A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination

Conflicts between transcription and cohesin-mediated loop extrusion can majorly influence 3D chromatin architecture but whether these structural changes affect biological function is unknown. Here, we show that a critical step in antibody class switch recombination (CSR) in activated B cells, namely, the juxtaposition (synapsis) of donor and acceptor switch (S) recombination sequences at the immunoglobulin heavy chain locus (Igh), occurs at the interface of a de novo topologically associating domain (TAD) boundary formed via transcriptional activity at acceptor S regions. Using Tri-C to capture higher-order multiway chromatin conformations, we find that synapsis occurs predominantly in the proximity of distal 3 CTCF-binding sites and that this multiway conformation is abolished upon downregulation of transcription and loss of the TAD boundary at the acceptor S region. Thus, an insulating de novo TAD boundary created by the conflict between transcription and loop extrusion plays a direct role in the mechanism of CSR.