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

Interactions between transcription and cohesin-mediated loop extrusion can influence 3D chromatin architecture. However, their relevance in biology is unclear. Here, we report a direct role for such interactions in the mechanism of antibody class switch recombination (CSR) at the murine immunoglobulin heavy chain locus (Igh). Using Tri-C to measure higher-order multiway interactions on single alleles, we find that the juxtaposition (synapsis) of transcriptionally active donor and acceptor Igh switch (S) sequences, an essential step in CSR, occurs via the interaction of loop extrusion complexes with a de novo topologically associating domain (TAD) boundary formed via transcriptional activity across S regions. Surprisingly, synapsis occurs predominantly in proximity to the 3′ CTCF-binding element (3′CBE) rather than the Igh super-enhancer, suggesting a two-step mechanism whereby transcription of S regions is not topologically coupled to synapsis, as has been previously proposed. Altogether, these insights advance our understanding of how 3D chromatin architecture regulates CSR. [Display omitted] • The multiway interactome of single Igh alleles undergoing CSR is revealed by Tri-C • Transcription of switch (S) regions is topologically uncoupled from S-S synapsis • Transcription creates a de novo TAD boundary in Igh S regions • Interaction of cohesin complexes with TAD boundaries underpins S-S synapsis CSR generates new antibody isotypes via deletional recombination between transcribed and juxtaposed (synapsed) switch (S) sequences of the immunoglobulin heavy chain genes. Here, the authors report that transcription creates a topological barrier that facilitates S-S synapsis, thereby revealing how interactions between cohesin and transcription complexes directly influence the mechanism of a major biological process. [ABSTRACT FROM AUTHOR]