Decapping of Long Noncoding RNAs Regulates Inducible Genes

Decapping represents a critical control point in regulating expression of protein coding genes. Here, we demonstrate that decapping also modulates expression of long noncoding RNAs (IncRNAs). Specifically, levels of >100 IncRNAs in yeast are controlled by decapping and are degraded by a pathway that occurs independent of decapping regulators. We find many IncRNAs degraded by DCP2 are expressed proximal to inducible genes. Of these, we show several genes required for galactose utilization are associated with IncRNAs that have expression patterns inversely correlated with their mRNA counterpart. Moreover, decapping of these IncRNAs is critical for rapid and robust induction of GAL gene expression. Failure to destabilize a IncRNA known to exert repressive histone modifications results in perpetuation of a repressive chromatin state that contributes to reduced plasticity of gene activation. We propose that decapping and IncRNA degradation serve a vital role in transcriptional regulation specifically at inducible genes.