Transcription levels of a long noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast

Abstract

Many long noncoding RNAs (lncRNAs) act in cis through transcription-coupled chromatin alterations that drive changes in local gene expression. How some cisacting lncRNAs promote and others repress gene expression remains poorly understood. Here we report that in S. cerevisiae transcription levels of the lncRNA IRT2, located upstream in the promoter of the inducer of meiosis gene, regulate opposing chromatin and transcription states. Low IRT2 transcription displays enhancer RNA-like features. At these levels, IRT2 promotes histone exchange delivering acetylated histone H3 lysine 56 to chromatin thereby facilitating recruitment of a transcription factor and consequently activating transcription.Conversely, increasing IRT2 transcription enhances chromatin assembly and transcriptional repression. The opposing functions of IRT2 direct a regulatory circuit, which ensures that cells expressing opposite, but not one of either, mating-type loci enter meiosis. Our data demonstrate that the transcription levels of an lncRNA are key to controlling gene expression and cell fate outcomes. Moretto et al.3

High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

“…To examine this systematically, we aggregated the data obtained from three pairs of comparisons representing each cell-fate transition: T1 (6h vs 2 h SPO), T2 (8h vs 6 h SPO) and T3 (60 min YPD vs 6 h SPO). We focussed on two features in the dataset: alternative TSS levels and distance between alternative-main TSS pairs, as both features have been described to affect gene expression, in multiple studies [34,42,64].…”

“…As quality check, we included spike-in controls for TSS-seq and TES-seq libraries as described previously [34,83]. In short, a pool of in vitro transcripts (IVTs) were used spike-in controls for both TSS-seq, and TES-seq libraries were prepared as previously described [46].…”

“…TSS-seq protocol was adapted and modified [20,43,44] and described previously [34,83]. In short, 50 ng of pooled IVTs were spiked into 1 mg of total RNA from each sample.…”

“…The TES-seq library preparation were adapted from previously described protocols [45,84], and were also described previously [34]. In short, from the same pool of fragmented mRNAs for each sample, at least 1 μg was used for TES-seq.…”

“…This process, known as transcriptional interference, is widespread in yeast, but also present in mammalian cells [28,[30][31][32]. Conversely, examples of upstream transcription activating downstream promoters have also been reported [33,34]. Thus, TSS/TES usage changes can have varying outcomes on gene expression.…”