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
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
KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin. [PDF]
J Virol, 2022 Abstract Eukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 base pair resolution and constructed a 3D KSHV genomic structural model with 2kb binning.
Campbell M +8 more
europepmc +5 more sources
MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions. [PDF]
PLoS Computational Biology, 2017 Genome-wide proximity ligation based assays such as Hi-C have revealed that eukaryotic genomes are organized into structural units called topologically associating domains (TADs).
Koon-Kiu Yan, Shaoke Lou, Mark Gerstein
doaj +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]
GenesOluwatosin Oluwadare +2 more
exaly +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
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
Clinical and Translational Medicine, 2022 Background During meiosis of mammalian cells, chromatin undergoes drastic reorganization. However, the dynamics of the three‐dimensional (3D) chromatin structure during the development of female germline stem cells (FGSCs) are poorly understood.
Geng G. Tian +3 more
doaj +1 more source