Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data

Eldad David Shulman*, Ran Elkon*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Alternative polyadenylation (APA) is emerging as an important layer of gene regulation because the majority of mammalian protein-coding genes contain multiple polyadenylation (pA) sites in their 3 UTR. By alteration of 3 UTR length, APA can considerably affect post-transcriptional gene regulation. Yet, our understanding of APA remains rudimentary. Novel single-cell RNA sequencing (scRNA-seq) techniques allow molecular characterization of different cell types to an unprecedented degree. Notably, the most popular scRNA-seq protocols specifically sequence the 3 end of transcripts. Building on this property, we implemented a method for analysing patterns of APA regulation from such data. Analyzing multiple datasets from diverse tissues, we identified widespread modulation of APA in different cell types resulting in global 3 UTR shortening/lengthening and enhanced cleavage at intronic pA sites. Our results provide a proof-of-concept demonstration that the huge volume of scRNA-seq data that accumulates in the public domain offers a unique resource for the exploration of APA based on a very broad collection of cell types and biological conditions.

Original languageEnglish
Pages (from-to)10027-10039
Number of pages13
JournalNucleic Acids Research
Issue number19
StatePublished - 4 Nov 2019


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