Structural Basis for Lesion Recognition and Commitment to Transcription-Coupled Repair

Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, plays important roles in the lesion-recognition steps of TC-NER. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles, how a lesion-arrested Pol II is committed to the recruitment of downstream repair factors, and what the fate is of a lesion-arrested Pol II remain unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles to establish a universal mechanism for the Rad26-mediated recognition of stalled Pol II. We also present a 3.1Å cryo-EM structure of lesion-arrested Pol II-Rad26 bound to a newly identified TC-NER factor, ELOF1/Elf1, that provides insights into its role in the commitment of lesion-arrested Pol II to TC-NER. Finally, we provide biochemical data revealing how Rad26 displaces a lesion-stalled Pol II during TC-NER. These results establish the structural basis of lesion-recognition, commitment to repair, and displacement of lesion-arrested Pol II during TC-NER