ArticleMolecular cell2019
A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins.
Article in Molecular cell, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed, 96 citations in OpenAlex.
- Decoding RNA-protein interactions using high-throughput methods.RNA biology · 2026Review
- Protocol for massively parallel RNA assay combined with immunoprecipitation for high-throughput analysis of RNA-protein interactions in cells.STAR protocols · 2026Article
- Automated high-throughput selection of DNA aptamers using a common optical next-generation sequencer.Nucleic acids research · 2026Article
- Biochemical principles of miRNA targeting in flies.Nature communications · 2026Article
- Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells.bioRxiv : the preprint server for biology · 2026Article
- Effective in vivo RNA base editing via engineered cytidine deaminase APOBECs fused with PUF proteins.Nature communications · 2025Article
- Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics.RNA (New York, N.Y.) · 2025Article
- Deaminase-based RNA recording enables high throughput mutational profiling of protein-RNA interactions.bioRxiv : the preprint server for biology · 2025Article
- Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display.Nature communications · 2025Article
- Significant roles in RNA-binding for the amino-terminal regions of Drosophila Pumilio and Nanos.PLoS genetics · 2025Article
- RNA ensembles from in vitro to in vivo: Toward predictive models of RNA cellular function.Current opinion in structural biology · 2024Review
- Systematic analysis of the target recognition and repression by the Pumilio proteins.Nucleic acids research · 2024Article
- Identification of leader-trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea.RNA (New York, N.Y.) · 2024Article
- FRET-guided modeling of nucleic acids.Nucleic acids research · 2024Article
- Pumilio-1 mediated translational control of claudin-5 at the blood-brain barrier.Fluids and barriers of the CNS · 2024Article
- Massively parallel dissection of RNA in RNA-protein interactions in vivo.Nucleic acids research · 2024Article
- PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans.Developmental cell · 2024Article
- RNA structure profiling at single-cell resolution reveals new determinants of cell identity.Nature methods · 2024Article
- Specificity, synergy, and mechanisms of splice-modifying drugs.Nature communications · 2024Article
- RNA molecular recording with an engineered RNA deaminase.Nature methods · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
High-throughput methodologies have enabled routine generation of RNA target sets and sequence motifs for RNA-binding proteins (RBPs). Nevertheless, quantitative approaches are needed to capture the landscape of RNA-RBP interactions responsible for cellular regulation. We have used the RNA-MaP platform to directly measure equilibrium binding for thousands of designed RNAs and to construct a predictive model for RNA recognition by the human Pumilio proteins PUM1 and PUM2. Despite prior findings of linear sequence motifs, our measurements revealed widespread residue flipping and instances of positional coupling. Application of our thermodynamic model to published in vivo crosslinking data reveals quantitative agreement between predicted affinities and in vivo occupancies. Our analyses suggest a thermodynamically driven, continuous Pumilio-binding landscape that is negligibly affected by RNA structure or kinetic factors, such as displacement by ribosomes. This work provides a quantitative foundation for dissecting the cellular behavior of RBPs and cellular features that impact their occupancies.
Indexed as
Identifiers
What OpenQuestion holds
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.