Gene regulation during development in the light of topologically associating domains
WIREs Developmental Biology, 2016 During embryonic development, complex transcriptional programs govern the precision of gene expression. Many key developmental genes are regulated via cis-regulatory elements that are located far away in the linear genome.
François Spitz +5 more
core +3 more sources
Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy [PDF]
Nature Communications, 2018 Accurate detection of TADs requires ultra-deep sequencing and sophisticated normalisation procedures, which limits the analysis of Hi-C data. Here the authors develop a normalisation-free method to decode the domains of chromosomes (deDoc) that utilizes ...
Angsheng Li +8 more
doaj +2 more sources
On the existence and functionality of topologically associating domains. [PDF]
Nat Genet, 2020 Genomes across a wide range of eukaryotic organisms fold into higher-order chromatin domains. Topologically associating domains (TADs) were originally discovered empirically in low-resolution Hi-C heat maps representing ensemble average interaction frequencies from millions of cells. Here, we discuss recent advances in high-resolution Hi-C, single-cell
Beagan JA, Phillips-Cremins JE.
europepmc +4 more sources
Functional Similarities of Protein-Coding Genes in Topologically Associating Domains and Spatially-Proximate Genomic Regions. [PDF]
Genes (Basel), 2022 Topologically associating domains (TADs) are the structural and functional units of the genome. However, the functions of protein-coding genes existing in the same or different TADs have not been fully investigated.
Zhao C, Liu T, Wang Z.
europepmc +2 more sources
Topologically associating domains and their role in the evolution of genome structure and function in Drosophila. [PDF]
Genome Res, 2021 Topologically associating domains (TADs) were recently identified as fundamental units of three-dimensional eukaryotic genomic organization, although our knowledge of the influence of TADs on genome evolution remains preliminary.
Liao Y +3 more
europepmc +2 more sources
A Comparison of Two Versions of the CRISPR-Sirius System for the Live-Cell Visualization of the Borders of Topologically Associating Domains [PDF]
CellsVladimir Viushkov +2 more
exaly +2 more sources
coiTAD: Detection of Topologically Associating Domains Based on Clustering of Circular Influence Features from Hi-C Data [PDF]
GenesDrew Houchens +2 more
exaly +2 more sources
Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation. [PDF]
Nucleic Acids ResKnowledge about transcription factor binding and regulation, target genes, cis-regulatory modules and topologically associating domains is not only defined by functional associations like biological processes or diseases but also has a determinative ...
Mulero-Hernández J +4 more
europepmc +2 more sources
A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains. [PDF]
Nat CommunTopologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy.
Xu J +13 more
europepmc +2 more sources
A critical assessment of topologically associating domain prediction tools [PDF]
Nucleic Acids Research, 2017 Topologically associating domains (TADs) have been proposed to be the basic unit of chromosome folding and have been shown to play key roles in genome organization and gene regulation. Several different tools are available for TAD prediction, but their properties have never been thoroughly assessed.
Dali, Rola, Blanchette, Mathieu
openaire +2 more sources