Abstract
SummaryEukaryotic genomes generate a heterogeneous ensemble of mRNAs and long noncoding RNAs (lncRNAs). LncRNAs and mRNAs are both transcribed by Pol II and acquire 5′ caps and poly(A) tails, but only mRNAs are translated into proteins. To address how these classes are distinguished, we identified the transcriptome-wide targets of 13 RNA processing, export, and turnover factors in budding yeast. Comparing the maturation pathways of mRNAs and lncRNAs revealed that transcript fate is largely determined during 3′ end formation. Most lncRNAs are targeted for nuclear RNA surveillance, but a subset with 3′ cleavage and polyadenylation features resembling the mRNA consensus can be exported to the cytoplasm. The Hrp1 and Nab2 proteins act at this decision point, with dual roles in mRNA cleavage/polyadenylation and lncRNA surveillance. Our data also reveal the dynamic and heterogeneous nature of mRNA maturation, and highlight a subset of “lncRNA-like” mRNAs regulated by the nuclear surveillance machinery.
Highlights
High-throughput transcriptome analyses in eukaryotes have revealed pervasive transcription at most, if not all, genomic loci
Transcriptome-wide Analysis of ribonucleoprotein particles (RNPs) Composition To establish how and when different classes of polymerase II (Pol II) transcripts are distinguished in the cell, we determined the transcriptomewide targets for 13 key mRNA biogenesis and turnover factors
Several cluster IV mRNAs overlap cryptic unstable transcripts (CUTs) (URA2, SER3, ADE12, IMD3, and LEU4) (Davis and Ares, 2006; Thiebaut et al, 2008), and we suggest that the ‘‘mixed’’ RNP profile of cluster IV reflects genes where mRNAs and long noncoding RNAs (lncRNAs) are transcribed concurrently
Summary
High-throughput transcriptome analyses in eukaryotes have revealed pervasive transcription at most, if not all, genomic loci. Many features are shared between lncRNAs and mRNAs; both classes of RNA possess 50-methylguanosine caps (Neil et al, 2009) and poly(A) tails (David et al, 2006) and have broadly similar lengths. Both are transcribed by RNA polymerase II (Pol II) from similar preinitiation complex assemblies (Rhee and Pugh, 2012) and can be regulated by common transcription factors. Despite these similarities, the fates and functions of lncRNAs and mRNAs are substantially different. Diverse nuclear functions have been attributed to lncRNAs, including the assembly of nuclear domains, directing chromatin-modification, resetting of epigenetic marks, and the regulation of mRNA transcription
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
