The RNA molecule or the Transcription process: which is critical in the regulation of fbp1 gene activation mediated by metabolic stress-induced lncRNA (mlonRNA) in fission yeast

Recent studies have revealed important roles of promoter-associated long noncoding RNAs (lncRNAs) in the regulation of adjacent genes. One of the first such RNA identified is the metabolic stress-induced lncRNA (mlonRNA) in fission yeast, which is involved in the activation of the fbp1 gene under glucose starvation. Whether this promoter-associated lncRNAs function through the RNA molecule itself or through the act of transcription remains a fundamental unresolved question. We here discriminate between a role of mlonRNA molecules and their transcriptional process by selectively inducing degradation of mlonRNA. To this end, we introduced hammerhead ribozyme, a self-cleaving RNA sequence, into the mlonRNA transcripts. We found that degradation of mlonRNA resulted in delayed chromatin remodeling, which was attributable to the delayed binding of a key transcription factor, Atf1 during the early phase of glucose starvation. In contrast, during the late phase of glucose starvation, when fbp1 is robustly induced, the mlonRNA degradation had no detectable effect on chromatin configuration or Atf1 binding. Notably, a mutant strain lacking mlonRNA transcription exhibited more severe defects in the chromatin remodeling and subsequent fbp1 induction. These results indicate that, in the mlonRNA-mediated regulation, the transcription process plays a pivotal role, whereas the mlonRNA molecules themselves function as a supportive regulator that facilitates a rapid response to stress. This study therefore provides a selective reevaluation of the mlonRNA molecules in fbp1 gene regulation by eliminating RNA transcripts without perturbing the transcriptional process. (235 words) • Hammerhead ribozyme enables ncRNA elimination without affecting transcription process • mlonRNA molecules facilitate rapid chromatin remodeling though Atf1 recruitment • Transcription process rather than transcripts plays dominant roles in fbp1 regulation