The spatial organization of transcriptional control
A Hafner, A Boettiger - Nature Reviews Genetics, 2023 - nature.com
In animals, the sequences for controlling gene expression do not concentrate just at the
transcription start site of genes, but are frequently thousands to millions of base pairs distal …
transcription start site of genes, but are frequently thousands to millions of base pairs distal …
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 …
Is euchromatin really open in the cell?
Genomic DNA is wrapped around a core histone octamer and forms a nucleosome. In
higher eukaryotic cells, strings of nucleosomes are irregularly folded as chromatin domains …
higher eukaryotic cells, strings of nucleosomes are irregularly folded as chromatin domains …
Loop stacking organizes genome folding from TADs to chromosomes
Although population-level analyses revealed significant roles for CTCF and cohesin in
mammalian genome organization, their contributions at the single-cell level remain …
mammalian genome organization, their contributions at the single-cell level remain …
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 …
Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes
AR Ringel, Q Szabo, AM Chiariello, K Chudzik… - Cell, 2022 - cell.com
Regulatory landscapes drive complex developmental gene expression, but it remains
unclear how their integrity is maintained when incorporating novel genes and functions …
unclear how their integrity is maintained when incorporating novel genes and functions …
CTCF mediates dosage-and sequence-context-dependent transcriptional insulation by forming local chromatin domains
Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily
conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but …
conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but …
MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution
The linear sequence of DNA provides invaluable information about genes and their
regulatory elements along chromosomes. However, to fully understand gene function and …
regulatory elements along chromosomes. However, to fully understand gene function and …
Genome modeling: from chromatin fibers to genes
The intricacies of the 3D hierarchical organization of the genome have been approached by
many creative modeling studies. The specific model/simulation technique combination …
many creative modeling studies. The specific model/simulation technique combination …
Predicting genome architecture: challenges and solutions
P Belokopytova, V Fishman - Frontiers in genetics, 2021 - frontiersin.org
Genome architecture plays a pivotal role in gene regulation. The use of high-throughput
methods for chromatin profiling and 3-D interaction mapping provide rich experimental data …
methods for chromatin profiling and 3-D interaction mapping provide rich experimental data …