a 3ê-end tailing reaction with biotin-16-dUTP. The biotinylated DNA is sonicated and captured with streptavidin-coated beads. The free DNA fragments are purified and used to prepare a sequencing.


  • Simple protocol


  • Not yet adopted widely by the scientific community


Illumina Library prep and Array Kit Selector


None available yet


Foulk M. S., Urban J. M., Casella C. and Gerbi S. A. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Res. 2015;25:725-735

Mukhopadhyay R., Lajugie J., Fourel N., et al. Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization. PLoS Genet. 2014;10:e1004319