Results 51 to 60 of about 2,288,208 (167)

Large scale genomic reorganization of topological domains at the HoxD locus

Genome Biology, 2017
Background The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster.
Pierre J. Fabre, Marion Leleu, Benjamin H. Mormann, Lucille Lopez-Delisle, Daan Noordermeer, Leonardo Beccari, Denis Duboule   +6 more
doaj   +1 more source

TOP1MT rs2293925 is an enhancer‐active regulatory SNP that shapes mitochondrial R‐loop dynamics

The FEBS Journal, EarlyView.
This study shows how a common genetic variant of mitochondrial topoisomerase 1 (TOP1MT rs2293925) can influence mitochondrial gene regulation, DNA topology, and formation of noncanonical nucleic acid structures such as R‐loops. By linking this enhancer‐active variant to mitochondrial nucleic acid stress in cellular contexts relevant to amyotrophic ...
Dóra Varga, Zsolt Ráduly, Beáta Boros‐Oláh, Éva Nagy, Zsolt Karányi, László Halász, Bálint László Bálint, György Vámosi, Emese Tóth, Péter Bai, Serena Santangelo, Patrizia Bossolasco, Antonia Ratti, Vincent Géli, Yves Pommier, Lóránt Székvölgyi   +15 more
wiley   +1 more source

Plant cis‐regulatory grammar: Decoding the multidimensional code of transcriptional regulation for programmable crop engineering

Journal of Integrative Plant Biology, EarlyView.
This review decodes the grammar of plant cis‐regulatory elements, revealing that their function emerges from sequence, chromatin accessibility, 3D topology, and cell type context. It highlights how single‐cell omics, CRISPR dissection, and AI‐driven design converge to enable predictive engineering and crop improvement. ABSTRACT Cis‐regulatory elements (
Libin Zhang, Maoteng Li
wiley   +1 more source

Additional file 3 of Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C

, 2022
Additional file 3: Table S2. Topologically Associating Domains (TADs) identified from this study. (A) TAD statistics of Hi-C, Micro-C, and promoter capture Micro-C data.
Zexun Wu (15169523), Beoung Hun Lee (15256370), Suhn K. Rhie (15169526)   +2 more
core   +1 more source

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

Genome Biology, 2019
The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most ...
Lin An, Tao Yang, Jiahao Yang, Johannes Nuebler, Guanjue Xiang, Ross C. Hardison, Qunhua Li, Yu Zhang   +7 more
doaj   +1 more source

Predicting scale-dependent chromatin polymer properties from systematic coarse-graining

Nature Communications, 2023
Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead ...
Sangram Kadam, Kiran Kumari, Vinoth Manivannan, Shuvadip Dutta, Mithun K. Mitra, Ranjith Padinhateeri   +5 more
doaj   +1 more source

The Arms Race Between Bacteria and Their Viruses: Update on Phage Countermeasures Against Bacterial Defence Systems

Microbial Biotechnology, Volume 19, Issue 11, November 2026.
Bacteria evolved anti‐phage systems such as Gabija defence that degrade the intracellular phage genome. Phages evolved counter‐defences such as the Gad1 protein which surrounds and inhibits the Gabija defence complex allowing phage replication. Many cases of phage anti‐defences were recently described.
Harald Brüssow
wiley   +1 more source

High‐quality genome of elite peanut cultivar ZH05 reveals subgenome asymmetry, pan‐genome diversity, and breeding insights

Journal of Integrative Plant Biology, Volume 68, Issue 11, Page 3977-3997, November 2026.
A high‐quality reference genome for the elite peanut cultivar Zhonghua No. 5 revealed differing evolutionary paths between the two peanut subgenomes. SubA has higher overall gene expression and more open chromatin, whereas SubB has stronger structural organization, higher DNA methylation, and greater adaptive diversity associated with peanut evolution ...
Taihua Yang, Nian Liu, Li Huang, Jianbin Guo, Xiaomeng Xue, Mingjun Wang, Xiaohan Zhang, Chengtao Quan, Enyou Feng, Jiazhuang Tan, Zhenzhen Zhang, Yu You, Youlin Xia, Dongxin Huai, Yuning Chen, Liying Yan, Kede Liu, Huifang Jiang, Yong Lei, Boshou Liao   +19 more
wiley   +1 more source

Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

Nature Communications, 2023
Cohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer–promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor ...
Ryuichiro Nakato, Toyonori Sakata, Jiankang Wang, Luis Augusto Eijy Nagai, Yuya Nagaoka, Gina Miku Oba, Masashige Bando, Katsuhiko Shirahige   +7 more
doaj   +1 more source

SRF promotes long-range chromatin loop formation and stem cell pluripotency [PDF]

Serum response factor (SRF) is a transcription factor essential for cell proliferation, differentiation, and migration and is required for primitive streak and mesoderm formation in the embryo.
Koch, F. ; https://orcid.org/, Scholze-Wittler, M. ; https://orcid.org/, Tsaytler, P. ; https://orcid.org/, Meierhofer, D. ; https://orcid.org/, Wittler, L. ; https://orcid.org/, Herrmann, B. ; https://orcid.org/, Blaess, G. ; https://orcid.org/   +6 more
core   +1 more source