ArticleNucleic acids research2017
Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed, 36 citations in OpenAlex.
- A chromatin-structure-guided framework for predictive and interpretable regulatory genomics.Briefings in bioinformatics · 2026Article
- A Chromatin-Structure-Guided Framework for Predictive and Interpretable Regulatory Genomics.bioRxiv : the preprint server for biology · 2025Article
- pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data.Nucleic acids research · 2025Article
- Energy landscape analysis of the development of the chromosome structure across the cell cycle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.Bioinformatics (Oxford, England) · 2025Article
- Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.Epigenetics & chromatin · 2023Article
- Compartmentalization with nuclear landmarks yields random, yet precise, genome organization.Biophysical journal · 2023Article
- Uncovering the Quantitative Relationships Among Chromosome Fluctuations, Epigenetics, and Gene Expressions of Transdifferentiation on Waddington Landscape.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Modeling and simulation of cell nuclear architecture reorganization process.Journal of computational physics · 2022Article
- Extracting multi-way chromatin contacts from Hi-C data.PLoS computational biology · 2021Article
- Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units.Current opinion in structural biology · 2021Review
- High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis.Nature communications · 2021Article
- A new precision medicine initiative at the dawn of exascale computing.Signal transduction and targeted therapy · 2021Review
- Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.Methods (San Diego, Calif.) · 2020Review
- Computing 3D Chromatin Configurations from Contact Probability Maps by Inverse Brownian Dynamics.Biophysical journal · 2020Article
- Bayesian inference of chromatin structure ensembles from population-averaged contact data.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells.Genome biology · 2020Article
- Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C.Biophysical journal · 2019Article
- Alterations in Chromatin Folding Patterns in Cancer Variant-Enriched Loci.... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics · 2019Article
- Computational Structural Biology: Successes, Future Directions, and Challenges.Molecules (Basel, Switzerland) · 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 2 institutions in 1 country.
Funding
Abstract
Conformation capture technologies measure frequencies of interactions between chromatin regions. However, understanding gene-regulation require knowledge of detailed spatial structures of heterogeneous chromatin in cells. Here we describe the nC-SAC (n-Constrained-Self Avoiding Chromatin) method that transforms experimental interaction frequencies into 3D ensembles of chromatin chains. nC-SAC first distinguishes specific from non-specific interaction frequencies, then generates 3D chromatin ensembles using identified specific interactions as spatial constraints. Application to α-globin locus shows that these constraints (∼20%) drive the formation of ∼99% all experimentally captured interactions, in which ∼30% additional to the imposed constraints is found to be specific. Many novel specific spatial contacts not captured by experiments are also predicted. A subset, of which independent ChIA-PET data are available, is validated to be RNAPII-, CTCF-, and RAD21-mediated. Their positioning in the architectural context of imposed specific interactions from nC-SAC is highly important. Our results also suggest the presence of a many-body structural unit involving α-globin gene, its enhancers, and POL3RK gene for regulating the expression of α-globin in silent cells.
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.