iPAR-CLIP

Our lab established a PAR-CLIP protocol for living C.elegans animals, called iPAR-CLIP. This allows to study RNA-binding protein interactions in vivo. Here, we list our published work, using this method. All sequencing data of published experiments are available through GEO.

In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target Sites

Anna-Carina Jungkamp, Marlon Stoeckius, Desirea Mecenas, Dominic Grün, Guido Mastrobuoni, Stefan Kempa, Nikolaus Rajewsky

Mol Cell. 2011 Dec 9;44(5):828-40. doi: 10.1016/j.molcel.2011.11.009.

PDF GEO raw data

Unambiguous identification of miRNA:target site interactions by different types of ligation reactions.

Grosswendt S, Filipchyk A, Manzano M, Klironomos F, Schilling M, Herzog M, Gottwein E, Rajewsky N.

Mol Cell. 2014 Jun 19;54(6):1042-54. doi: 10.1016/j.molcel.2014.03.049. Epub 2014 May 22.

PDF GEO raw data

A variety of dicer substrates in human and C. elegans.

Rybak-Wolf A, Jens M, Murakawa Y, Herzog M, Landthaler M, Rajewsky N

Cell. 2014 Nov 20;159(5):1153-67. doi: 10.1016/j.cell.2014.10.040.

PDF GEO raw data

 

A note on RNA thio labeling

The above papers utilized 4-thiouridine for RNA-labeling and crosslinking. We have also attempted to use 4-thiouracil as an alternative to 4-thiouridine for iPAR-CLIP in C.elegans. The raw data can be made available upon request by E-mail to Nikolaus Rajewsky.