Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing

Zhiping Zhang, Bongmin Bae, Winston H. Cuddleston and Pedro Miura ()
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Zhiping Zhang: University of Connecticut School of Medicine
Bongmin Bae: University of Nevada, Reno
Winston H. Cuddleston: University of Nevada, Reno
Pedro Miura: University of Connecticut School of Medicine

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract Nervous system development is associated with extensive regulation of alternative splicing (AS) and alternative polyadenylation (APA). AS and APA have been extensively studied in isolation, but little is known about how these processes are coordinated. Here, the coordination of cassette exon (CE) splicing and APA in Drosophila was investigated using a targeted long-read sequencing approach we call Pull-a-Long-Seq (PL-Seq). This cost-effective method uses cDNA pulldown and Nanopore sequencing combined with an analysis pipeline to quantify inclusion of alternative exons in connection with alternative 3’ ends. Using PL-Seq, we identified genes that exhibit significant differences in CE splicing depending on connectivity to short versus long 3’UTRs. Genomic long 3’UTR deletion was found to alter upstream CE splicing in short 3’UTR isoforms and ELAV loss differentially affected CE splicing depending on connectivity to alternative 3’UTRs. This work highlights the importance of considering connectivity to alternative 3’UTRs when monitoring AS events.

Date: 2023
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DOI: 10.1038/s41467-023-41207-8

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