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Disambiguating Transcriptional Effects from Post-Transcriptional Effects of Genetic Variants with an Inferred Stability Optimized Massively Parallel Reporter Assay (ISOMPRA).

ABSTRACT: Some widely used methods to study functional effects of DNA sequence on transcription cannot readily disambiguate these from post-transcriptional impacts of the same element on RNA. Therefore, we developed an approach enabling assessment of DNA/RNA regulatory elements in parallel: Inferred Stability Optimized Massively Parallel Reporter Assay (ISOMPRA). ISOMPRA quantifies pre-spliced RNA to more directly assess transcription rate, and spliced RNA, corrected for transcription rate, to correctly identify RNA stability-altering 3’ UTR elements. We benchmark ISOMPRA with both predicted enhancers and 3’ UTR elements, selected regions containing autism patient mutations. We identify numerous functional enhancers/UTRs, and discover a subset with high impact mutations. We further show failing to consider both potential transcriptional and post transcriptional effects results in numerous false-positives and false-negatives. Finally, we adapt ISOMPRA for in vivo analysis of element effects via AAV transduction. Combined with Cre-dependent priming sites, this permits analyses of both transcriptional and post-transcriptional effects within specific cell types of the brain, and further enables measurement of regulatory impacts of in vivo traits, such as sex.

ORGANISM(S): Mus musculus Escherichia coli Adeno-associated virus 9 Homo sapiens

PROVIDER: GSE295080 | GEO | 2025/12/12

REPOSITORIES: GEO

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