Mohsen Khorshid

TL;DR: This study developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs and revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions.

TL;DR: The results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites.

TL;DR: A powerful cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs that is termed PAR-CliP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) is developed.

TL;DR: The CLIPZ database and analysis environment, available at http://www.clipz.ch, aims to provide an open access repository of information for post-transcriptional regulatory elements, and can be visualized at the level of the genome and of individual transcripts.

TL;DR: By introducing photoreactive nucleosides that generate characteristic sequence changes upon crosslinking, this protocol allows one to separate RNA segments bound by the protein of interest from the background un-crosslinked RNAs.