ArticleNature communications2018
Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assay.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed, 60 citations in OpenAlex.
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- Decoding biology with massively parallel reporter assays and machine learning.Genes & development · 2024Review
- Massively parallel screen uncovers many rare 3' UTR variants regulating mRNA abundance of cancer driver genes.Nature communications · 2024Article
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- Design and Analysis of Massively Parallel Reporter Assays Using FORECAST.Methods in molecular biology (Clifton, N.J.) · 2023Article
- High-throughput identification of RNA localization elements in neuronal cells.Nucleic acids research · 2022Article
- A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons.Nucleic acids research · 2022Article
- A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA.Nucleic acids research · 2022Article
- Transcriptome-scale methods for uncovering subcellular RNA localization mechanisms.Biochimica et biophysica acta. Molecular cell research · 2022Review
- Cloning of DNA oligo pools forSTAR protocols · 2022Article
- Relative specificity as an important consideration in the big data era.Frontiers in genetics · 2022Article
- Effects of sequence motifs in the yeast 3' untranslated region determined from massively parallel assays of random sequences.Genome biology · 2021Article
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- Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes.Nature communications · 2021Article
- Conservation of Differential Animal MicroRNA Processing by Drosha and Dicer.Frontiers in molecular biosciences · 2021Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Despite extensive research, the sequence features affecting microRNA-mediated regulation are not well understood, limiting our ability to predict gene expression levels in both native and synthetic sequences. Here we employed a massively parallel reporter assay to investigate the effect of over 14,000 rationally designed 3' UTR sequences on reporter construct repression. We found that multiple factors, including microRNA identity, hybridization energy, target accessibility, and target multiplicity, can be manipulated to achieve a predictable, up to 57-fold, change in protein repression. Moreover, we predict protein repression and RNA levels with high accuracy (R = 0.84 and R = 0.80, respectively) using only 3' UTR sequence, as well as the effect of mutation in native 3' UTRs on protein repression (R = 0.63). Taken together, our results elucidate the effect of different sequence features on miRNA-mediated regulation and demonstrate the predictability of their effect on gene expression with applications in regulatory genomics and synthetic biology.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.