A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon

We investigated the post-transcriptional landscape in Halobacterium salinarum NRC-1. For that, we built an atlas of the transcriptome, ribosome footprints, and proteome using samples collected over a growth curve in bulk culture. Further, for each gene, we overlaid SmAP1 binding sites, putative cis-acting antisense RNAs (asRNA), putative transcript processing sites (TPS), and differential expression in one RNase knockout mutant (VNG2099C). To observe the effect of SmAP1 knockout on the activity of putatively post-transcriptionally regulated transposase transcripts, we performed long-read DNA sequencing. We made available the raw SmAP1 RIP-Seq and SmAP1 knockout DNA-Seq data in this BioProject.