Structural basis of RNA-guided transcription by a dCas12f–σE–RNAP complex

Nature

by Renjian Xiao

March 4, 2026

In both natural and engineered biological systems, RNA-guided proteins have emerged as critical transcriptional regulators by modulating RNA polymerase (RNAP) and its associated factors1–3. In bacteria, diverse clades of repurposed TnpB and CRISPR-associated proteins repress gene expression by blocking transcription initiation or elongation, enabling non-canonical modes of regulatory control and adaptive immunity1,4,5. A distinct class of nuclease-dead Cas12f homologues (dCas12f) instead activates gene expression through its association with unique extracytoplasmic function sigma factors (σE)6, although the molecular basis has remained elusive. Here we reveal a new mode of RNA-guided transcription initiation by determining the cryo-electron microscopy structures of the dCas12f–σE system from Flagellimonas taeanensis. We captured multiple conformational and compositional states, including the DNA-bound dCas12f–σE–RNAP holoenzyme complex, revealing how RNA-guided DNA binding leads to σE–RNAP recruitment and nascent mRNA synthesis at a precisely defined distance downstream of the R-loop. Rather than following the classical paradigm of σE-dependent promoter recognition, these studies show that recognition of the −35 element is largely supplanted by CRISPR–Cas targeting, whereas the melted −10 element is stabilized through unusual stacking interactions rather than insertion into the typical recognition pocket. Collectively, this work provides high-resolution insights into an unexpected mechanism of RNA-guided transcription, expanding our understanding of bacterial gene regulation and opening new avenues for programmable transcriptional control. Cryogenic electron microscopy reveals how dCas12f with σE recruits RNAP to targeted DNA, initiating transcription at a fixed downstream distance, bypassing canonical −35 recognition and stabilizing the −10 element in an unusual manner.

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Originally published on Nature on 3/4/2026