ArticlePLoS computational biology2016
MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT00137111 (Total XV - Total Therapy Study XV for Newly Diagnosed Patients With Acute Lymphoblastic Leukemia), which is not on this map. Cited by 39 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.
Total XV - Total Therapy Study XV for Newly Diagnosed Patients With Acute Lymphoblastic Leukemia
Who cites it
39 citing papers in PubMed, 88 citations in OpenAlex.
- The paradox of nuclear miRNAs: Mechanisms, therapeutic potential, and future directions.Non-coding RNA research · 2026Review
- 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
- Functional Genomic Evidence for Candidate Small Viral RNA-Mediated Epigenetic Interference in SARS-CoV-1 and SARS-CoV-2.Computational and structural biotechnology journal · 2026Article
- Triplexes Color the Chromaverse by Modulating Nucleosome Phasing and Anchoring Chromatin Condensates.International journal of molecular sciences · 2025Review
- MicroRNAs as Endocrine Modulators of Breast Cancer.International journal of molecular sciences · 2025Review
- Epigenetic Regulation of Chromatin Functions by MicroRNAs and Long Noncoding RNAs and Implications in Human Diseases.Biomedicines · 2025Review
- Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism.Nucleic acids research · 2025Article
- Easy triplex: An online tool for predicting the formation of DNA-RNA triple helices.Computational and structural biotechnology journal · 2025Article
- Nuclear miRNAs: Gene Regulation Activities.International journal of molecular sciences · 2024Review
- Participation of miR165a in the Phytochrome Signal Transduction in Maize (International journal of molecular sciences · 2024Article
- Special Issue "Bioinformatics of Unusual DNA and RNA Structures".International journal of molecular sciences · 2024Article
- The human PTGR1 gene expression is controlled by TE-derived Z-DNA forming sequence cooperating with miR-6867-5p.Scientific reports · 2024Article
- Noncanonical functions of microRNAs in the nucleus.Acta biochimica et biophysica Sinica · 2024Review
- Non-Canonical Targets of MicroRNAs: Role in Transcriptional Regulation, Disease Pathogenesis and Potential for Therapeutic Targets.MicroRNA (Shariqah, United Arab Emirates) · 2024Review
- Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation.The Journal of biological chemistry · 2023Review
- The effects of RNA.DNA-DNA triple helices on nucleosome structures and dynamics.Biophysical journal · 2023Article
- Computational Methods to Study DNA:DNA:RNA Triplex Formation by lncRNAs.Non-coding RNA · 2023Review
- Deciphering the RNA universe in sperm in its role as a vertical information carrier.Environmental epigenetics · 2022Review
- Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growth.Journal of ovarian research · 2021Article
- The Importance of Epigenetics in Diagnostics and Treatment of Major Depressive Disorder.Journal of personalized medicine · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors at 3 institutions in 2 countries.
Funding
Abstract
MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA) and typically down-regulating their stability or translation. Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence (i.e., NMR, FRET, SPR) that purine or pyrimidine-rich microRNAs of appropriate length and sequence form triple-helical structures with purine-rich sequences of duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident) to search genome-wide for potential triplex-forming sites and show that several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, p<2.2 × 10(-16)) for genes whose expression is positively correlated with expression of microRNAs targeting triplex binding sequences. This work has thus revealed a new mechanism by which microRNAs could interact with gene promoter regions to modify gene transcription.
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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.