Histone readers MLLT1 and MLLT3 concentrate AID to confer locus specificity

Activation-induced deaminase (AID) drives antibody diversification through class-switch recombination and somatic hypermutation of the immunoglobulin (Ig) genes, but its off-target mutagenic activity contributes to B cell lymphoma^1-5. How AID selectively mutates Ig loci and a restricted set of other genes remains unknown. Transcription is required for AID activity, but most transcribed genes are not mutated^1,5-7, and AID occupies more loci than it mutates^7-9. Here we identify the super elongation complex histone readers MLLT1 and MLLT3 as determinants of selective AID activity. Combined loss of MLLT1 and MLLT3 abolishes all AID-dependent mutagenic processes, recapitulating AID deficiency. AID-mutated genomic regions in mouse and human B cells are precisely marked by high MLLT1 and MLLT3 occupancy (MLLT1/MLLT3^high). Transcriptional changes after deleting both readers are modest and cannot explain the AID activity loss. Mechanistically, MLLT1 and MLLT3 are dispensable for global AID chromatin tethering but locally enrich AID downstream from promoter regions. Both readers bind to AID and act redundantly, but MLLT1 has a dominant role in mice through its intrinsically disordered region, which promotes condensates that selectively concentrate AID. Fusing AID to MLLT1 or MLLT3 is sufficient to restore class-switch recombination and mutagenesis in Mllt1^-/-Mllt3^-/- cells. These findings reveal that local MLLT1/MLLT3^high-dependent enrichment licenses AID at a restricted subset of genomic regions by spatially confining and concentrating its activity, probably through condensate formation.