ArticlePLoS genetics2015
Probing Xist RNA Structure in Cells Using Targeted Structure-Seq.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 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
81 citing papers in PubMed, 130 citations in OpenAlex.
- Exploring the functional role of XIST in breast cancer from mechanisms to clinical implications.Discover oncology · 2026Review
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Challenges and opportunities in technologies and methods for lncRNA structure determination.Cell & bioscience · 2025Review
- An evolving landscape of PRC2-RNA interactions in chromatin regulation.Nature reviews. Molecular cell biology · 2025Review
- Human XIST: Origin and Divergence of aNon-coding RNA · 2025Review
- The Unpaved Road of Non-Coding RNA Structure-Function Relationships: Current Knowledge, Available Methodologies, and Future Trends.Non-coding RNA · 2025Review
- Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity.Nature structural & molecular biology · 2025Article
- Recruitment of chromatin remodelers by XIST B-repeat region is variably dependent on HNRNPK.Human molecular genetics · 2025Article
- RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding.Chemical reviews · 2024Review
- Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA.RNA (New York, N.Y.) · 2024Article
- RNA structure: implications in viral infections and neurodegenerative diseases.Advanced biotechnology · 2024Review
- Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.Nucleic acids research · 2023Article
- RNA structure determination: From 2D to 3D.Fundamental research · 2023Review
- RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure.PLoS computational biology · 2023Article
- Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.bioRxiv : the preprint server for biology · 2023Article
- Targeting RNA with small molecules: lessons learned from Xist RNA.RNA (New York, N.Y.) · 2023Article
- RNAsmc: A integrated tool for comparing RNA secondary structure and evaluating allosteric effects.Computational and structural biotechnology journal · 2023Article
- Targeting RNA structures with small molecules.Nature reviews. Drug discovery · 2022Review
21 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function.
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.