Statistical analysis supports pervasive RNA subcellular localization and alternative 3’ UTR regulation

Abstract

Targeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Further, these studies link localization to RNA isoform expression, especially 3' Untranslated Region (UTR) regulation. The recent introduction of genome-wide spatial transcriptomics techniques enable the potential to test if subcellular localization is regulated in situ pervasively. In order to do this, robust statistical measures of subcellular localization and alternative poly-adenylation (APA) at single cell resolution are needed. Developing a new statistical framework called SPRAWL, we detect extensive cell-type specific subcellular RNA localization regulation in the mouse brain and to a lesser extent mouse liver. We integrated SPRAWL with a new approach to measure cell-type specific regulation of alternative 3' UTR processing and detected examples of significant correlations between 3' UTR length and subcellular localization. Included examples, Timp3, Slc32a1, Cxcl14, and Nxph1 have subcellular localization in the brain highly correlated with regulated 3' UTR processing that includes use of unannotated, but highly conserved, 3' ends. Together, SPRAWL provides a statistical framework to integrate multi-omic single-cell resolved measurements of gene-isoform pairs to prioritize an otherwise impossibly large list of candidate functional 3' UTRs for functional prediction and study. SPRAWL predicts 3' UTR regulation of subcellular localization may be more pervasive than currently known.

Pharmacological inhibition of tyrosine protein-kinase 2 reduces islet inflammation and delays type 1 diabetes onset in mice

“…Most notably, cytoplasmic CD274 mRNA was increased in TYK2i-treated RIP-LCMV-GP mice at day 14 and in NOD mice, suggesting that changes in subcellular localization of mRNAs may be influenced by reducing inflammation (74). Of note, changes in mRNA localization have been linked with changes in mRNA translation in several disease models (75,76). Interestingly, PDL-1 protein was reduced in islets from TYK2i-treated RIP-LCMV-GP mice at day 3 and 7, but levels were not different between vehicle-and TYK2i-treated mice at day 14.…”

Analysis of RNA processing directly from spatial transcriptomics data reveals previously unknown regulation

“…These methods each require a matched dataset for RNA processing analysis in ST data, which makes them inapplicable to most of the ST datasets publicly available. There has been some analysis of 3' UTR localization in subcellular spatial data (Bierman & Salzman, 2022), but most relies on seqFISH experiments rather than ST data (Cassella & Ephrussi, 2022). Up to this point, analysis of RNA processing directly from ST data has been out of reach.…”