4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?
Genome-wide sequencing technologies enable investigations of the structural properties of the genome in various spatial dimensions. Here, we review computational techniques developed to model the three-dimensional genome in single cells versus ensembles of cells and assess their underlying assumptions. We further address approaches to study the spatio-temporal aspects of genome organization from single-cell data.
Nucleic Acid Conformation
1. 3D computational reconstruction of tissues with hollow spherical morphologies using single-cell gene expression data.
2. Spatially resolved transcriptomics in neuroscience.
3. The 4D nucleome project.
4. Spatially resolved transcriptomics adds a new dimension to genomics.
5. Understanding development and stem cells using single cell-based analyses of gene expression.
1. Single cell Hi-C reveals cell-to-cell variability in chromosome structure
2. Single-cell chromatin accessibility data using scATAC-seq
3. Global Reorganization of Chromatin Architecture during Embronic Stem Cell Differentiation
4. Pseudo-temporal ordering of individual cells reveals regulators of differentiation
5. Comparative gene expression profiling of human PGP1 iPS, lymphocyte, donor fibroblasts