ArticleJournal of translational medicine2017
Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome.
Article in Journal of translational medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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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.
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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
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 45 citations in OpenAlex.
- Six polymorphisms in the lncRNA H19 gene and the risk of cancer: a systematic review and meta-analysis.BMC cancer · 2023Pooled it
- The Chromaverse Is Colored by Triplexes Formed Through the Interactions of Noncoding RNAs with HNPRNPU, TP53, AGO, REL Proteins, Intrinsically-Disordered Regions, and Flipons.International journal of molecular sciences · 2026Article
- Triplexes Color the Chromaverse by Modulating Nucleosome Phasing and Anchoring Chromatin Condensates.International journal of molecular sciences · 2025Review
- MiR-128-3p - a gray eminence of the human central nervous system.Molecular therapy. Nucleic acids · 2024Review
- Non-Coding RNA Performs Its Biological Function by Interacting with Macromolecules.International journal of molecular sciences · 2023Article
- Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo.International journal of molecular sciences · 2023Review
- LncRNA-AP006284.1 promotes prostate cancer cell growth and motility by forming RNA-DNA triplexes and recruiting GNL3/SFPQ complex to facilitate RASSF7 transcription.Genes & diseases · 2023Article
- Computational Methods to Study DNA:DNA:RNA Triplex Formation by lncRNAs.Non-coding RNA · 2023Review
- Identification of Long Noncoding RNAs That Exert Transcriptional Regulation by Forming RNA-DNA Triplexes in Prostate Cancer.International journal of molecular sciences · 2023Article
- 3plex enables deep computational investigation of triplex forming lncRNAs.Computational and structural biotechnology journal · 2023Article
- HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex.Nature communications · 2022Article
- Long Non-coding RNA HOTAIR in Central Nervous System Disorders: New Insights in Pathogenesis, Diagnosis, and Therapeutic Potential.Frontiers in molecular neuroscience · 2022Review
- Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL.Nucleic acids research · 2021Article
- Seq'ing identity and function in a repeat-derived noncoding RNA world.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Review
- Article
- Functional Prediction of Candidate MicroRNAs for CRC Management Using in Silico Approach.International journal of molecular sciences · 2019Article
- LncRNA Riken-201 and Riken-203 modulates neural development by regulating the Sox6 through sequestering miRNAs.Cell proliferation · 2019Article
- Isolation and genome-wide characterization of cellular DNA:RNA triplex structures.Nucleic acids research · 2019Article
- Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture.Biotechnology and bioengineering · 2019Article
- Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOnly a handful of long noncoding RNAs have been functionally characterized. They are known to modulate regulation through interacting with other biomolecules in the cell: DNA, RNA and protein. Though there have been detailed investigations on lncRNA-miRNA and lncRNA-protein interactions, the interaction of lncRNAs with DNA have not been studied extensively. In the present study, we explore whether lncRNAs could modulate genomic regulation by interacting with DNA through the formation of highly stable DNA:DNA:RNA triplexes.
methodsWe computationally screened 23,898 lncRNA transcripts as annotated by GENCODE, across the human genome for potential triplex forming sequence stretches (PTS). The PTS frequencies were compared across 5'UTR, CDS, 3'UTR, introns, promoter and 1000 bases downstream of the transcription termination sites. These regions were annotated by mapping to experimental regulatory regions, classes of repeat regions and transcription factors. We validated few putative triplex mediated interactions where lncRNA-gene pair interaction is via pyrimidine triplex motif using biophysical methods.
resultsWe identified 20,04,034 PTS sites to be enriched in promoter and intronic regions across human genome. Additional analysis of the association of PTS with core promoter elements revealed a systematic paucity of PTS in all regulatory regions, except TF binding sites. A total of 25 transcription factors were found to be associated with PTS. Using an interaction network, we showed that a subset of the triplex forming lncRNAs, have a positive association with gene promoters. We also demonstrated an in vitro interaction of one lncRNA candidate with its predicted gene target promoter regions.
conclusionsOur analysis shows that PTS are enriched in gene promoter and largely associated with simple repeats. The current study suggests a major role of a subset of lncRNAs in mediating chromatin organization modulation through CTCF and NSRF proteins.
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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.