A web-based atlas for exploring post-transcriptional regulation in the archaeon Sulfolobus acidocaldarius

The archaeal domain contains organisms that are well-adapted to extreme conditions and changes in their habitat. Post-transcriptional regulation plays a key role in environmental adaptation, including rapid molecular responses to stress conditions. To understand the importance of RNA-based post-transcriptional regulation for these processes, a comprehensive analysis of the presence and processing of regulatory RNAs, as well as their interactions with other RNAs and proteins, is indispensable. Here, we combine the analysis of several RNA sequencing approaches to reveal the presence of a set of novel non-coding RNAs (ncRNAs), their expression in various conditions, processing, and molecular interactions in the transcriptome of Sulfolobus acidocaldarius, a model organism for Archaea. We expand its annotation by 102 intergenic ncRNAs (sRNAs) and 1,048 antisense RNAs (asRNAs), add the location and motifs of over 6,000 transcript processing sites, and determine the interaction of transcripts with Sm-like archaeal proteins (SmAPs), known RNA chaperones involved in RNA-based regulatory systems. We determined the correlation between the expression patterns of asRNAs and their cognate mRNAs, suggesting transcript-based regulation patterns in gene expression, particularly in response to changing environmental conditions. Additionally, we observed differential binding preferences of SmAP1 and SmAP2 toward mRNA and ncRNAs, suggesting a distribution of regulating roles of these chaperones. Finally, we provide an overview of our post-transcriptional data analysis results, optimized for custom exploration, in the form of a web-based transcriptome atlas (https://vicentebr.github.io/Sulfolobus_atlas/).

Post‑transcriptional regulation is a key control layer in gene expression. Yet, resources integrating antisense RNAs (asRNAs), RNA processing sites, and RNA-protein interactions are scarce for archaeal organisms. Here, we combine multiple RNA‑seq strategies and RIP‑seq to expand the Sulfolobus acidocaldarius transcriptome with 1,048 asRNAs, thousands of transcript processing sites, and the interactomes of the essential RNA chaperones Sm-like archaeal protein (SmAP)1 and SmAP2. Integrating the novel generated data for the re‑analysis of heat‑shock transcriptomics reveals a consistent upregulation of asRNAs and antagonistic expression profiles with their cognate mRNAs. Moreover, our publicly accessible web atlas provides a community platform to explore these datasets and assist in the formulation of new hypotheses about archaeal RNA regulation.