On the existence and functionality of topologically associating domains

JA Beagan, JE Phillips-Cremins - Nature genetics, 2020 - nature.com
Genomes across a wide range of eukaryotic organisms fold into higher-order chromatin
domains. Topologically associating domains (TADs) were originally discovered empirically …

HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions

XT Wang, W Cui, C Peng - Nucleic acids research, 2017 - academic.oup.com
A current question in the high-order organization of chromatin is whether topologically
associating domains (TADs) are distinct from other hierarchical chromatin domains …

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

B Bintu, LJ Mateo, JH Su, NA Sinnott-Armstrong… - Science, 2018 - science.org
INTRODUCTION Chromatin adopts an intricate three-dimensional (3D) organization in the
nucleus that is critical for many genome processes, from gene regulation to genome …

[HTML][HTML] Chromatin-driven behavior of topologically associating domains

F Ciabrelli, G Cavalli - Journal of molecular biology, 2015 - Elsevier
Metazoan genomes are highly organized inside the cell nucleus. Topologically associating
domains (TADs) represent the building blocks of genome organization, but their linear …

Comparison of computational methods for the identification of topologically associating domains

M Zufferey, D Tavernari, E Oricchio, G Ciriello - Genome biology, 2018 - Springer
Background Chromatin folding gives rise to structural elements among which are clusters of
densely interacting DNA regions termed topologically associating domains (TADs). TADs …

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

J Fraser, C Ferrai, AM Chiariello… - Molecular systems …, 2015 - embopress.org
Mammalian chromosomes fold into arrays of megabase‐sized topologically associating
domains (TAD s), which are arranged into compartments spanning multiple megabases of …

Defining functionally relevant spatial chromatin domains: it is a TAD complicated

N Sikorska, T Sexton - Journal of molecular biology, 2020 - Elsevier
Chromosome conformation capture and orthologous methods uncovered the spatial
organization of metazoan chromosomes into autonomously folded substructures, often …

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

SV Ulianov, EE Khrameeva, AA Gavrilov… - Genome …, 2016 - genome.cshlp.org
Recent advances enabled by the Hi-C technique have unraveled many principles of
chromosomal folding that were subsequently linked to disease and gene regulation. In …

Principles of genome folding into topologically associating domains

Q Szabo, F Bantignies, G Cavalli - Science advances, 2019 - science.org
Understanding the mechanisms that underlie chromosome folding within cell nuclei is
essential to determine the relationship between genome structure and function. The recent …

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

Y Zhan, L Mariani, I Barozzi, EG Schulz… - Genome …, 2017 - genome.cshlp.org
Understanding how regulatory sequences interact in the context of chromosomal
architecture is a central challenge in biology. Chromosome conformation capture revealed …