Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB)

2 ARTICLES PUBLISHED IN JoVE

Biology

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Markus Hafner¹, Markus Landthaler², Lukas Burger³, Mohsen Khorshid³, Jean Hausser⁴, Philipp Berninger⁴, Andrea Rothballer¹, Manuel Ascano¹, Anna-Carina Jungkamp², Mathias Munschauer², Alexander Ulrich¹, Greg S. Wardle¹, Scott Dewell⁵, Mihaela Zavolan³, Thomas Tuschl¹

¹Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, ²Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, ³Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB), ⁴Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB), ⁵Genomics Resource Center, Rockefeller University

RNA transcripts are subject to extensive posttranscriptional regulation that is mediated by a multitude of trans-acting RNA-binding proteins (RBPs). Here we present a generalizable method to identify precisely and on a transcriptome-wide scale the RNA binding sites of RBPs.

Biology

3' End Sequencing Library Preparation with A-seq2

Georges Martin¹, Ralf Schmidt¹, Andreas J. Gruber¹, Souvik Ghosh¹, Walter Keller¹, Mihaela Zavolan^1,2

¹Computational and Systems Biology, Biozentrum, University of Basel, ²Swiss Institute of Bioinformatics, Biozentrum, University of Basel

This protocol describes a method for mapping pre-mRNA 3' end processing sites.