The RNA-binding protein Puf5 contributes to buffering of mRNA upon chromatin-mediated changes in nascent transcription.

Gene expression involves regulation of chromatin structure and transcription, as well as processing of the transcribed mRNA. While there are feedback mechanisms, it is not clear whether these include crosstalk between chromatin architecture and mRNA decay. To address this, we performed a genome-wide genetic screen using a Saccharomyces cerevisiae strain harbouring the H3K56A mutation, which is known to perturb chromatin structure and nascent transcription. We identified Puf5 (also known as Mpt5) as essential in an H3K56A background. Depletion of Puf5 in this background leads to downregulation of Puf5 targets. We suggest that Puf5 plays a role in post-transcriptional buffering of mRNAs, and support this by transcriptional shutoff experiments in which Puf5 mRNA targets are degraded slower in H3K56A cells compared to wild-type cells. Finally, we show that post-transcriptional buffering of Puf5 targets is widespread and does not occur only in an H3K56A mutant, but also in an H3K4R background, which leads to a global increase in nascent transcription. Our data suggest that Puf5 determines the fate of its mRNA targets in a context-dependent manner acting as an mRNA surveillance hub balancing deregulated nascent transcription to maintain physiological mRNA levels.

Nhp2 is a reader of H2AQ105me and part of a network integrating metabolism with rRNA synthesis.

Ribosome biogenesis is an essential cellular process that requires integration of extracellular cues, such as metabolic state, with intracellular signalling, transcriptional regulation and chromatin accessibility at the ribosomal DNA. Here, we demonstrate that the recently identified histone modification, methylation of H2AQ105 (H2AQ105me), is an integral part of a dynamic chromatin network at the rDNA locus. Its deposition depends on a functional mTor signalling pathway and acetylation of histone H3 at position K56, thus integrating metabolic and proliferative signals. Furthermore, we identify a first epigenetic reader of this modification, the ribonucleoprotein Nhp2, which specifically recognizes H2AQ105me. Based on functional and proteomic data, we suggest that Nhp2 functions as an adapter to bridge rDNA chromatin with components of the small subunit processome to efficiently coordinate transcription of rRNA with its post-transcriptional processing. We support this by showing that an H2AQ105A mutant has a mild defect in early processing of rRNA.