RC-Seq

RC-Seq

Retrotransposon capture sequencing (RC-Seq) is a high-throughput protocol to map and study retrotransposon insertions . In this method, after genomic DNA is fractionated, retrotransposon binding sites on DNA hybridize to transposon binding sites on a microarray. Deep sequencing provides accurate information that can be aligned to a reference sequence to discover novel retrotransposition events.

Pros:

• Ability to clearly identify and detect novel retrotransposition events
• Can specifically study transposon binding sites of interest
• High-throughput protocol

Cons:

• Different types of MEI require separate PCR experiments with different primers
• Hybridization errors can lead to sequencing unwanted DNA fragments
• PCR biases can underrepresent GC-rich templates
• Similar transposition binding sites can lead

• RC-Seq: Baillie J. K., Barnett M. W., Upton K. R., Gerhardt D. J., Richmond T. A., et al. (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479: 534-537

1. Upton K. R., Gerhardt D. J., Jesuadian J. S., Richardson S. R., Sanchez-Luque F. J., et al. (2015) Ubiquitous L1 mosaicism in hippocampal neurons. Cell 161: 228-239
2. Shukla R., Upton K. R., Munoz-Lopez M., Gerhardt D. J., Fisher M. E., et al. (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153: 101-111