TC-Seq

TC-Seq

Translocation-capture sequencing (TC-Seq) is a method developed to study chromosomal rearrangements and translocations . In this method, cells are infected with retrovirus expressing l-Scel sites in cells with and without activation-induced cytidine deaminase (AICDA or AID) protein. Genomic DNA from cells is sonicated, linker-ligated, purified, and amplified via semi-nested LM-PCR. The linker is then cleaved and the DNA is sequenced. Any AID-dependent chromosomal rearrangement will be amplified by LM-PCR, while AID-independent translocations will be discarded.

Pros:

• Can study chromosomal translocations within a given model or environment
• Random sonication generates unique linker ligation points, and deep sequencing allows reading through rearrangement breakpoints

Cons:

• PCR amplification errors
• Non-linear PCR amplification can lead to biases affecting reproducibility
• PCR biases can underrepresent GC-rich templates

• TC-Seq: Klein I. A., Resch W., Jankovic M., Oliveira T., Yamane A., et al. (2011) Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes. Cell 147: 95-106

1. Pefanis E., Wang J., Rothschild G., Lim J., Chao J., et al. (2014) Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. Nature 514: 389-393
2. Jankovic M., Feldhahn N., Oliveira T. Y., Silva I. T., Kieffer-Kwon K. R., et al. (2013) 53BP1 alters the landscape of DNA rearrangements and suppresses AID-induced B cell lymphoma. Mol Cell 49: 623-631