We have ablated the cellular RNA degradation machinery in differentiated B cells and pluripotent embryonic stem (ES) cells by conditional mutagenesis of core (Exosc3) and nuclear RNase (Exosc10) components of RNA exosome and identified a vast number of long non-coding RNAs (lncRNAs) and enhancer RNAs (eRNAs) with emergent functionality. Unexpectedly, eRNA-expressing regions accumulate R-loop structures upon RNA exosome ablation, thus demonstrating the role of RNA exosome in resolving deleterious DNA/RNA hybrids arising from active enhancers. We have uncovered a distal divergent eRNA-expressing element (lncRNA-CSR) engaged in long-range DNA interactions and regulating IgH 3′ regulatory region super-enhancer function. CRISPR-Cas9 mediated ablation of lncRNA-CSR transcription decreases its chromosomal looping-mediated association with the IgH 3′regulatory region super-enhancer and leads to decreased class switch recombination efficiency. We propose that the RNA exosome protects divergently transcribed lncRNA expressing enhancers, by resolving deleterious transcription-coupled secondary DNA structures, while also regulating long-range super-enhancer chromosomal interactions important for cellular function.

The transcription factor Batf controls TH17 differentiation by regulating the expression of both RORγt and RORγt target genes such as Il17. Here, we report the mechanism by which Batf controls in vivo class switch recombination (CSR). In T cells, Batf directly controls expression of the transcription factors Bcl-6 and c-Maf, both of which are needed for development of T follicular helper (TFH) cells. Restoring TFH activity to Batf−/− T cells in vivo requires co-expression of both Bcl-6 and c-Maf. In B cells, Batf directly controls the expression of both activation-induced cytidine deaminase (AID) and of IH-CH germline transcripts. Thus, Batf functions at multiple hierarchical levels across two cell types to globally regulate in vivo switched antibody responses.

No abstract