Results 91 to 100 of about 2,288,208 (167)

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

, 2017
BackgroundThe 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.
Miguel A. Andrade-Navarro, Jonas Ibn-Salem, Jan Krefting   +2 more
core   +1 more source

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry

Cell Reports
Summary: The transcription factor ZNF143 contains a central domain of seven zinc fingers in a tandem array and is involved in 3D genome construction. However, the mechanism by which ZNF143 functions in chromatin looping remains unclear.
Mo Zhang, Haiyan Huang, Jingwei Li, Qiang Wu   +3 more
doaj   +1 more source

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

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   +1 more source

Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure

Nature Communications
In eukaryotes, structural maintenance of chromosomes (SMC) complexes form topologically associating domains (TADs) by extruding DNA loops and being stalled by roadblock proteins.
Kodai Yamaura, Naomichi Takemata, Masashi Kariya, Ayami Osaka, Sonoko Ishino, Masataka Yamauchi, Tomonori Tamura, Itaru Hamachi, Shoji Takada, Yoshizumi Ishino, Haruyuki Atomi   +10 more
doaj   +1 more source

Mandibular Prognathism in Dolang Sheep: Hi-C Evidence for Localized TAD Remodeling at Craniofacial Loci

Animals
Mandibular prognathism (Class III malocclusion) is a craniofacial anomaly characterized by an anteriorly positioned mandible, a concave facial profile and impaired mastication, and appears unusually frequently in Dolang sheep (Ovis aries).
Chao Fang, Hang Cao, Lingling Liu, Wujun Liu   +3 more
doaj   +1 more source

Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus

Genome Medicine
Background X-linked acrogigantism (X-LAG; MIM: 300942) is a severe form of pituitary gigantism caused by chromosome Xq26.3 duplications involving GPR101.
Adrian F. Daly, Leslie A. Dunnington, David F. Rodriguez-Buritica, Erica Spiegel, Francesco Brancati, Giovanna Mantovani, Vandana M. Rawal, Fabio Rueda Faucz, Hadia Hijazi, Jean-Hubert Caberg, Anna Maria Nardone, Mario Bengala, Paola Fortugno, Giulia Del Sindaco, Marta Ragonese, Helen Gould, Salvatore Cannavò, Patrick Pétrossians, Andrea Lania, James R. Lupski, Albert Beckers, Constantine A. Stratakis, Brynn Levy, Giampaolo Trivellin, Martin Franke   +24 more
doaj   +1 more source

Benchmarking DNA foundation models for genomic and genetic tasks

Nature Communications
The rapid evolution of DNA foundation models promises to revolutionize genomics, yet comprehensive evaluations are lacking. Here, we present a comprehensive, unbiased benchmark of five models (DNABERT-2, Nucleotide Transformer V2, HyenaDNA, Caduceus-Ph ...
Haonan Feng, Lang Wu, Bingxin Zhao, Chad Huff, Jianjun Zhang, Jia Wu, Lifeng Lin, Peng Wei, Chong Wu   +8 more
doaj   +1 more source

Molecular mechanisms of TAD boundary formation

, 2017
International audienceOver the last decade, it is increasingly appreciated that the 3D organization of the genome in the cell nucleus contributes to gene regulation, genome stability and chromosome inheritance.
Dekker, Job, Valton, Anne-Laure
core   +1 more source

Single‐Cell Hi‐C Technologies and Computational Data Analysis

Advanced Science
Single‐cell chromatin conformation capture (scHi‐C) techniques have evolved to provide significant insights into the structural organization and regulatory mechanisms in individual cells.
Madison A Dautle, Yong Chen
doaj   +1 more source

CREPT is required for the metastasis of triple-negative breast cancer through a co-operational-chromatin loop-based gene regulation

Molecular Cancer
Triple-negative breast cancer (TNBC) is recognized for its aggressiveness, yet the mechanism underlying metastasis remains unclear. Here, we report that CREPT/RPRD1B, which exhibits somatic gene copy-number amplifications and elevated expression ...
Jianghua Li, Lu Xu, Jiayu Wang, Xuning Wang, Yuting Lin, Alex Yutian Zou, Fangli Ren, Yinyin Wang, Jun Li, Zhijie Chang   +9 more
doaj   +1 more source