Functional characterization of dynamic nascent RNA folding ensembles in real time

TL;DR

This study uses advanced imaging to observe how RNA molecules fold and how cellular factors influence their function in real time.

Contribution

A new method for tracking up to eight RNA types in real time, revealing how specific factors modulate RNA folding.

Findings

Ribosomal proteins, RNA modification enzymes, and antisense oligonucleotides modulate specific RNA folding classes.

Increased RNA accessibility correlates with ribosomal protein chaperoning during ribosome assembly.

The study provides a framework to link dynamic RNA folding and misfolding to function.

Abstract

RNA structure starts forming cotranscriptionally as the nascent RNA emerges from the RNA polymerase and is dynamically modulated by cellular factors. How individual RNA conformations, out of an ensemble of RNA molecules, relate to function is not well understood. Here, developing multicolor single-molecule fluorescence microscopy experiments, we track in real time nascent RNA structure formation, functionally characterizing up to eight different types of RNA molecules. We find that ribosomal proteins, RNA modification enzymes or antisense oligonucleotides specifically modulate a subset of the RNA folding classes. For example, we provide direct evidence that increased local RNA accessibility at specific sites correlates with the chaperoning activity of ribosomal proteins during ribosome assembly. These experiments provide a general framework to study how dynamic RNA folding, and misfolding, relates to function.

Single-molecule imaging shows the role of various factors in selectively reshaping nascent RNA molecules to modulate function.

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