Genome BiologyThe tight correlation between topologically associating domains (TADs) and epigenetic domains in Drosophila suggests that the epigenome contributes to define TADs. However, it is still unknown whether histone modifications are essential for TAD formation
Sandrine Denaud +5 more
doaj +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
Topologically Associating Domains in 3D Chromatin Organization
The spatial organization of the genome within the nucleus is crucial in regulating gene expression, DNA replication, and other cellular processes. Topologically Associating Domains (TADs) is a important feature, and is the compartmentalization of the ...
Abdullah Choudhary, Murari Ambati
core +2 more sources
Identification of differential topologically associating domains from low sequencing depth and pseudobulk chromatin contact maps. [PDF]
Genome ResTopologically associating domains (TADs) are fundamental units of 3D genome architecture that shape gene regulation. Comparative analyses of TADs across biological conditions have revealed their involvement in development and disease. However, accurately
Li J, Xu H, Chen H, Lin J, Ye Y, Gao L.
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]
CellsViushkov VS, Lomov NA, Rubtsov MA.
europepmc +2 more sources
coiTAD: Detection of Topologically Associating Domains Based on Clustering of Circular Influence Features from Hi-C Data. [PDF]
Genes (Basel)Houchens D, Chowdhury HMAM, Oluwadare O.
europepmc +2 more sources
Entropy gives rise to topologically associating domains. [PDF]
Nucleic Acids Res, 2016 We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape ...
Vasquez PA +5 more
europepmc +4 more sources
Three-dimensional chromatin folding into topologically associating domains
, 2019 Mon projet de thèse a consisté à étudier les mécanismes du repliement tridimensionnel du génome dans les cellules eucaryotes. L’organisation des chromosomes est étroitement liée à la régulation de nombreuses fonctions biologiques, telles que le contrôle ...
Szabo, Quentin
core +2 more sources
, 2023 <p>Codes for reproducing results in the manuscript "Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk".</p ...
Honda, Kurara +7 more
core +1 more source
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