Results 21 to 30 of about 2,265,648 (271)

A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains

Nature Communications
Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy.
Jingxuan Xu, Xiang Xu, Dandan Huang, Yawen Luo, Lin Lin, Xuemei Bai, Yang Zheng, Qian Yang, Yu Cheng, An Huang, Jingyi Shi, Xiaochen Bo, Jin Gu, Hebing Chen   +13 more
doaj   +2 more sources

Measuring the three-dimensional structural properties of topologically associating domains

2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018
Genome topologically associating domains (TADs) are mega base pair (Mbp) sized genomic regions that may be the structural and functional units of the genome.
Liu, Tong, Wang, Zheng
core   +3 more sources

Deciphering chromatin domain, domain community and chromunity for 3D genome maps with Mactop

Communications Biology
Advanced high-throughput chromosome conformation capture techniques, like Hi-C, reveal genome organization into structural units like topologically associating domains (TADs), which are crucial in gene expression regulation.
Ran Duan, Dachang Dang, Shichen Fan, Shaowen Yao, Shihua Zhang   +4 more
doaj   +2 more sources

A critical assessment of topologically associating domain prediction tools. [PDF]

Nucleic Acids Res, 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 R, Blanchette M.
europepmc   +4 more sources

Effects of topological domain disruption on transcriptional regulation are chromatin context dependent

Epigenetics & Chromatin
Background Three-dimensional genome organization helps coordinate enhancer-promoter communication while insulating loci from inappropriate regulatory contacts. CTCF and cohesin contribute to this organization by forming topologically associating domains.
Ángel Josué Cerecedo-Castillo, Diana Itzé Mojica-Santamaría, Hober Nelson Núñez-Martínez, Carlos Alberto Peralta-Alvarez, Gustavo Tapia-Urzúa, Georgina Guerrero, Rodrigo Gacel Arzate-Mejía, Félix Recillas-Targa   +7 more
doaj   +2 more sources

Mutations of PDS5 genes enhance TAD-like domain formation in Arabidopsis thaliana [PDF]

Nature Communications
In eukaryotes, topologically associating domains (TADs) organize the genome into functional compartments. While TAD-like structures are common in mammals and many plants, they are challenging to detect in Arabidopsis thaliana.
Anna-Maria Göbel, Sida Zhou, Zhidan Wang, Sofia Tzourtzou, Axel Himmelbach, Shiwei Zheng, Mónica Pradillo, Chang Liu, Hua Jiang   +8 more
doaj   +2 more sources

Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function [PDF]

, 2021
Summary Topologically associating domain (TAD) boundaries are thought to partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotype 1–
Akeza, Adyam, Fukuda-Yuzawa, Yoko, Afzal, Veena, Novak, Catherine S, Godoy, Janeth, Tran, Stella, Blow, Matthew J, von Maydell, Kianna, Talkowski, Michael E, Plajzer-Frick, Ingrid, Harrington, Anne N, Meky, Eman M, Ren, Bing, Kelman, Guy, Rajderkar, Sudha, Zhang, Yanxiao, Pham, Quan, Barozzi, Iros, Li, Bin, Pennacchio, Len A, Zhu, Yiwen, Dickel, Diane E, Visel, Axel, Hu, Rong, Lloyd, KC Kent, Sudha Rajderkar, Diane E. Dickel, Iros Barozzi, Anne N. Harrington, Yanxiao Zhang, Catherine S. Novak, Veena Afzal, Adyam Akeza, Kianna von Maydell, Matthew J. Blow, Ingrid Plajzer-Frick, Janeth Godoy, Len A. Pennacchio, Michael E. Talkowski, Rong Hu, K. C. Kent Lloyd, Yoko Fukuda-Yuzawa, Stella Tran, Yiwen Zhu, Bing Ren, Guy Kelman, Bin Li, Eman M. Meky, Quan Pham, Axel Visel   +49 more
core   +1 more source

Principles of genome folding into topologically associating domains [PDF]

Science Advances, 2019
This review discusses the features of TADs across species, and their role in chromosome organization, genome function, and evolution.
Szabo, Quentin, Bantignies, Frédéric, Cavalli, Giacomo   +2 more
openaire   +2 more sources

Entropy gives rise to topologically associating domains [PDF]

Nucleic Acids Research, 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, Paula A., Hult, Caitlin, Adalsteinsson, David, Lawrimore, Josh, Forest, Mark G., Bloom, Kerry   +5 more
openaire   +2 more sources

TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription

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   +1 more source