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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
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Dynamic landscape of alternative polyadenylation during retinal development
Wenyan Hu1, Shengguo Li2, Ji Yeon Park3
1State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 500040, China.
Cellular and Molecular Life Sciences : CMLS
|December 20, 2016
Summary
Alternative polyadenylation (APA) dynamically regulates gene expression during mouse retinal development. This process impacts RNA-binding protein and miRNA targeting, crucial for central nervous system (CNS) development and visual function.
Area of Science:
- Neuroscience
- Developmental Biology
- Genetics
- Molecular Biology
Background:
- Central nervous system (CNS) development requires precise control over neuron production.
- RNA alternative polyadenylation (APA) generates transcriptome diversity and regulates gene expression.
- Previous studies on APA in the CNS focused on tissue specificity and whole-organism development, lacking systematic surveys during specific developmental stages.
Purpose of the Study:
- To conduct a global analysis of APA during mouse retinal development.
- To identify stage-specific polyadenylation (pA) sites and their associated genes.
- To investigate the role of APA in regulating gene expression during CNS development.
Main Methods:
- Global analysis of APA during mouse retinal development.
- Identification and characterization of stage-specific pA sites.
- Analysis of 3' untranslated region (3'UTR) and intronic pA site usage.
- Examination of polyadenylated long non-coding RNA (lncRNA) co-expression.
Main Results:
- Identified stage-specific pA sites enriched in genes critical for retinal development and visual perception.
- Observed 3'UTR lengthening and increased intronic pA site usage during development, leading to novel RNA-binding protein (RBP) and microRNA (miRNA) target sites.
- Found that a significant number of polyadenylated lncRNAs are co-expressed with protein-coding genes involved in retinal development and function.
Conclusions:
- APA is highly and dynamically regulated during mouse retinal development and maturation.
- APA contributes to transcriptome diversity by altering 3'UTR lengths and RBP/miRNA binding sites.
- APA represents a crucial gene regulatory mechanism underlying CNS development.
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