[HTML][HTML] A compendium of chromatin contact maps reveals spatially active regions in the human genome

AD Schmitt, M Hu, I Jung, Z Xu, Y Qiu, CL Tan, Y Li… - Cell reports, 2016 - cell.com
The three-dimensional configuration of DNA is integral to all nuclear processes in
eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide …

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

VC Seitan, AJ Faure, Y Zhan, RP McCord… - Genome …, 2013 - genome.cshlp.org
Chromosome conformation capture approaches have shown that interphase chromatin is
partitioned into spatially segregated Mb-sized compartments and sub-Mb-sized topological …

Resolving the 3D landscape of transcription-linked mammalian chromatin folding

THS Hsieh, C Cattoglio, E Slobodyanyuk, AS Hansen… - Molecular cell, 2020 - cell.com
Whereas folding of genomes at the large scale of epigenomic compartments and
topologically associating domains (TADs) is now relatively well understood, how chromatin …

Principles of 3D compartmentalization of the human genome

MH Nichols, VG Corces - Cell reports, 2021 - cell.com
Chromatin is organized in the nucleus via CTCF loops and compartmental domains. Here,
we compare different cell types to identify distinct paradigms of compartmental domain …

[HTML][HTML] 4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis

PHL Krijger, G Geeven, V Bianchi, CRE Hilvering… - Methods, 2020 - Elsevier
Chromosome conformation capture (3C) methods measure DNA contact frequencies based
on nuclear proximity ligation, to uncover in vivo genomic folding patterns. 4C–seq is a …

Chromatin loops, gene positioning, and gene expression

S Holwerda, W Laat - Frontiers in genetics, 2012 - frontiersin.org
Technological developments and intense research over the last years have led to a better
understanding of the 3D structure of the genome and its influence on genome function …

CTCF and cohesin in genome folding and transcriptional gene regulation

M Merkenschlager, EP Nora - Annual review of genomics and …, 2016 - annualreviews.org
Genome function, replication, integrity, and propagation rely on the dynamic structural
organization of chromosomes during the cell cycle. Genome folding in interphase provides …

Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops

S Liu, Y Cao, K Cui, Q Tang, K Zhao - Nature communications, 2022 - nature.com
The three-dimensional genomic structure plays a critical role in gene expression, cellular
differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin …

Higher-order chromosomal structures mediate genome function

I Jerković, Q Szabo, F Bantignies, G Cavalli - Journal of Molecular Biology, 2020 - Elsevier
How chromosomes are organized within the tridimensional space of the nucleus and how
can this organization affect genome function have been long-standing questions on the path …

Loop stacking organizes genome folding from TADs to chromosomes

A Hafner, M Park, SE Berger, SE Murphy, EP Nora… - Molecular cell, 2023 - cell.com
Although population-level analyses revealed significant roles for CTCF and cohesin in
mammalian genome organization, their contributions at the single-cell level remain …