ArticleRNA (New York, N.Y.)2012
RNA-ID, a highly sensitive and robust method to identify cis-regulatory sequences using superfolder GFP and a fluorescence-based assay.
Article in RNA (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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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.
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Who cites it
22 citing papers in PubMed, 32 citations in OpenAlex.
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- Translation Inhibition by Rocaglamide A Enhances Susceptibility of Yeasts to Caspofungin.bioRxiv : the preprint server for biology · 2025Article
- 40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion.RNA (New York, N.Y.) · 2025Article
- Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.Molecular cell · 2024Article
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- Frameshifting at collided ribosomes is modulated by elongation factor eEF3 and by integrated stress response regulators Gcn1 and Gcn20.RNA (New York, N.Y.) · 2022Article
- Replacing the eleven native tryptophans by directed evolution produces an active P-glycoprotein with site-specific, non-conservative substitutions.Scientific reports · 2020Article
- Impacts of uORF codon identity and position on translation regulation.Nucleic acids research · 2019Article
- Multi-protein bridging factor 1(Mbf1), Rps3 and Asc1 prevent stalled ribosomes from frameshifting.eLife · 2018Article
- Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA.RNA (New York, N.Y.) · 2018Article
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- High-throughput discovery of post-transcriptional cis-regulatory elements.BMC genomics · 2016Article
- RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences.Methods in enzymology · 2016Article
- Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats.RNA (New York, N.Y.) · 2015Article
- Functional importance of Ψ38 and Ψ39 in distinct tRNAs, amplified for tRNAGln(UUG) by unexpected temperature sensitivity of the s2U modification in yeast.RNA (New York, N.Y.) · 2015Article
- Methodology for the High-Throughput Identification and Characterization of tRNA Variants That Are Substrates for a tRNA Decay Pathway.Methods in enzymology · 2015Article
- Quantitative analysis of mammalian translation initiation sites by FACS-seq.Molecular systems biology · 2014Article
- Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis.Genes & development · 2014Article
- Translation of CGA codon repeats in yeast involves quality control components and ribosomal protein L1.RNA (New York, N.Y.) · 2013Article
- Matrix metalloproteinase (MMP) 9 transcription in mouse brain induced by fear learning.The Journal of biological chemistry · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed a robust and sensitive method, called RNA-ID, to screen for cis-regulatory sequences in RNA using fluorescence-activated cell sorting (FACS) of yeast cells bearing a reporter in which expression of both superfolder green fluorescent protein (GFP) and yeast codon-optimized mCherry red fluorescent protein (RFP) is driven by the bidirectional GAL1,10 promoter. This method recapitulates previously reported progressive inhibition of translation mediated by increasing numbers of CGA codon pairs, and restoration of expression by introduction of a tRNA with an anticodon that base pairs exactly with the CGA codon. This method also reproduces effects of paromomycin and context on stop codon read-through. Five key features of this method contribute to its effectiveness as a selection for regulatory sequences: The system exhibits greater than a 250-fold dynamic range, a quantitative and dose-dependent response to known inhibitory sequences, exquisite resolution that allows nearly complete physical separation of distinct populations, and a reproducible signal between different cells transformed with the identical reporter, all of which are coupled with simple methods involving ligation-independent cloning, to create large libraries. Moreover, we provide evidence that there are sequences within a 9-nt library that cause reduced GFP fluorescence, suggesting that there are novel cis-regulatory sequences to be found even in this short sequence space. This method is widely applicable to the study of both RNA-mediated and codon-mediated effects on expression.
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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.