title: Noncoding RNA transcription targets AID to divergently transcribed loci in B cells.
abstract: The vast majority of the mammalian genome has the potential to express noncoding RNA (ncRNA). The 11-subunit RNA exosome complex is the main source of cellular 3'-5' exoribonucleolytic activity and potentially regulates the mammalian noncoding transcriptome. Here we generated 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 and somatic hypermutation, two mutagenic DNA 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-RNAs, transcription start site (TSS)-associated antisense transcripts that can exceed 500 base pairs in length and are transcribed divergently from cognate coding gene transcripts. xTSS-RNAs are most strongly expressed at genes that 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 single-strand DNA structures containing RNA-DNA hybrids. We propose that RNA exosome regulation of ncRNA recruits AID to single-strand DNA-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.
authors.affiliation: 1] Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA [2] Regeneron Pharmaceuticals, Tarrytown, New York 10591, USA [3].
authors.forename: Evangelos
authors.initials: E
authors.lastname: Pefanis
authors.affiliation: 1] Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA [2] Department of Systems Biology and Department of Biomedical Informatics, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA [3].
authors.forename: Jiguang
authors.initials: J
authors.lastname: Wang
authors.affiliation: 1] Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA [2].
authors.forename: Gerson
authors.initials: G
authors.lastname: Rothschild
authors.affiliation: Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA.
authors.forename: Junghyun
authors.initials: J
authors.lastname: Lim
authors.affiliation: Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA.
authors.forename: Jaime
authors.initials: J
authors.lastname: Chao
authors.affiliation: Department of Systems Biology and Department of Biomedical Informatics, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA.
authors.forename: Raul
authors.initials: R
authors.lastname: Rabadan
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, New York 10591, USA.
authors.forename: Aris N
authors.initials: AN
authors.lastname: Economides
authors.affiliation: Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA.
authors.forename: Uttiya
authors.initials: U
authors.lastname: Basu
mesh_terms: D000818:Animals; D001402:B-Lymphocytes / Q000378:metabolism*; D020029:Base Pairing; D003564:Cytidine Deaminase / Q000378:metabolism*; D053903:DNA Breaks, Double-Stranded; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D063326:Exosome Multienzyme Ribonuclease Complex / Q000172:deficiency / Q000235:genetics; D055354:Exosomes / Q000378:metabolism; D005260:Female; D016678:Genome / Q000235:genetics; D042822:Genomic Instability / Q000235:genetics; D017578:Immunoglobulin Class Switching / Q000235:genetics; D007143:Immunoglobulin Heavy Chains / Q000235:genetics; D008297:Male; D051379:Mice; D009693:Nucleic Acid Hybridization; D016372:RNA, Antisense / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics; D027041:Somatic Hypermutation, Immunoglobulin / Q000235:genetics; D013379:Substrate Specificity; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000235:genetics*; D014178:Translocation, Genetic / Q000235:genetics; D000098830:AICDA (Activation-Induced Cytidine Deaminase)
chemical_list: D004277:DNA, Single-Stranded; C000592923:Exosc3 protein, mouse; D007143:Immunoglobulin Heavy Chains; D016372:RNA, Antisense; D022661:RNA, Untranslated; D016601:RNA-Binding Proteins; D063326:Exosome Multienzyme Ribonuclease Complex; D000098830:AICDA (Activation-Induced Cytidine Deaminase); D003564:Cytidine Deaminase