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 …
Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations
PR Cook, D Marenduzzo - Nucleic acids research, 2018 - academic.oup.com
Current models for the folding of the human genome see a hierarchy stretching down from
chromosome territories, through A/B compartments and topologically-associating domains …
chromosome territories, through A/B compartments and topologically-associating domains …
[HTML][HTML] The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery
HG Stunnenberg, S Abrignani, D Adams, M de Almeida… - Cell, 2016 - cell.com
The International Human Epigenome Consortium (IHEC) coordinates the generation of a
catalog of high-resolution reference epigenomes of major primary human cell types. The …
catalog of high-resolution reference epigenomes of major primary human cell types. The …
[HTML][HTML] Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts
Abstract Current three-dimensional (3D) genome modeling platforms are limited by their
inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user …
inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user …
Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription
Intrinsic dynamics of chromatin contribute to gene regulation. How chromatin mobility
responds to genomic processes, and whether this response relies on coordinated chromatin …
responds to genomic processes, and whether this response relies on coordinated chromatin …
Epigenetic and transcriptional variability shape phenotypic plasticity
Epigenetic and transcriptional variability contribute to the vast diversity of cellular and
organismal phenotypes and are key in human health and disease. In this review, we …
organismal phenotypes and are key in human health and disease. In this review, we …
[HTML][HTML] Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states
The transition from naive to primed pluripotency is accompanied by an extensive
reorganisation of transcriptional and epigenetic programmes. However, the role of …
reorganisation of transcriptional and epigenetic programmes. However, the role of …
Deciphering Hi-C: from 3D genome to function
S Kong, Y Zhang - Cell biology and toxicology, 2019 - Springer
Hi-C is a commonly used technology in 3D genomics which can depict global chromatin
interactions across eukaryotic genome. Integrating with different datasets, it can also be …
interactions across eukaryotic genome. Integrating with different datasets, it can also be …
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells
K Jodkowska, V Pancaldi, M Rigau… - Nucleic Acids …, 2022 - academic.oup.com
In mammalian cells, chromosomal replication starts at thousands of origins at which
replisomes are assembled. Replicative stress triggers additional initiation events from …
replisomes are assembled. Replicative stress triggers additional initiation events from …
[HTML][HTML] Network models of chromatin structure
V Pancaldi - Current Opinion in Genetics & Development, 2023 - Elsevier
Highlights•Networks are a useful framework to study chromatin structure
datasets.•Chromatin networks can be used to visualize the 3D epigenome and integrate …
datasets.•Chromatin networks can be used to visualize the 3D epigenome and integrate …