Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data

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.

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.

Graphical abstract

Keywords

alternative polyadenylation / brain cells / RNA-seq / scRNA-seq

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SUPPLEMENTARY MATERIALS

The supplementary materials can be found online with this article at https://doi.org/ 10.1007/s40484-018-0148-3.

AUTHOR CONTRIBUTIONS

Aysegul Guvenek and Bin Tian conceived of and designed the experiments. Aysegul Guvenek analyzed the data. Aysegul Guvenek and Bin Tian wrote the paper.

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.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Aysegul Guvenek and Bin Tian declare that they have no conflict of interests.

This article does not contain any studies with human or animal subjects performed by any of the authors.

RIGHTS & PERMISSIONS

2018 Higher Education Press and Springer-Verlag GmbH Germany, part of Springer Nature