Identification of non-coding transcripts regulated by Rap1 and other transcription factors by RNA-seq analysis

Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. Here we identify that in Saccharomyces cerevisiae, the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes, and characterize them in the context of other non-coding RNAs regulated by chromatin and transcription related factors. Overall design: RNA-seq analysis of Saccharomyces cerevisiae S288C strains. Data include gene deletion strains (spt10?, spt21?, rlf2?), strains transformed with OsTIR1 ligase and auxin-inducible degron (IAA7) tagged proteins (Rap1, Spt6, Spt16), Rap1 auxin-inducible degron strains expressing depletion-insensitive Rap1 mutant proteins, or wild-type control strains. 2 biological replicates for each sample type and condition were analyzed. For each biological replicate, cells were grown overnight in YPD media, diluted, and treated with DMSO or 500 µM 3-indole-acetic acid (3-IAA, auxin). Samples for auxin-inducible degron strains were taken 2 hours after treatment with DMSO or 3-IAA. For wild-type and gene deletion strains, samples were taken in mid-logarithmic growth. RNA was subjected to rRNA depletion to generate TOTAL RNA-seq libraries, respectively.