Identification of RNA 3' ends in archaea

Transcription is the first of two steps in gene expression and is a highly regulated process in all domains of life. The transcription cycle can generally be divided into the three steps initiation, elongation and termination, with the latter being of high importance. Termination sets the 3' end of a transcript and an efficient termination mechanism is a prerequisite to prevent readthrough into downstream coding sequences, which can otherwise lead to conflicts between transcription and replication. This is of particular importance in prokaryotes, which are characterized by densely packed, operon-structured genomes. In contrast to termination, archaeal initiation and elongation are part of many studies and are nowadays widely understood. Recently, the b-CASP ribonuclease aCPSF1 was identified as the first ubiquitously distributed termination factor in archaea, capable of disrupting a processive transcription elongation complex. The factor was shown to recognize consecutive poly(U) signals, representing the archaeal intrinsic termination signal, in the nascentRNAand subsequently trigger cleavage downstreamof the termination site. This cooperative interaction between aCPSF1 and the intrinsic terminators appears to be one of the major determinants of termination efficiency, suggesting a 'two-in-one' termination mode to be present in archaea. In this study, we looked into RNA 3' end formation using Term-seq and Nanopore PCR-cDNA sequencing.