Results 31 to 40 of about 2,265,648 (271)

Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk

, 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, Takata, Atsushi, Kazuno, An-a, Nakamura, Takumi, Mizuno, Shota, Ueda, Junko, Hara, Tomonori, Yamamoto, Hirona   +7 more
core   +1 more source

Three‐dimensional genome structure and function

MedComm, 2023
Linear DNA undergoes a series of compression and folding events, forming various three‐dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop.
Hao Liu, Hsiangyu Tsai, Maoquan Yang, Guozhi Li, Qian Bian, Gang Ding, Dandan Wu, Jiewen Dai   +7 more
doaj   +1 more source

SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information

Genome Biology, 2021
Topologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees.
Yu Wei Zhang, Meng Bo Wang, Shuai Cheng Li   +2 more
doaj   +1 more source

Capture Hi-C reveals the influence on dynamic three-dimensional chromosome organization perturbed by genetic variation or vanillin stress in Saccharomyces cerevisiae

Frontiers in Microbiology, 2022
Studying the mechanisms of resistance to vanillin in microorganisms, which is derived from lignin and blocks a major pathway of DNA double-strand break repair in yeast, will benefit the design of robust cell factories that produce biofuels and chemicals ...
Xinning Wang, Xinning Wang, Bolun Yang, Weiquan Zhao, Wenyan Cao, Yu Shen, Zailu Li, Xiaoming Bao   +7 more
doaj   +1 more source

Exploring the 2D and 3D structural properties of topologically associating domains [PDF]

BMC Bioinformatics, 2019
Abstract Background Topologically associating domains (TADs) are genomic regions with varying lengths. The interactions within TADs are more frequent than those between different TADs. TADs or sub-TADs are considered the structural and functional units of the mammalian genomes. Although TADs are important for understanding how genomes function, we have
Tong Liu, Zheng Wang
openaire   +4 more sources

HPV16 genome integration does not disrupt host topologically associating domain (TAD) boundaries at the integration site in W12 clones G2 and D2.

, 2021
(A, D) Hi-C data for W12 clone G2 is compared to (B, E) Hi-C data for W12 clone D2 using (C, F) an insulation score interpreting the boundaries of topologically associating domains (TADs) for HPV16 integration sites within W12 clone G2 (Chr5: 50–55 Mbp ...
Emma L. A. Drane (11331464), Csilla Várnai (3720010), Ian J. Groves (8703930), Marco Michalski (5007890), Cinzia G. Scarpini (11331470), Giovanni Bussotti (45579), Jack M. Monahan (11331467), Peter Fraser (32141), Stefan Schoenfelder (115930), Nicholas Coleman (95937), Stephen P. Smith (11331473), Anton J. Enright (11331476)   +11 more
core   +1 more source

The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers

Computational and Structural Biotechnology Journal, 2021
Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown.
Guifang Du, Hao Li, Yang Ding, Shuai Jiang, Hao Hong, Jingbo Gan, Longteng Wang, Yuanping Yang, Yinyin Li, Xin Huang, Yu Sun, Huan Tao, Yaru Li, Xiang Xu, Yang Zheng, Junting Wang, Xuemei Bai, Kang Xu, Yaoshen Li, Qi Jiang, Cheng Li, Hebing Chen, Xiaochen Bo   +22 more
doaj   +1 more source

DiffDomain Enables Identification of Structurally Reorganized Topologically Associating Domains

Nature Communications, 2022
Abstract Topologically associating domains (TADs) are critical structural units in three-dimensional genome organization of mammalian genome. Dynamic reorganizations of TADs between health and disease states are associated with essential genome functions. However, computational methods for identifying reorganized TADs are still in the
Dunming Hua, Ming Gu, Yanyi Du, Li Qi, Xiangjun Du, Zhidong Bai, Xiaopeng Zhu, Dechao Tian   +7 more
openaire   +5 more sources

The CTCF Anatomy of Topologically Associating Domains [PDF]

, 2019
Abstract Topologically associated domains (TADs) are defined as regions of self-interaction. To date, it is unclear how to reconcile TAD structure with CTCF site orientation, which is known to coordinate chromatin loops anchored by Cohesin rings at convergent CTCF site pairs.
Nanni, Luca, Wang, Cheng, Manders, Freek, Groh, Laszlo, Haro, Paula, Oldenkamp, Roel, Ceri, Stefano, Logie, Colin   +7 more
openaire   +1 more source

Disruption of topologically associating domains by structural variations in tetraploid cottons

Genomics, 2021
Structural variations (SVs) are recognized to have an important role in transcriptional regulation, especially in the light of resolved 3D genome structure using high-throughput chromosome conformation capture (Hi-C) technology in mammals. However, the effect of SVs on 3D genome organization in plants remains rarely understood.
Yuexuan, Long, Zhenping, Liu, Pengcheng, Wang, Hang, Yang, Yuejin, Wang, Sainan, Zhang, Xianlong, Zhang, Maojun, Wang   +7 more
openaire   +2 more sources