RNA pol II assembly affects ncRNA expression
Pervasive transcription of RNA pol II has been addressed in several organisms. In S. cerevisiae, ncRNAs derived from pervasive transcription of RNA pol II have been further classified based on their sensitivity to different decay pathways, transcription termination pathways, or specific conditions for their expression. In this study, we demonstrate that altering RNA pol II assembly by using an rpb1 mutant, leads to a general drop in ncRNA transcription. We provide evidences that defects in RNA pol II assembly lead to a reduction in cryptic transcription, mainly of CUTs, a feature which is not influenced by the levels of its bidirectional open reading frame (ORF).  This feature is not dependent on a defect of exosome function. We propose that a defect in transcription termination could account for the reduction in ncRNAs in the rpb1 mutant. Overall design: Two independent biological replicates of each Saccharomyces cerevisiae strain were cultured in YPD liquid medium at 30ºC  until OD600 of about 0.8. After RNA extraction, sequencing cDNA libraries were performed using the QuantSeq 3' mRNA-Seq Library Prep Kit form Illumina following the manufacturer instructions.