Extensive Involvement of Alternative Polyadenylation in Single-Nucleus Neurons

Abstract

Cleavage and polyadenylation are essential processes that can impact many aspects of mRNA fate. Most eukaryotic genes have alternative polyadenylation (APA) events. While the heterogeneity of mRNA polyadenylation isoform choice has been studied in specific tissues, less attention has been paid to the neuronal heterogeneity of APA selection at single-nucleus resolution. APA is highly controlled during development and neuronal activation, however, to what extent APA events vary in a specific neuronal cell population and the regulatory mechanisms are still unclear. In this paper, we investigated dynamic APA usage in different cell types using snRNA-seq data of 1424 human brain cells generated by single-cell 3′ RNA sequencing. We found that distal APA sites are not only favored by global neuronal cells, but that their usage also varies between the principal types of neuronal cell populations (excitatory neurons and inhibitory neurons). A motif analysis and a gene functional analysis indicated the enrichment of RNA-binding protein (RBP) binding sites and neuronal functions for the set of genes with neuron-enhanced distal PAS usage. Our results revealed the extensive involvement of APA regulation in neuronal populations at the single-nucleus level, providing new insights into roles for APA in specific neuronal cell populations, as well as utility in future functional studies.

On the function and relevance of alternative 3′‐UTRs in gene expression regulation

“…Notably, genes with long 3′‐UTRs show enrichment in neuronal functions. In accordance with what was observed in different brain cell types and tissues (Braz et al, 2017), both excitatory neurons and inhibitory neurons show differential usage of PASs for the same genes, showing that APA regulation is a cell‐type‐ and context‐specific mechanism (Wang et al, 2020). In a global analysis of APA during mouse retinal development, lengthening of the 3′‐UTR and increased usage of intronic PASs was also detected, suggesting a role for APA in the regulation of retinal development and maturation (Hu et al, 2017).…”

“…In mouse and human neural tissues, distal PASs are also preferentially selected, producing long 3′‐UTRs (Miura et al, 2013). As in Drosophila , the 3′‐UTR extensions had numerous conserved miRNA target sites that were enriched for known neural miRNAs, suggesting that posttranscriptional regulation of longer 3′‐UTRs by miRNAs and RBPs has a particular influence in the nervous system (Miura et al, 2013; Wang et al, 2020). Notably, genes with long 3′‐UTRs show enrichment in neuronal functions.…”

Selective poly adenylation predicts the efficacy of immunotherapy in patients with lung adenocarcinoma by multiple omics research

“…In summary, eight model genes were used in the gene set for this analysis, and it was found that they were regulated by multiple transcription factors and other common mechanisms [37][38][39]. Transcription factor NFAT5 was the main regulator of gene concentration, and there was statistical significance in the difference of survival prognosis and immune cell infiltration in LUAD (P < 0.05).…”