Topological and transcriptional control of TCRβ antigen receptor diversification

Abstract

Abstract Antigen receptor (AgR) loci undergo distinct developmentally regulated changes that include a transcriptional burst and locus compaction to facilitate recombination between V and (D)J gene segments during the primary diversification process. In order to understand how this contributes to diverse AgR repertoires, we generated mice lacking T cell receptor beta (TCRβ) cis-regulatory and CTCF binding elements (CBEs) with potential to serve as locus loop anchors. We then systematically compared epigenetics, transcriptomes, and 3D genome topologies of wild-type and mutant thymocytes populations coupled with their TCRβ repertoires. We find that in DN thymocytes, contacts to the recombination center (RC) are limited to other transcriptionally active chromatin comprising of all Vβ segments, while excluding neighboring heterochromatic regions, supporting our prediction that compaction is driven by homotypic chromatin forces. We identify CBEs and cis regulatory elements that either a) serve as boundary elements, b) control select Vβ accessibility and interaction with the RC, or c) control proximal versus distal skewing of the repertoire. Collectively, our results reveal mechanisms by which CBEs cement TCRβ topological structures and allow efficient recombination of the distal Vβs during AgR diversification.