Dynamic landscape of alternative polyadenylation during retinal development

Wenyan Hu, Shengguo Li, Ji Yeon Park, Sridhar Boppana, Ting Ni, Miaoxin Li, Jun Zhu, Bin Tian, Zhi Xie, Mengqing Xiang

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

The development of the central nervous system (CNS) is a complex process that must be exquisitely controlled at multiple levels to ensure the production of appropriate types and quantity of neurons. RNA alternative polyadenylation (APA) contributes to transcriptome diversity and gene regulation, and has recently been shown to be widespread in the CNS. However, the previous studies have been primarily focused on the tissue specificity of APA and developmental APA change of whole model organisms; a systematic survey of APA usage is lacking during CNS development. Here, we conducted global analysis of APA during mouse retinal development, and identified stage-specific polyadenylation (pA) sites that are enriched for genes critical for retinal development and visual perception. Moreover, we demonstrated 3′UTR (untranslated region) lengthening and increased usage of intronic pA sites over development that would result in gaining many different RBP (RNA-binding protein) and miRNA target sites. Furthermore, we showed that a considerable number of polyadenylated lncRNAs are co-expressed with protein-coding genes involved in retinal development and functions. Together, our data indicate that APA is highly and dynamically regulated during retinal development and maturation, suggesting that APA may serve as a crucial mechanism of gene regulation underlying the delicate process of CNS development.

Original languageEnglish (US)
Pages (from-to)1721-1739
Number of pages19
JournalCellular and Molecular Life Sciences
Volume74
Issue number9
DOIs
StatePublished - May 1 2017

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Molecular Biology
  • Pharmacology
  • Cellular and Molecular Neuroscience
  • Cell Biology

Keywords

  • Central nervous system
  • Cleavage and polyadenylation-associated factor
  • PA-seq
  • Post-transcriptional gene regulation
  • RNA stability
  • Transcriptome

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