Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation [PDF]
Nature Communications, 2017 Metazoan genomes contain many clusters of conserved noncoding elements. Here, the authors provide evidence that these clusters coincide with distinct topologically associating domains in humans and Drosophila, revealing a conserved regulatory genomic ...
Nathan Harmston +5 more
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Principles of genome folding into topologically associating domains. [PDF]
Sci Adv, 2019 International audienceUnderstanding the mechanisms that underlie chromosome folding within cell nuclei is essential to determine the relationship between genome structure and function.
Szabo Q, Bantignies F, Cavalli G.
europepmc +5 more sources
Methods for the Analysis of Topologically Associating Domains (TADs)
, 2021 Chromatin folding in the 3D space of the nucleus can be explored through high-throughput chromosome conformation capture (Hi-C) approaches. These experiments quantify the number of interactions between any pair of genomic loci in the genome and, thus ...
Giovanni Ciriello +5 more
core +4 more sources
Form and function of topologically associating genomic domains in budding yeast [PDF]
Proceedings of the National Academy of Sciences, 2017 Significance In metazoans, topological domains are regions in the genome that more frequently associate with themselves than with neighboring regions. These domains are important for regulating transcription and replication.
Devon Chandler-Brown +6 more
core +3 more sources
Finding Topologically Associating Domains [PDF]
, 2015 In this thesis, we propose a new method for finding Topologically Associating Domains, which are contiguous segments of chromatin, ranging in size from thousands to millions of base pairs.
Grytten, Ivar
core +2 more sources
An Investigation of Segmental Duplications across Topologically Associating Domains [PDF]
, 2022 High-throughput chromosome conformation capture (Hi-C) reveals organization within genomes. Topologically associating domains (TADs) make up one level of organization and are identified by applying algorithms to Hi-C data.
Bell, Sara
core +2 more sources
Mapping chromosome neighborhoods
BioTechniques, 2015 The discovery of topologically associating domains (TADs) changed the way researchers think about gene expression and chromosome structure. Jeffrey Perkel takes a closer look into these “chromosome neighborhoods.”
Jeffrey Perkel
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Evolutionary stability of topologically associating domains is associated with conserved gene regulation [PDF]
BMC Biology, 2017 BackgroundThe human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts.
Miguel A. Andrade-Navarro +2 more
core +4 more sources
The hierarchical folding dynamics of topologically associating domains during early embryo development [PDF]
BMC BiologyBackground Recent research has indicated a close connection between the three-dimensional (3D) structure of chromatin and early embryo development, with precise higher-order chromatin folding playing a significant role in mediating gene expression ...
Xuemei Bai +20 more
doaj +2 more sources
TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription [PDF]
Genome Biology, 2020 We present TADsplimer, the first computational tool to systematically detect topologically associating domain (TAD) splits and mergers across the genome between Hi-C samples.
Guangyu Wang +11 more
doaj +2 more sources