ReviewChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology2011
Structure determination of genomic domains by satisfaction of spatial restraints.
Review in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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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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Who cites it
24 citing papers in PubMed, 45 citations in OpenAlex.
- Biology and Model Predictions of the Dynamics and Heterogeneity of Chromatin-Nuclear Lamina Interactions.Frontiers in cell and developmental biology · 2022Review
- Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data.Briefings in functional genomics · 2020Article
- Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs.Nature communications · 2020Article
- TAD fusion score: discovery and ranking the contribution of deletions to genome structure.Genome biology · 2019Article
- Semi-nonparametric modeling of topological domain formation from epigenetic data.Algorithms for molecular biology : AMB · 2019Article
- Computational 3D genome modeling using Chrom3D.Nature protocols · 2018Article
- Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings.Nucleic acids research · 2017Article
- Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae.Nature communications · 2017Article
- Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization.Scientific reports · 2016Article
- Population-based 3D genome structure analysis reveals driving forces in spatial genome organization.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Inferring 3D chromatin structure using a multiscale approach based on quaternions.BMC bioinformatics · 2015Article
- Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes.Nucleus (Austin, Tex.) · 2015Article
- Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization.Genes & development · 2014Article
- Uncertainty in integrative structural modeling.Current opinion in structural biology · 2014Review
- The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease.Journal of cellular physiology · 2014Review
- Article
- Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly--a model based approach.PloS one · 2014Article
- Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.Nature reviews. Genetics · 2013Review
- Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data.Quantitative biology (Beijing, China) · 2013Article
- The hierarchy of the 3D genome.Molecular cell · 2013Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The three-dimensional (3D) architecture of a genome is non-random and known to facilitate the spatial colocalization of regulatory elements with the genes they regulate. Determining the 3D structure of a genome may therefore probe an essential step in characterizing how genes are regulated. Currently, there are several experimental and theoretical approaches that aim at determining the 3D structure of genomes and genomic domains; however, approaches integrating experiments and computation to identify the most likely 3D folding of a genome at medium to high resolutions have not been widely explored. Here, we review existing methodologies and propose that the integrative modeling platform (http://www.integrativemodeling.org), a computational package developed for structurally characterizing protein assemblies, could be used for integrating diverse experimental data towards the determination of the 3D architecture of genomic domains and entire genomes at unprecedented resolution. Our approach, through the visualization of looping interactions between distal regulatory elements, will allow for the characterization of global chromatin features and their relation to gene expression. We illustrate our work by outlining the recent determination of the 3D architecture of the α-globin domain in the human genome.
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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.