ArticleNucleic acids research2014
Dissecting the chromatin interactome of microRNA genes.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed.
- The Life of MicroRNAs: Biogenesis, Function and Decay in Cancer.Biomolecules · 2025Review
- Genome-Wide Detection of Leukemia Biomarkers from lincRNA-Protein-Coding Gene Interaction Networks in the Three-Dimensional Chromatin Structure.Current issues in molecular biology · 2025Article
- Bioinformatics Methods for Modeling microRNA Regulatory Networks in Cancer.Advances in experimental medicine and biology · 2022Article
- Chromatin Hubs: A biological and computational outlook.Computational and structural biotechnology journal · 2022Review
- A microRNA-microRNA crosstalk network inferred from genome-wide single nucleotide polymorphism variants in natural populations ofFrontiers in plant science · 2022Article
- Review
- Small RNAs, Big Diseases.International journal of molecular sciences · 2020Review
- Review
- Article
- Article
- A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions.Scientific reports · 2016Article
- Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.PLoS computational biology · 2015Article
- Loregic: a method to characterize the cooperative logic of regulatory factors.PLoS computational biology · 2015Article
- Genome-wide identification of microRNA expression quantitative trait loci.Nature communications · 2015Article
- Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application.BMC genomics · 2014Article
- Continuing analysis of microRNA origins: Formation from transposable element insertions and noncoding RNA mutations.Mobile genetic elements · 2013Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
Our knowledge of the role of higher-order chromatin structures in transcription of microRNA genes (MIRs) is evolving rapidly. Here we investigate the effect of 3D architecture of chromatin on the transcriptional regulation of MIRs. We demonstrate that MIRs have transcriptional features that are similar to protein-coding genes. RNA polymerase II-associated ChIA-PET data reveal that many groups of MIRs and protein-coding genes are organized into functionally compartmentalized chromatin communities and undergo coordinated expression when their genomic loci are spatially colocated. We observe that MIRs display widespread communication in those transcriptionally active communities. Moreover, miRNA-target interactions are significantly enriched among communities with functional homogeneity while depleted from the same community from which they originated, suggesting MIRs coordinating function-related pathways at posttranscriptional level. Further investigation demonstrates the existence of spatial MIR-MIR chromatin interacting networks. We show that groups of spatially coordinated MIRs are frequently from the same family and involved in the same disease category. The spatial interaction network possesses both common and cell-specific subnetwork modules that result from the spatial organization of chromatin within different cell types. Together, our study unveils an entirely unexplored layer of MIR regulation throughout the human genome that links the spatial coordination of MIRs to their co-expression and 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.