Transcription pause and elongation regulators mediate somatic hypermutation

Somatic hypermutation (SHM) creates point mutations in the variable regions of immunoglobulin genes in activated B cells to support antibody affinity maturation1. SHM is initiated by activation-induced deaminase (AID), and the single-stranded DNA substrate of this cytosine deaminase is thought to arise during RNA polymerase II (PolII) transcription, perhaps in the context of PolII stalling2,3. The factors and mechanisms that mediate AID chromatin recruitment and generate its putative stalled PolII substrate during SHM are unknown. Negative elongation factor (NELF) stabilizes PolII in a paused state near the transcription start site. Release of NELF from PolII and the PolII elongation-versus-termination decision are regulated by opposing super elongation complex (SEC) kinase and integrator–protein phosphatase 2A (INT–PP2A) activities4. Here we demonstrate that NELF, the SEC components MLLT1 and MLLT3 and the INT–PP2A phosphatase module are required for SHM. We show that NELF can associate with PolII in the AID target window in the gene body and that, in the absence of NELF, AID fails to deaminate its targets despite efficient recruitment to chromatin and transcription by PolII. MLLT1 and MLLT3 interact with AID through their histone-binding YEATS domain and are required for AID enrichment at its target sites. We propose a physiological function for the NELF–PolII association in gene bodies in creating the stalled PolII substrate for AID action during SHM. The molecular factors and mechanisms that mediate the chromatin recruitment of activation-induced deaminase and the generation of its stalled polymerase II substrate during somatic hypermutation are identified.