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Biol."],"published-print":{"date-parts":[[2018,9]]},"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Most eukaryotic protein\u2010coding genes exhibit alternative cleavage and polyadenylation (APA), resulting in mRNA isoforms with different 3\u2032 untranslated regions (3\u2032 UTRs). Studies have shown that brain cells tend to express long 3\u2032 UTR isoforms using distal cleavage and polyadenylation sites (PASs).<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Using our recently developed, comprehensive PAS database PolyA_DB, we developed an efficient method to examine APA, named Significance Analysis of Alternative Polyadenylation using RNA\u2010seq (SAAP\u2010RS). We applied this method to study APA in brain cells and neurogenesis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We found that neurons globally express longer 3\u2032 UTRs than other cell types in brain, and microglia and endothelial cells express substantially shorter 3\u2032 UTRs. We show that the 3\u2032 UTR diversity across brain cells can be corroborated with single cell sequencing data. Further analysis of APA regulation of 3\u2032 UTRs during differentiation of embryonic stem cells into neurons indicates that a large fraction of the APA events regulated in neurogenesis are similarly modulated in myogenesis, but to a much greater extent.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Together, our data delineate APA profiles in different brain cells and indicate that APA regulation in neurogenesis is largely an augmented process taking place in other types of cell differentiation.<\/jats:p><\/jats:sec>","DOI":"10.1007\/s40484-018-0148-3","type":"journal-article","created":{"date-parts":[[2018,9,5]],"date-time":"2018-09-05T11:48:08Z","timestamp":1536148088000},"page":"253-266","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA\u2010seq 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