ArticleNucleic acids research2024
Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 14 papers.
What it found
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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.
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.
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Who cites it
14 citing papers in PubMed, 16 citations in OpenAlex.
- Scanning transcriptomes for nonlinear, domain-level similarities using hmSEEKR.bioRxiv : the preprint server for biology · 2026Article
- Direct roles of long non-coding RNAs in transcription activation.Nature structural & molecular biology · 2026Review
- An EGFR co-amplified lncRNA HELDR promotes glioblastoma malignancy through KAT7-driven gene programs.Nature cell biology · 2026Article
- Genome-wide identification of eQTL-associated lncRNAs in melon and their role in fruit cracking.Scientific reports · 2026Article
- Functional Characterization of Long Non-Coding RNAs Associated with Reproductive Fitness in Pura Raza Española Mares.Animals : an open access journal from MDPI · 2026Article
- Article
- Functional characterization of DNAAF3-AS1 in chromatin remodeling and H3K36me3 distribution.bioRxiv : the preprint server for biology · 2025Article
- LncRNA CISTR-ACT regulates cell size in human and mouse by guiding FOSL2.Nature communications · 2025Article
- Take the bull by the horns: A computational framework to predict lncRNA function.Cell genomics · 2025Article
- EGFR-induced lncRNAProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comprehensive analysis of lncRNAs and mRNAs revealed potential participants in the process of avian reovirus infection.Frontiers in microbiology · 2025Article
- MIR193BHG inhibits the proliferation, migration and invasion of trophoblasts by upregulating p53.Experimental and therapeutic medicine · 2024Article
- The pancancer overexpressed NFYC Antisense 1 controls cell cycle mitotic progression through in cis and in trans modes of action.Cell death & disease · 2024Article
- Localization is the key to action: regulatory peculiarities of lncRNAs.Frontiers in genetics · 2024Review
Corrections and comments
- Erratum issued
Authors and funding
15 authors at 5 institutions in 5 countries.
Funding
Abstract
A key attribute of some long noncoding RNAs (lncRNAs) is their ability to regulate expression of neighbouring genes in cis. However, such 'cis-lncRNAs' are presently defined using ad hoc criteria that, we show, are prone to false-positive predictions. The resulting lack of cis-lncRNA catalogues hinders our understanding of their extent, characteristics and mechanisms. Here, we introduce TransCistor, a framework for defining and identifying cis-lncRNAs based on enrichment of targets amongst proximal genes. TransCistor's simple and conservative statistical models are compatible with functionally defined target gene maps generated by existing and future technologies. Using transcriptome-wide perturbation experiments for 268 human and 134 mouse lncRNAs, we provide the first large-scale survey of cis-lncRNAs. Known cis-lncRNAs are correctly identified, including XIST, LINC00240 and UMLILO, and predictions are consistent across analysis methods, perturbation types and independent experiments. We detect cis-activity in a minority of lncRNAs, primarily involving activators over repressors. Cis-lncRNAs are detected by both RNA interference and antisense oligonucleotide perturbations. Mechanistically, cis-lncRNA transcripts are observed to physically associate with their target genes and are weakly enriched with enhancer elements. In summary, TransCistor establishes a quantitative foundation for cis-lncRNAs, opening a path to elucidating their molecular mechanisms and biological significance.
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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.