ArticleNature communications2018
Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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
30 citing papers in PubMed, 57 citations in OpenAlex.
- Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy.Cell genomics · 2025Article
- Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits.Nucleic acids research · 2025Article
- Article
- Improving Hi-C contact matrices using genome graphs.bioRxiv : the preprint server for biology · 2023Article
- Transcription factor expression is the main determinant of variability in gene co-activity.Molecular systems biology · 2023Article
- Integrative omics approaches for biosynthetic pathway discovery in plants.Natural product reports · 2022Review
- Article
- Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Cell and Tissue Structure, Function, and Phenotype.Results and problems in cell differentiation · 2022Review
- Regulation of 3D Organization and Its Role in Cancer Biology.Frontiers in cell and developmental biology · 2022Review
- Time-Based Systems Biology Approaches to Capture and Model Dynamic Gene Regulatory Networks.Annual review of plant biology · 2021Review
- Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome.Cell research · 2021Article
- Exons and introns exhibit transcriptional strand asymmetry of dinucleotide distribution, damage formation and DNA repair.NAR genomics and bioinformatics · 2021Article
- Artificial intelligence in sepsis early prediction and diagnosis using unstructured data in healthcare.Nature communications · 2021Article
- Integrated Analysis of Whole Genome and Epigenome Data Using Machine Learning Technology: Toward the Establishment of Precision Oncology.Frontiers in oncology · 2021Review
- Transcriptionally active enhancers in human cancer cells.Molecular systems biology · 2021Article
- Three-dimensional genome: developmental technologies and applications in precision medicine.Journal of human genetics · 2020Article
- Analysis of the structural variability of topologically associated domains as revealed by Hi-C.NAR genomics and bioinformatics · 2020Article
- Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction.Computational and structural biotechnology journal · 2020Review
- Monitoring the prolonged Tnf stimulation in space and time with topological-functional networks.Computational and structural biotechnology journal · 2020Article
- Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer.Genes, chromosomes & cancer · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Transcriptional regulation is tightly coupled with chromosomal positioning and three-dimensional chromatin architecture. However, it is unclear what proportion of transcriptional activity is reflecting such organisation, how much can be informed by RNA expression alone and how this impacts disease. Here, we develop a computational transcriptional decomposition approach separating the proportion of expression associated with genome organisation from independent effects not directly related to genomic positioning. We show that positionally attributable expression accounts for a considerable proportion of total levels and is highly informative of topological associating domain activities and organisation, revealing boundaries and chromatin compartments. Furthermore, expression data alone accurately predict individual enhancer-promoter interactions, drawing features from expression strength, stabilities, insulation and distance. We characterise predictions in 76 human cell types, observing extensive sharing of domains, yet highly cell-type-specific enhancer-promoter interactions and strong enrichments in relevant trait-associated variants. Overall, our work demonstrates a close relationship between transcription and chromatin architecture.
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.