ArticleNucleic acids research2018
Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Annotating Interchromosomal Interactions at Sub-Megabase Resolution Using Network Clustering Coefficients.bioRxiv : the preprint server for biology · 2026Article
- Molecular Behavior of Human β Defensin Type 3 Embedded in Different Model Lipid Membranes.Journal of chemical information and modeling · 2026Article
- Conformational transition of a polycationic hinge domain contributes to DNA binding.Biophysical chemistry · 2026Article
- Extrinsic heterogeneity: Collectivity in isotropic conformational fluctuations of chromosomes.Biophysical journal · 2025Article
- Chromosome compartmentalization: causes, changes, consequences, and conundrums.Trends in cell biology · 2024Review
- Article
- An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line.STAR protocols · 2022Article
- Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling.Scientific reports · 2022Article
- Statistical Analysis of Protein-Ligand Interaction Patterns in Nuclear Receptor RORγ.Frontiers in molecular biosciences · 2022Article
- Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation.Biophysical chemistry · 2021Article
- Protein conformational switch discerned via network centrality properties.Computational and structural biotechnology journal · 2021Article
- Inferring chromosome radial organization from Hi-C data.BMC bioinformatics · 2020Article
- Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function.Molecular cell · 2020Review
- Using contact statistics to characterize structure transformation of biopolymer ensembles.Physical review. E · 2020Article
- Disorder Mediated Oligomerization ofThe journal of physical chemistry. B · 2019Article
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4 authors.
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Abstract
Conformational ensembles of biopolymers, whether proteins or chromosomes, can be described using contact matrices. Principal component analysis (PCA) on the contact data has been used to interrogate both protein and chromosome structures and/or dynamics. However, as these fields have developed separately, variants of PCA have emerged. Previously, a variant we hereby term Implicit-PCA (I-PCA) has been applied to chromosome contact matrices and revealed the spatial segregation of active and inactive chromatin. Separately, Explicit-PCA (E-PCA) has previously been applied to proteins and characterized their correlated structure fluctuations. Here, we swapped analysis methods (I-PCA and E-PCA), applying each to a different biopolymer type (chromosome or protein) than the one for which they were initially developed. We find that applying E-PCA to chromosome distance matrices derived from microscopy data can reveal the dominant motion (concerted fluctuation) of these chromosomes. Further, by applying E-PCA to Hi-C data across the human blood cell lineage, we isolated the aspects of chromosome structure that most strongly differentiate cell types. Conversely, when we applied I-PCA to simulation snapshots of proteins, the major component reported the consensus features of the structure, making this a promising approach for future analysis of semi-structured proteins.
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