ArticleProceedings of the National Academy of Sciences of the United States of America2016
SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 155 papers.
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Who cites it
155 citing papers in PubMed.
- UFold-X: an enhanced Dual & Dynamic U-Mamba model for long-range RNA secondary structure prediction.Nucleic acids research · 2026Article
- Pnky lncRNA secondary structure maps identify functional regions that control neurogenesis in neural stem cells.Cell reports · 2026Article
- Correlated protein-RNA associations and a requirement for HNRNPU in the long-range recruitment of Polycomb Repressive Complexes by the lncRNAs Airn and Kcnq1ot1.PLoS genetics · 2026Article
- Conserved structural features of the lncRNA HOTAIR in breast cancer cells.bioRxiv : the preprint server for biology · 2026Article
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Xist in X chromosome inactivation: mechanisms and disease relevance.Cell communication and signaling : CCS · 2025Review
- The lncRNA PACER Regulates Lung Adenocarcinoma Phenotypes via COX-2 Signaling and RNA Structural Dynamics.bioRxiv : the preprint server for biology · 2025Article
- Challenges and opportunities in technologies and methods for lncRNA structure determination.Cell & bioscience · 2025Review
- LncRNA SChLAP1 Promotes Cancer Cell Proliferation and Invasion Via Its Distinct Structural Domains and Conserved Regions.Journal of molecular biology · 2025Article
- G-quadruplex structural motifs modulate protein-RNA interactions within the transcriptome.Genome biology · 2025Article
- Structural basis for the function of long noncoding RNAbioRxiv : the preprint server for biology · 2025Article
- Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion.RNA (New York, N.Y.) · 2025Article
- Immiscible proteins compete for RNA binding to order condensate layers.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Illuminating biomolecular assemblies in gene regulation.Biophysical reviews · 2025Review
- Article
- Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP.Nucleic acids research · 2025Article
- Human XIST: Origin and Divergence of aNon-coding RNA · 2025Review
- Biomolecules Interacting with Long Noncoding RNAs.Biology · 2025Review
- Article
- Article
95 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
Abstract
The 18-kb Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation during female eutherian mammalian development. Global structural architecture, cell-induced conformational changes, and protein-RNA interactions within Xist are poorly understood. We used selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) to examine these features of Xist at single-nucleotide resolution both in living cells and ex vivo. The Xist RNA forms complex well-defined secondary structure domains and the cellular environment strongly modulates the RNA structure, via motifs spanning one-half of all Xist nucleotides. The Xist RNA structure modulates protein interactions in cells via multiple mechanisms. For example, repeat-containing elements adopt accessible and dynamic structures that function as landing pads for protein cofactors. Structured RNA motifs create interaction domains for specific proteins and also sequester other motifs, such that only a subset of potential binding sites forms stable interactions. This work creates a broad quantitative framework for understanding structure-function interrelationships for Xist and other lncRNAs in cells.
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