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lncRNAs promote gene expression, too

GAL lncRNAs in yeast induce gene transcription by enabling gene looping through the formation of RNA-DNA hybrids. Long noncoding RNAs (lncRNAs) are mainly associated with transcriptional silencing. The inducible GAL gene cluster in Saccharomyces cerevisiae is repressed when the yeast are grown in glucose-rich medium by glucose-dependent repressors. Upon switching the yeast to a galactose-rich medium, two lncRNAs, GAL 10 lncRNA and GAL 10s lncRNA (collectively referred to as GAL lncRNA and both expressed from the GAL gene cluster), promote the induction of the repressed GAL genes, such as GAL1, GAL10, and GAL7. Cloutier et al. investigated the mechanism of lncRNA-mediated induction of repressed GAL genes. Comparing DBP2– yeast, which lacked the RNA helicase DBP2, with wild-type yeast showed that DBP2– promoted a greater increase in GAL gene cluster transcripts during the nutrient switch. In addition, Northern blotting analysis showed faster induction and increased abundance of GAL1, GAL10, and GAL7 transcripts in DBP2– and DBP2– trans GAL lncRNA (a strain in which the GAL lncRNA gene had been inactivated in the GAL gene cluster and inserted in a distant location) strains compared with wild-type or DBP2– GAL lncRNA– double-mutant strains, suggesting that the GAL lncRNA-coding sequences did not have to be within the GAL gene cluster to function. Yeast strains with a plasmid expressing RNaseH, an enzyme that degrades DNA-RNA hybrids termed R-loops, had reduced induction of GAL cluster genes, which suggested that GAL lncRNA may induce the formation of an R-loop structure to promote expression of the GAL cluster. Indeed, both wild-type and DBP2– yeast formed R-loops at the GAL cluster, which were detected by DNA-RNA immunoprecipitation (DRIP) assay. Yeast in which Dpb2 was depleted from the nucleus had increased R-loop structures in the DRIP assay compared with wild-type strains. Comparison of publicly available transcript data and DRIP data revealed that transcripts with increased expression in DBP2– yeast cells were associated with R-loop–associated genes in wild-type cells, consistent with an inhibitory effect of DBP2 on R-loop structure formation. Chromatin confirmation capture analysis, a method that identifies gene looping, showed a time-dependent increase in promoter-terminator looping in DBP2– strains compared with GAL lncRNA– or DBP2– GAL lncRNA– strains after nutrient switching. GAL lncRNA– strains had increased binding of transcriptional repressors at the GAL gene cluster promoters. Last, yeast lacking GAL lncRNA grew less well than did wild-type yeast when provided galactose as the carbon source. Thus, lncRNAs can induce gene expression by enabling the formation of R-loop structures. S. C. Cloutier, S. Wang, W. K. Ma, N. Al Husini, Z. Dhoondia, A. Ansari, P. E. Pascuzzi, E. J. Tran, Regulated formation of lncRNA-DNA hybrids enables faster transcriptional induction and environmental adaptation. Mol. Cell 61, 393–404 (2016). [PubMed]