ArticleNature methods2024
RNA structure profiling at single-cell resolution reveals new determinants of cell identity.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed, 19 citations in OpenAlex.
- Multiomic proximity labeling in vivo by D-amino-acid-activated peroxidase reaction.Nature chemical biology · 2026Article
- Modtector: ultra-fast modification signal mining on mapped sequencing reads.Bioinformatics (Oxford, England) · 2026Article
- Nuclear RNA clusters are dynamic structural entities in Huntington's disease.Communications biology · 2026Article
- Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell.Nature methods · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Translational Regulation of Plant Stress Responses: Mechanisms, Pathways, and Applications in Bioengineering.Annual review of phytopathology · 2025Review
- TAS-seq enables subcellular single-stranded adenosine profiling by signal peptide-assisted adenosine deamination.Cell reports methods · 2025Article
- Transcriptome-wide RNA accessibility mapping reveals structured RNA elements and pervasive conformational rearrangements under stress.bioRxiv : the preprint server for biology · 2025Article
- Sequencing technologies to measure translation in single cells.Nature reviews. Molecular cell biology · 2025Review
- Angle-controllable RNA tiles for programable array assembly and RNA sensing.Nature communications · 2025Article
- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.Nature reviews. Genetics · 2025Review
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- RNA Metabolism and the Role of Small RNAs in Regulating Multiple Aspects of RNA Metabolism.Non-coding RNA · 2024Review
- Nexus between RNA conformational dynamics and functional versatility.Current opinion in structural biology · 2024Review
- The RNA Revolution in the Central Molecular Biology Dogma Evolution.International journal of molecular sciences · 2024Review
- Identifying cell types by lasso-constraint regularized Gaussian graphical model based on weighted distance penalty.Briefings in bioinformatics · 2024Article
- Conserved intronic secondary structures with concealed branch sites regulate alternative splicing of poison exons.Nucleic acids research · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA structure is critical for multiple steps in gene regulation. However, how the structures of transcripts differ both within and between individual cells is unknown. Here we develop a SHAPE-inspired method called single-cell structure probing of RNA transcripts that enables simultaneous determination of transcript secondary structure and abundance at single-cell resolution. We apply single-cell structure probing of RNA transcripts to human embryonic stem cells and differentiating neurons. Remarkably, RNA structure is more homogeneous in human embryonic stem cells compared with neurons, with the greatest homogeneity found in coding regions. More extensive heterogeneity is found within 3' untranslated regions and is determined by specific RNA-binding proteins. Overall RNA structure profiles better discriminate cell type identity and differentiation stage than gene expression profiles alone. We further discover a cell-type variable region of 18S ribosomal RNA that is associated with cell cycle and translation control. Our method opens the door to the systematic characterization of RNA structure-function relationships at single-cell resolution.
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.