Transcription-coupled AID Deamination Damage Depends on ELOF1-associated RNA Polymerase II [RNA-seq]

In adaptive immunity, transcription-coupled damage is introduced into antibody genes by activation-induced cytidine deaminase (AID) to diversify antibody repertoire. However, the coordination between transcription and DNA damage/repair remains elusive. Here, we find that transcription elongation factor 1 (ELOF1) stabilizes paused RNA polymerase II (RNAPII) at transcription barriers, providing a platform for transcription-coupled DNA damage/repair. Using a genetic screen, we discover that ELOF1 is required for AID targeting and that ELOF1 deficiency results in defective antibody class switch recombination and somatic hypermutation in mice. While downstream transcription-coupled repair factors are dispensable for AID-damage, ELOF1 mechanistically facilitates both transcription-coupled damage and repair by stabilizing chromatin-bound RNAPII. In ELOF1-deficient cells, paused RNAPII tends to detach from chromatin and fails to recruit factors to induce or repair DNA damage. Our study places ELOF1 at the center of transcription-coupled DNA metabolism processes and suggests a transition of RNAPII from elongation to a DNA damage/repair scaffold. RNA-seq of ELOF1 proficient and deficient CH12F3 cells and splenic primary B cells. CH12F3 cells were stimulated with α-CD40, IL4, TGF-β for 1.5, 3 or 7 days before experiments. Splenic primary B cells were stimulated with IL4 and LPS for 2.5 or 3.5 days. For each sample, polyA RNA from Drosophia S2 cells were added at a ratio of 76ng/million cells as spike-in control. The library were prepared with NEB kits (E7770S, E7400L) using rRNA depletion method.