Diverse cell-specific patterns of alternative polyadenylation in Drosophila Journal Article

Authors: Lee, S.; Chen, Y. C.; FCA Consortium; Gillen, A. E.; Taliaferro, J. M.; Deplancke, B.; Li, H.; Lai, E. C.
Article Title: Diverse cell-specific patterns of alternative polyadenylation in Drosophila
Abstract: Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs conditional, and can also alter protein sequences via alternative last exon (ALE) isoforms. We previously used 3'-sequencing from diverse Drosophila samples to define multiple tissue-specific APA landscapes. Here, we exploit comprehensive single nucleus RNA-sequencing data (Fly Cell Atlas) to elucidate cell-type expression of 3' UTRs across >250 adult Drosophila cell types. We reveal the cellular bases of multiple tissue-specific APA/ALE programs, such as 3' UTR lengthening in differentiated neurons and 3' UTR shortening in spermatocytes and spermatids. We trace dynamic 3' UTR patterns across cell lineages, including in the male germline, and discover new APA patterns in the intestinal stem cell lineage. Finally, we correlate expression of RNA binding proteins (RBPs), miRNAs and global levels of cleavage and polyadenylation (CPA) factors in several cell types that exhibit characteristic APA landscapes, yielding candidate regulators of transcriptome complexity. These analyses provide a comprehensive foundation for future investigations of mechanisms and biological impacts of alternative 3' isoforms across the major cell types of this widely-studied model organism. © 2022. The Author(s).
Keywords: sequence analysis; genetics; animal; animals; drosophila; 3' untranslated region; sequence analysis, rna; isoprotein; protein isoforms; 3' untranslated regions; polyadenylation; male
Journal Title: Nature Communications
Volume: 13
ISSN: 2041-1723
Publisher: Nature Publishing Group  
Date Published: 2022-09-13
Start Page: 5372
Language: English
DOI: 10.1038/s41467-022-32305-0
PUBMED: 36100597
PROVIDER: scopus
PMCID: PMC9470587
Notes: Article -- Export Date: 3 October 2022 -- Source: Scopus
Citation Impact
MSK Authors
  1. Eric C Lai
    146 Lai
  2. Seungjae Lee
    5 Lee