Results 21 to 30 of about 1,018,957 (214)

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, Qingshu Meng, Bo Xia, Shuo Zhang, Jie Lv, Dongyu Zhao, Yanqiang Li, Xin Wang, Lili Zhang, John P. Cooke, Qi Cao, Kaifu Chen   +11 more
doaj   +2 more sources

Evolutionary stability of topologically associating domains is associated with conserved gene regulation [PDF]

BMC Biology, 2018
Background The 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.
Jan Krefting, Miguel A. Andrade-Navarro, Jonas Ibn-Salem   +2 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, Xianchen Yin, Bingxiang Xu, Danyang Wang, Jimin Han, Yi Wei, Yun Deng, Ying Xiong, Zhihua Zhang   +8 more
doaj   +2 more sources

KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin. [PDF]

J Virol, 2022
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 bp resolution and constructed a
Campbell M, Chantarasrivong C, Yanagihashi Y, Inagaki T, Davis RR, Nakano K, Kumar A, Tepper CG, Izumiya Y.   +8 more
europepmc   +2 more sources

Topologically associating domains of chromatin on single-cell Hi-C data: a survey of bioinformatic tools and applications in the light of artificial intelligence [PDF]

Frontiers in Genetics
Lyu H, Li Y, Chen X, Liu Y, Liu E, Cheng X.   +5 more
exaly   +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]

Cells
Vladimir Viushkov, Nikolai Lomov, Mikhail Rubtsov   +2 more
exaly   +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, Zhang X, Chakraborty M, Emerson JJ.   +3 more
europepmc   +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   +1 more source

coiTAD: Detection of Topologically Associating Domains Based on Clustering of Circular Influence Features from Hi-C Data [PDF]

Genes
Oluwatosin Oluwadare, Drew William Houchens   +1 more
exaly   +2 more sources

Exploring mammalian chromatin architecture and its impact on gene regulation [PDF]

, 2023
Mammalian chromatin architecture appears hierarchically organised and is composed of chromosome territories, compartments, topologically associating domains (TADs), loops and nucleosomes.
Long, Helen
core   +1 more source