Poster abstracts
Poster number 85 submitted by Tina Jiayu Fu
Upstream RNA structure tunes intrinsic termination
Tina Jiayu Fu (Interdisciplinary Biological Sciences, Northwestern University), Julius Beau Lucks (Chemical and Biological Engineering, Northwestern University)
Abstract:
Intrinsic transcription termination is a widespread mechanism of bacterial gene regulation in which co-transcriptional formation of an RNA hairpin promotes release of the transcription complex. While the sequence and energetic features of intrinsic terminators have been extensively characterized, less is understood about how RNA structures formed upstream of the terminator influence this process, particularly beyond the immediately adjacent sequence context. Our lab recently found that an independently folding upstream RNA structure can suppress intrinsic termination if it noes not direct overlap with the terminator in sequence, suggesting that nascent RNA folding outside the canonical terminator can influence the termination decision. Here, we systematically investigate the structural features that determine this effect.
Using complementary in vivo reporter and single-round in vitro transcription assays, we perturb upstream RNA structure while independently varying its predicted stability, the position and topology of structural disruptions, and the strength of the downstream terminator. We find that changes in upstream structure can produce large differences in transcriptional readthrough, but these effects are not explained by folding free energy alone. Variants with similar predicted stability can exhibit substantially different termination behavior depending on where structural perturbations are introduced, with positions proximal to the terminator showing particularly strong effects. These results suggest that the organization of the folded upstream RNA, in addition to its overall thermodynamic stability, contributes to its ability to modulate termination. We are further extending this framework to compact tertiary RNA structures to test how higher-order structural features influence termination.
Together, this work establishes upstream nascent RNA structure as a tunable component of intrinsic termination and provides a framework for understanding how RNA folding beyond the canonical terminator contributes to transcriptional regulation.
Keywords: intrinsic termination, cotranscriptional RNA folding, RNA structurefunction