RT Journal
A1 Wang, Isabel X.
A1 Grunseich, Christopher
A1 Chung, Youree G.
A1 Kwak, Hojoong
A1 Ramrattan, Girish
A1 Zhu, Zhengwei
A1 Cheung, Vivian G.
T1 RNA–DNA sequence differences in Saccharomyces cerevisiae
JF Genome Research 
JO Genome Research 
YR 2016 
FD November 01 
VO 26 
IS 11 
SP 1544 
OP 1554 
DO 10.1101/gr.207878.116 
UL http://genome.cshlp.org/content/26/11/1544.abstract 
AB 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.