In collaboration with Jernej Ule’s group at the Francis Crick Institute in London, UK, the Zarnack lab explores how different experimental steps can constrain the identification of RBP binding sites in CLIP experiments. To this end, they analysed publicly available and newly generated data for the RBPs PTBP1, eIF4A3 and U2AF65 that were produced with multiple different CLIP protocols, including iCLIP, eCLIP and irCLIP. Based on these comparisons, they present experimental considerations and computational approaches to enable an accurate identification of RBP crosslink sites.
Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K$, Ule J$
($ shared correspondence)
Insights into the design and interpretation of iCLIP experiments
Genome Biology (2017) 18:7. doi: 10.1186/s13059-016-1130-x