Pan, X.-B. | bioRxiv Science

bioRxiv2024

Multi-tissue transition of A-to-I RNA editing pattern and its regulatory relevance in transcription, splicing, and translation during development

Previous studies have shown that A-to-I RNA editing can occur in various organs and tissues under normal physiological conditions. However, the dynamics of RNA editing and its functional relevance in multiple tissues and organs during the embryo-to-adult transition in mammals remain to be elucidated. Here, we performed a comprehensive analysis of RNA-Seq and Ribo-Seq data from six mouse tissues at embryonic and adult stages to elucidate the A-to-I RNA editing transition during development and to validate it in additional mouse brain datasets spanning multiple developmental stages. Our results revealed a general transition of up-regulated A-to-I RNA editing activity across numerous tissue types during embryonic-adult development, indicated by significantly increased average RNA editing levels. Consistently, differential RNA editing (DRE) analysis showed more up-regulated than down-regulated RNA editing sites in all six tissue types. Furthermore, such RNA editing transitions during development could contribute to differential gene expression (DEG) at both transcriptional and translational levels, as well as differential alternative splicing (DAS) across multiple tissues. Differentially edited genes with DEG or DAS could be involved not only in tissue-specific biological functions but also in common routine biological processes during development. Notably, Adarb1 was found to be a more important player than Adar in the CNS (the brain and retina), with its expression levels increasing gradually and correlating with the A-to-I RNA editing activity. Our study demonstrates the potential role of A-to-I editing during development across multiple tissues, providing new insights into its regulatory relevance in both transcriptional and translational landscapes.

genomics↗

bioRxiv2020

Novel missense mutation E585K in retinitis pigmentosa leads to compromised RPGR splicing diversity

Mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene, are the major cause of X-linked retinitis pigmentosa (RP). Herein we used whole-exome sequencing to screen possible novel RPGR mutations in RP patients, and identified a novel missense mutation E585K in a patient with early onset but slow disease progression, and a frameshift deletion E998Gfs*78 in a patient with RP sine pigmento and high myopia. Intriguingly, bioinformatic analysis indicated that E585K probably affected RPGR RNA splicing instead of the protein sequence directly. Mini-gene assays in 293T cells revealed that splicing events of the E585K mutant were found to be also exist in wildtype, but with a shifted pattern. In the E585K mini-gene usage of an upstream alternative 5' splice site (5' ss) of exon 14 was enhanced, and other splicing events were suppressed, including the canonical 5' ss of exon 14, skipping of exon 14/15 and retention of intron 14. As a result, RPGR splicing products of the E585K mini-gene were predominated by transcripts containing a 4-bp deletion, with a small fraction of in-frame transcripts containing a retended intron 14, which might explain the slow disease progression in the patient carrying the mutation. RNA-Seq analysis further confirmed existence of these splicing events in endogenous RPGR RNA in human retina, pointing to compromised splicing diversity in the E585K mutant. Our findings thus added to the understanding of genotype-phenotype correlation in RP, and suggested that compromised RPGR splicing diversity might play a role in molecular mechanism of the disease.

genetics↗