Integrative transcriptomic analysis of S. acidocaldarius

Post-transcriptional regulation plays a key role in environmental adaptation, including rapid molecular responses to stress conditions. Archaea represent a domain containing well-adapted organisms to extreme conditions and changes in their habitat. To understand the importance of RNA-based post-transcriptional actions, a full-scale analysis of the presence of regulatory RNAs, their processing and interactions with other RNAs and proteins is indispensable. Here, we use the analytical combination of several RNA sequencing approaches to reveal the presence of a set of 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 expanded the annotation by 160 ncRNAs and 990 anti-sense RNAs (asRNAs), the location and motifs of over 6000 transcript processing sites, and the interaction of transcripts with Sm-like archaeal proteins (SmAPs). We found numerous correlated expression patterns for asRNAs to cognate mRNAs hinting a transcript-based regulation in gene expression, specifically in changing environmental conditions. Additionally, we observed differential binding preferences of SmAP1 and SmAP2 towards mRNA and ncRNAs suggesting a distribution of regulating roles of these chaperones. 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/).