Two modes of cis-activation of switch transcription by the IgH superenhancer

Abstract

Significance Immunoglobulin isotype switching plays an important role in adaptive immune responses. It requires transcription of switch regions from inducible promoters controlled by a long-range superenhancer (3′RR). Most stimuli induce more than one promoter on both chromosomes. Thus, it is unknown whether isotype (I) promoters compete for the 3′RR on the same chromosome. By performing allele-specific RT-qPCR assays, we show that the 3′RR activates promoters by either co-activation or competition and that the nature of the inducing signal plays a pivotal role in determining the activation mode. The two activation paths may have evolved to cope with different kinetics of primary immune responses. B cell isotype switching plays an important role in modulating adaptive immune responses. It occurs in response to specific signals that often induce different isotype (I) promoters driving transcription of switch regions, located upstream of the Ig heavy chain (IgH) constant genes. The transcribed switch regions can recombine, leading to a change of the constant gene and, consequently, of antibody isotype. Switch transcription is controlled by the superenhancer 3′ regulatory region (3′RR) that establishes long-range chromatin cis-interactions with I promoters. Most stimuli induce more than one I promoter, and switch transcription can occur on both chromosomes. Therefore, it is presently unknown whether induced I promoters compete for the 3′RR on the same chromosome. Here we performed single-chromosome RT-qPCR assays to examine switch transcription monoallelically in the endogenous context. We show that there are two modes of 3′RR-mediated activation of I promoters: coactivation and competition. The nature of the inducing signal plays a pivotal role in determining the mode of activation. Furthermore, we provide evidence that, in its endogenous setting, the 3′RR has a bidirectional activity. We propose that the coactivation and competition modes mediated by the 3′RR may have evolved to cope with the different kinetics of primary immune responses.