Mapping of Rpo21 RNA-binding sites in Saccharomyces cerevisiae with abrogated binding of Nab3 to PIC2

Using CRAC, we compared the transcriptomic occupancy of Rpo21 in a Saccharomyces cerevisiae BY4741 parental strain (PIC2-GFP) and two derived mutants lacking Nab3 RNA-binding sites in PIC2. The purpose of the experiment was to determine that changes in the abundance of differentially expressed transcripts, which had been previously identified by RNA-sequencing, were not caused by alterations in Rpo21 occupancy and transcription. Sequencing outputs were processed using the pyCRAC pipeline and peak calling was performed with DBPeaks, our newly developed package for identification and comparison of binding sites defined by RNA-binding footprinting techniques (e.g., CRAC, iCLIP, PAR-CLIP, etc.).