Abstract
Background
Most eukaryotic protein-coding genes exhibit alternative cleavage and polyadenylation (APA), resulting in mRNA isoforms with different 3′ untranslated regions (3′ UTRs). Studies have shown that brain cells tend to express long 3′ UTR isoforms using distal cleavage and polyadenylation sites (PASs).
Methods
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-seq (SAAP-RS). We applied this method to study APA in brain cells and neurogenesis.
Results
We found that neurons globally express longer 3′ UTRs than other cell types in brain, and microglia and endothelial cells express substantially shorter 3′ UTRs. We show that the 3′ UTR diversity across brain cells can be corroborated with single cell sequencing data. Further analysis of APA regulation of 3′ 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.
Conclusion
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.
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Acknowledgments
We thank members of Bin Tian lab for helpful discussions. This work was supported by grants from NIH (Nos. R01 GM084089 and R21 NS097992) and a grant from the Rutgers Brain Health Institute.
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Author summary: Most eukaryotic protein-coding genes express isoforms with different 3′ UTR lengths. Studies have shown that transcripts expressed in brain tend to have longer 3′ UTRs compared to other tissues. We have developed an efficient computational method to analyze 3′ UTR isoforms using RNA-seq data. We show that neurons have the longest 3′ UTRs among all brain cell types and 3′ UTRs are the shortest in microglia and endothelial cells. This finding is also supported by single cell sequencing data. We further show that 3′ UTRs lengthen in neurogenesis, similar to that in myogenesis. However, 3′ UTR lengthening is much potent in differentiating neurons.
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Guvenek, A., Tian, B. Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data. Quant Biol 6, 253–266 (2018). https://doi.org/10.1007/s40484-018-0148-3
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DOI: https://doi.org/10.1007/s40484-018-0148-3