FRAG-Seq
FRAG-Seq
Fragmentation sequencing (FRAG-Seq) is a method for probing RNA structure. In this method, RNA is digested using nuclease P1, followed by reverse transcription. Deep sequencing of the cDNA provides high-resolution single-stranded reads, which can be used to determine the structure of RNA by mapping P1 endonuclease digestion sites.
- FRAG-Seq: Underwood J. G., Uzilov A. V., Katzman S., Onodera C. S., Mainzer J. E., et al. (2010) FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods 7: 995-1001
- Imig J., Brunschweiger A., Brummer A., Guennewig B., Mittal N., et al. (2015) miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat Chem Biol 11: 107-114
- Luna J. M., Scheel T. K., Danino T., Shaw K. S., Mele A., et al. (2015) Hepatitis C virus RNA functionally sequesters miR-122. Cell 160: 1099-1110
- Wang P., Ning S., Zhang Y., Li R., Ye J., et al. (2015) Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer. Nucleic Acids Res 43: 3478-3489
- Grosswendt S., Filipchyk A., Manzano M., Klironomos F., Schilling M., et al. (2014) Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. Mol Cell 54: 1042-1054
- Newie I., Sokilde R., Persson H., Grabau D., Rego N., et al. (2014) The HER2-encoded miR-4728-3p regulates ESR1 through a non-canonical internal seed interaction. PLoS One 9: e97200