RNA–DNA sequence differences in Saccharomyces cerevisiae

Abstract

Alterations of RNA sequences and structures, such as those from editing and alternative splicing, result in two or more RNA transcripts from a DNA template. It was thought that in yeast, RNA editing only occurs in tRNAs. Here, we found that Saccharomyces cerevisiae have all 12 types of RNA-DNA sequence differences (RDDs) in the mRNA. We showed these sequence differences are propagated to proteins, as we identified peptides encoded by the RNA sequences in addition to those by the DNA sequences at RDD sites. RDDs are significantly enriched at regions with R-loops. A screen of yeast mutants showed that RDD formation is affected by mutations in genes regulating R-loops. Loss-of-function mutations in ribonuclease H, senataxin, and topoisomerase I that resolve RNA-DNA hybrids lead to increases in RDD frequency. Our results demonstrate that RDD is a conserved process that diversifies transcriptomes and proteomes and provide a mechanistic link between R-loops and RDDs.

RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system

“…Therefore, our work sets the stage for investigating RNA editing in other bacterial species that harbor this enzyme. Moreover, tadA's orthologs (such as Tad1p and ADAT) are found in eukaryotes (yeast [Wang et al 2016] and human [Grice and Degnan 2015], for example). Since we now implicated tadA in mRNA editing, in addition to its established role in tRNA editing, future studies should examine whether its orthologs are involved in mRNA editing in other organisms too.…”

“…Inosine in turn can be identified by the translational or genetic machinery (e.g., reverse transcriptase) as a guanosine (G). A-to-I editing can recode proteins in eukaryotes (for example, humans and fungi) (Knoop 2011;Liu et al 2016;Wang et al 2016). The majority of editing events found in humans occur in untranslated regions, while only a small fraction of editing events are found in coding regions, of which only a few lead to nonsynonymous recoding (Ramaswami and Li 2014).…”

“…Recent advances in sequencing technologies have facilitated the discovery of RNA modifications and edited sites in an unprecedented level both in the nucleus (Ramaswami et al 2013;Bazak et al 2014;Schwartz et al 2014;Liu et al 2016;Wang et al 2016) and within organelles (Bar-Yaacov et al 2013;Bentolila et al 2013;Oldenkott et al 2014). However, editing events in mRNA were so far not reported in bacteria.…”

RNA abasic sites in yeast and human cells

“…Cells have different mechanisms to resolve R-loops, including the use of RNase H enzymes to cleave the RNA in the hybrids ( 39 – 41 ) and topoisomerase to unwind the DNA ( 41 , 42 ). Yeast deletion mutants of genes that encode these enzymes are known to accumulate more R-loops ( 41 – 43 ). Thus, detailed mapping showed a genome-wide increase in R-loops when genes encoding the RNase H enzymes were deleted in yeast ( 44 ).…”

Systematic Nucleotide Exchange Analysis of ESTs From the Human Cancer Genome Project Report: Origins of 347 Unknown ESTs Indicate Putative Transcription of Non-Coding Genomic Regions

“…Several types of RNAs with no sequence homology to template genomes exist. This includes RNA-DNA differences (Blank et al, 1986;Ninio, 1991;Li et al, 2011;Bahn et al, 2012;Strathern et al, 2012;Bar-Yaacov et al, 2013;Knippa and Peterson, 2013;Zhou et al, 2013;Wang et al, 2016), post-transcriptional editing (Bass, 2002;Schaub and Keller, 2002;Chen and Bundschuh, 2012;Park et al, 2012;Wang IX et al, 2014a;Lee et al, 2015), post-transcriptional hyper editing (Porath et al, 2014) and polymerase template switching (Lee et al, 2007;Löytynoja and Goldma n, 20 17). Transcript fusion exp lains some noncanonical RNAs (Kumar et al, 2016;López-Nieva et al, 2019;Singh et al, 2019).…”