We were able to show a striking similarity between the mechanisms of transcription termination by RNA Polymerase I (which transcribes the rRNA precursors and RNA Polymerase II (which transcribes mRNA precursors. The results reveal potentially important links between the transcriptional and post-transcriptional steps in rRNA synthesis, and between ribosome biogenesis and mRNA synthesis. In both cases, the 5’ exonuclease Rat1 and its cofactor Rai1 act as a “torpedo” - degrading the nascent transcript and terminating transcription when they catch the transcribing polymerase.
Negative torsion behind transcribing polymerases can lead to opening of the DNA helix followed by hybridization of the nascent pre-rRNA to the template strand, forming an R-loop. Analyses of links between pre-rRNA transcription and processing showed that the loss of Topisomerase 1 enhances inherent R-loop formation on the rDNA, particularly over the 5’ region, imposing persistent transcription blocks when RNase H is limiting (El Hage et al., 2010).
A genome-wide screen for synthetic lethal (sl) interactions with loss of the nuclear exosome cofactors Rrp47/Lrp1 or Air1 identified 3’->5’ exonucleases, the THO complex required for mRNP assembly and Ynr024w (Mpp6). Sl-interactions with mpp6∆ were confirmed for rrp47∆ and nuclear exosome component Rrp6. Bioinformatic analyses revealed homology between Mpp6 and a human exosome cofactor, underlining the high conservation of the RNA surveillance system. Mpp6 is physically associated with the exosome and was localized to the nucleus. Functional analyses demonstrated roles for Mpp6 in the surveillance of both pre-rRNA and pre-mRNAs, and in the degradation of “cryptic” non-coding RNAs (ncRNAs) derived from intergenic regions and the rDNA spacer heterochromatin. Strikingly, these ncRNAs are also targeted by other exosome cofactors Rrp47, the TRAMP complex (which includes Air1) and the Nrd1/Nab3 complex, and are degraded by both Rrp6 and the core exosome. Heterochromatic transcripts and other ncRNAs are characterized by very rapid degradation and we predict that functional redundancy is an important feature of ncRNA metabolism (Milligan et al. 2008).