Results 1 to 10 of about 5,250 (92)

HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets [PDF]

Computational and Structural Biotechnology Journal, 2023
High-throughput chromatin conformation capture technologies, such as Hi-C and Micro-C, have enabled genome-wide view of chromatin spatial organization.
Armen Abnousi, Jiawen Chen, Jia Wen
exaly   +4 more sources

Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease [PDF]

Frontiers in Cell and Developmental Biology, 2021
Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as
Juan J Tena, JOSÉ M Santos-Pereira
exaly   +4 more sources

Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains [PDF]

Frontiers in Genetics, 2023
Transcription-factor binding to cis-regulatory regions regulates the gene expression program of a cell, but occupancy is often a poor predictor of the gene response.
Christophe Tav, Christophe Tav, Christophe Tav, Éric Fournier, Éric Fournier, Éric Fournier, Michèle Fournier, Michèle Fournier, Fatemeh Khadangi, Fatemeh Khadangi, Audrey Baguette, Maxime C. Côté, Maxime C. Côté, Maruhen A. D. Silveira, Maruhen A. D. Silveira, Félix-Antoine Bérubé-Simard, Félix-Antoine Bérubé-Simard, Guillaume Bourque, Guillaume Bourque, Arnaud Droit, Arnaud Droit, Arnaud Droit, Arnaud Droit, Steve Bilodeau, Steve Bilodeau, Steve Bilodeau, Steve Bilodeau   +26 more
doaj   +2 more sources

Pattern recognition of topologically associating domains using deep learning [PDF]

BMC Bioinformatics, 2022
Background Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have been shown to be a chromosomal ...
Jhen Yuan Yang, Jia-Ming Chang
doaj   +2 more sources

Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency [PDF]

Genome Biology, 2021
Background Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and
Yongzheng Li, Boxin Xue, Mengling Zhang, Liwei Zhang, Yingping Hou, Yizhi Qin, Haizhen Long, Qian Peter Su, Yao Wang, Xiaodong Guan, Yanyan Jin, Yuan Cao, Guohong Li, Yujie Sun   +13 more
doaj   +2 more sources

Identifying topologically associating domains using differential kernels. [PDF]

PLoS Computational Biology
Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication.
Luka Maisuradze, Megan C King, Ivan V Surovtsev, Simon G J Mochrie, Mark D Shattuck, Corey S O'Hern   +5 more
doaj   +2 more sources

RobusTAD: reference panel based annotation of nested topologically associating domains [PDF]

Genome Biology
Topologically associating domains (TADs) are fundamental units of 3D genomes and play essential roles in gene regulation. Hi-C data suggests a hierarchical organization of TADs.
Yanlin Zhang, Rola Dali, Mathieu Blanchette   +2 more
doaj   +2 more sources

DiffDomain enables identification of structurally reorganized topologically associating domains [PDF]

Nature Communications
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,
Dunming Hua, Ming Gu, Xiao Zhang, Yanyi Du, Hangcheng Xie, Li Qi, Xiangjun Du, Zhidong Bai, Xiaopeng Zhu, Dechao Tian   +9 more
doaj   +2 more sources

The hierarchical folding dynamics of topologically associating domains during early embryo development [PDF]

BMC Biology
Background Recent research has indicated a close connection between the three-dimensional (3D) structure of chromatin and early embryo development, with precise higher-order chromatin folding playing a significant role in mediating gene expression ...
Xuemei Bai, Xiaohan Tang, Yuyang Wang, Shutong Yue, Xiang Xu, Pengzhen Hu, Jingxuan Xu, Yaru Li, Junting Wang, Huan Tao, Yang Zheng, Bijia Chen, Mengge Tian, Lin Lin, Ruiqing Wang, Yu Sun, Chao Ren, Xiaochen Bo, Hao Li, Hebing Chen, Meisong Lu   +20 more
doaj   +2 more sources

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

BMC Bioinformatics, 2019
Background Topologically associating domains (TADs) are genomic regions with varying lengths. The interactions within TADs are more frequent than those between different TADs.
Tong Liu, Zheng Wang
doaj   +2 more sources