Bubble-Seq
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.
Advantages:
- Simple protocol
Disadvantages:
- Not yet adopted widely by the scientific community
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
None available yet
References:
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