Results 11 to 20 of about 2,288,208 (167)

Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries [PDF]

Nature Communications, 2023
Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered ...
Li-Hsin Chang, Sourav Ghosh, Andrea Papale, Jennifer M. Luppino, Mélanie Miranda, Vincent Piras, Jéril Degrouard, Joanne Edouard, Mallory Poncelet, Nathan Lecouvreur, Sébastien Bloyer, Amélie Leforestier, Eric F. Joyce, David Holcman, Daan Noordermeer   +14 more
doaj   +23 more sources

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

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

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

TAD boundaries and gene activity are uncoupled. [PDF]

Elife
Topologically associating domains (TADs) are prominent features of genome organization. A proposed function of TADs is to contribute to gene regulation by promoting chromatin interactions within a TAD and by suppressing interactions between TADs.
Almansour F, Fursova NA, Keikhosravi A, Reed KSM, Larson DR, Pegoraro G, Misteli T.   +6 more
europepmc   +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

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

Multi-Layer Transcriptomic Comparison Across Human, Pig, and Mouse Informs Tissue- and Trait-Specific Animal Model Selection. [PDF]

Adv Sci (Weinh)
We integrated RNA‐seq data from humans, pigs, and mice across 15 matched tissues based on 14 910 one‐to‐one orthologous genes. Cross‐species similarity was systematically evaluated across multiple regulatory layers, including global co‐expression conservation, co‐expression networks, tissue‐specific programs, and 3D genome architecture.
Dou J, Liao Y, Shen X, Huang X, Tang Z, Gou Y, Zhou H, Xu J, Liu H, Wang Y, Liang K, Liu J, Zhang X, Li C, Wang S, Fu L, Yin L, Li X, Zhao S, Liu X, Li J, Fu Y.   +21 more
europepmc   +2 more sources

TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

Genome Biology, 2021
Background Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been shown to depend on cohesin in a loop-extrusion mechanism.
Yubao Cheng, Miao Liu, Mengwei Hu, Siyuan Wang   +3 more
doaj   +1 more source

Methods for the Analysis of Topologically Associating Domains (TADs)

, 2021
Chromatin folding in the 3D space of the nucleus can be explored through high-throughput chromosome conformation capture (Hi-C) approaches. These experiments quantify the number of interactions between any pair of genomic loci in the genome and, thus ...
Giovanni Ciriello, Tavernari, D., Zufferey, M., Ciriello, G., Marie Zufferey, Daniele Tavernari   +5 more
core   +1 more source