Computational methods for analysing multiscale 3D genome organization
Recent progress in whole-genome mapping and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …
characterization of the spatial organization and folding of the genome in the nucleus. In …
Whole-cell models and simulations in molecular detail
Comprehensive data about the composition and structure of cellular components have
enabled the construction of quantitative whole-cell models. While kinetic network–type …
enabled the construction of quantitative whole-cell models. While kinetic network–type …
Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes
Genetic studies promise to provide insight into the molecular mechanisms underlying type 2
diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer …
diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer …
GRID-seq reveals the global RNA–chromatin interactome
Higher eukaryotic genomes are bound by a large number of coding and non-coding RNAs,
but approaches to comprehensively map the identity and binding sites of these RNAs are …
but approaches to comprehensively map the identity and binding sites of these RNAs are …
Capsid-CPSF6 interaction licenses nuclear HIV-1 trafficking to sites of viral DNA integration
V Achuthan, JM Perreira, GA Sowd, M Puray-Chavez… - Cell Host & Microbe, 2018 - cell.com
HIV-1 integration into the host genome favors actively transcribed genes. Prior work
indicated that the nuclear periphery provides the architectural basis for integration site …
indicated that the nuclear periphery provides the architectural basis for integration site …
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding
Loop-extrusion and phase-separation have been proposed as mechanisms that shape
chromosome spatial organization. It is unclear, however, how they perform relative to each …
chromosome spatial organization. It is unclear, however, how they perform relative to each …
Polymer simulations of heteromorphic chromatin predict the 3D folding of complex genomic loci
Chromatin folded into 3D macromolecular structures is often analyzed by chromosome
conformation capture (3C) and fluorescence in situ hybridization (FISH) techniques, but …
conformation capture (3C) and fluorescence in situ hybridization (FISH) techniques, but …
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations
A multitude of sequencing-based and microscopy technologies provide the means to
unravel the relationship between the three-dimensional organization of genomes and key …
unravel the relationship between the three-dimensional organization of genomes and key …
Evaluating the role of the nuclear microenvironment in gene function by population-based modeling
The nuclear folding of chromosomes relative to nuclear bodies is an integral part of gene
function. Here, we demonstrate that population-based modeling—from ensemble Hi-C data …
function. Here, we demonstrate that population-based modeling—from ensemble Hi-C data …
Chromatin architectural changes during cellular senescence and aging
Chromatin 3D structure is highly dynamic and associated with many biological processes,
such as cell cycle progression, cellular differentiation, cell fate reprogramming, cancer …
such as cell cycle progression, cellular differentiation, cell fate reprogramming, cancer …