UMMS Affiliation

RNA Therapeutics Institute; Department of Biochemistry and Molecular Pharmacology

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Biochemistry, Biophysics, and Structural Biology | Genetics and Genomics


Many RNAs, including pre-mRNAs and long non-coding RNAs, can be thousands of nucleotides long and undergo complex post-transcriptional processing. Multiple sites of alternative splicing within a single gene exponentially increase the number of possible spliced isoforms, with most human genes currently estimated to express at least ten. To understand the mechanisms underlying these complex isoform expression patterns, methods are needed that faithfully maintain long-range exon connectivity information in individual RNA molecules. In this study, we describe SeqZip, a methodology that uses RNA-templated DNA-DNA ligation to retain and compress connectivity between distant sequences within single RNA molecules. Using this assay, we test proposed coordination between distant sites of alternative exon utilization in mouse Fn1, and we characterize the extraordinary exon diversity of Drosophila melanogaster Dscam1.


D. melanogaster, Dscam1, RNA-templated, alternative splicing, chromosomes, fibronectin, genes, isoform, ligation, mouse

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Copyright © 2015, Roy et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

DOI of Published Version



Elife. 2015 Apr 13;4:e03700. doi: 10.7554/eLife.03700. Link to article on publisher's site

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Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.