Antisense non-coding RNA transcription targets AID to divergently transcribed genes in the B cell genome. Mus musculus strain:C57BL6

The vast majority of the mammalian genome has the potential to express non-coding RNA (ncRNA). The eleven subunit RNA exosome complex is the main source of cellular 3’-5’ exoribonucleolytic activity and can potentially regulate the mammalian non-coding transcriptome. We report the generation of a mouse model in which the essential subunit Exosc3 of the RNA exosome complex can be conditionally deleted. Exosc3-deficient B cells lack the ability to undergo normal levels of class switch recombination (CSR) and somatic hypermutation (SHM), two DNA mutagenesis processes used to generate antibody diversity via the B cell mutator protein Activation Induced cytidine Deaminase (AID). The transcriptome of Exosc3-deficient B cells has revealed the presence of many novel RNA exosome substrate ncRNAs. RNA exosome substrate RNAs include xTSS-RNA, transcription start site associated antisense transcripts that can exceed 500 base pairs in length and are transcribed divergently from cognate coding gene transcripts. xTSS-RNA are most strongly expressed at genes which accumulate AID mediated somatic mutations and/or are frequent translocation partners of DNA double strand breaks generated at IgH in B cells. Strikingly, translocations near TSSs or within gene bodies occur over regions of RNA exosome substrate ncRNA expression. These RNA exosome regulated, antisense transcribed regions of the B cell genome recruit AID and accumulate ssDNA structures containing RNA/DNA hybrids. We propose that RNA exosome regulation of ncRNA recruits AID to ssDNA forming sites of antisense and divergent transcription in the B cell genome, thereby creating a link between ncRNA transcription and overall maintenance of B cell genomic integrity.