Transcriptome maps of general eukaryotic RNA degradation factors

Abstract

RNA degradation pathways enable RNA processing, the regulation of RNA levels, and the surveillance of aberrant or poorly functional RNAs in cells. Here we provide transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in the yeast Saccharomyces cerevisiae. The profiles reveal the distribution of degradation factors between different RNA classes. They are consistent with the canonical degradation pathway for closed-loop forming mRNAs after deadenylation. Modeling based on mRNA half-lives suggests that most degradation factors bind intact mRNAs, whereas decapping factors are recruited only for mRNA degradation, consistent with decapping being a rate-limiting step. Decapping factors preferentially bind mRNAs with non-optimal codons, consistent with rapid degradation of inefficiently translated mRNAs. Global analysis suggests that the nuclear surveillance machinery, including the complexes Nrd1/Nab3 and TRAMP4, targets aberrant nuclear RNAs and processes snoRNAs.

The Ccr4-Not complex monitors the translating ribosome for codon optimality

“…Such a handover could be beneficial since anchoring the complex to the Esite of an 80S ribosome located on the start codon would be an ideal way to assemble and activate the decapping machinery within spatial proximity to the 5' cap, while probably inhibiting further initiation. In line with this idea, recent RNA-binding studies of deadenylation and decapping factors showed an interesting distributed allocation on the 5'-and 3'-ends of the transcripts (8).…”

The Integrator complex terminates promoter-proximal transcription at protein-coding genes

“…Similar termination mechanisms are recognized in the yeast Saccharomyces cerevisiae, where the Nrd1-Nab3-Sen1 (NNS) complex directs termination using coordinated RNA binding and helicase activities (Bresson and Tollervey, 2018). Intriguingly, the NNS complex, which predominantly drives termination of non-coding RNAs, has also been implicated in premature termination at select mRNA loci (Merran and Corden, 2017;Porrua and Libri, 2015;Sohrabi-Jahromi et al, 2019). However, despite the regulatory potential of promoter-proximal attenuation, a similar phenomenon has not yet been described in metazoan cells.…”

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

“…Deep profiling of RBPs associated with a specific RNA processing pathway can yield unique insights into the specialization of RBPs. For example, profiling of 30 RBPs associated with RNA degradation gave insights into specific RNP complex variants with roles targeting specific subtypes of RNAs, providing a comprehensive view of how the wide array of RNAs in the cell are turned over [8]. In contrast, the relatively unbiased selection of 150 RBPs profiled here enabled us to query across a wide variety of RBP functions and binding modalities and, at a broad level, address the basic question of whether RNA targets identified by CLIP can generally predict the likely function of the RBP of interest.…”

“…Analyses of single RBP binding profiles by CLIP have provided unique insights into basic mechanisms of RNA processing, as well as identified downstream effectors that drive human diseases [5][6][7]. Further efforts to profile multiple human RBPs in the same family or regulatory function by CLIP illustrated coordinated and complex auto-and cross-regulatory interactions among RBPs and their targets [8][9][10]. Rising interest in organizing public deeply sequenced CLIP datasets to enable the community to extract novel RNA biology is apparent from newly available computational databases and integrative methods [11,12].…”