Results 111 to 120 of about 94,335 (243)

Combinatorics and topological weights of chromatin loop networks

Physical Review E
Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop networks, both in the case where TUs are labeled and where they are unlabeled.
Andrea Bonato, Michael Chiang, Dom Corbett, Sergey Kitaev, Davide Marenduzzo, Alexander Morozov, Enzo Orlandini   +6 more
openaire   +5 more sources

Stem Cell Differentiation Disperses Transcriptional Clusters via a Conserved Surface‐Condensate Trajectory

Advanced Science, EarlyView.
Stem cell differentiation follows a conserved surface condensate trajectory: H3K27ac super enhancers nucleate large RNA polymerase II clusters that grow and unfold before transcriptional activity disperses them. This work reveals how biophysical forces at enhancer surfaces dynamically build and dismantle stem cell transcription hubs, reshaping cell ...
Tim Klingberg, Irina Wachter, Agnieszka Pancholi, Matthias Akyel, Yomna Gohar, Priya Kumar, Ana Miguel Fernandes, Yuzhi Bao, Alica Schmidt‐Heydt, Marcel Piepers, Alicia Günthel, Marcel Sobucki, Elisa Kämmer, Süheyla Eroğlu‐Kayıkçı, Stephan Allgeier, Sylvia Erhardt, Vasily Zaburdaev, Carmelo Ferrai, Lennart Hilbert   +18 more
wiley   +1 more source

Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion

Genome Biology
Background Inhomogeneous patterns of chromatin-chromatin contacts within 10–100-kb-sized regions of the genome are a generic feature of chromatin spatial organization.
Tianyu Yuan, Hao Yan, Kevin C. Li, Ivan Surovtsev, Megan C. King, Simon G. J. Mochrie   +5 more
doaj   +1 more source

A Lightweight Framework For Chromatin Loop Detection at the Single-Cell Level. [PDF]

Adv Sci (Weinh), 2023
Wang F, Alinejad-Rokny H, Lin J, Gao T, Chen X, Zheng Z, Meng L, Li X, Wong KC.   +8 more
europepmc   +1 more source

Accurately Deciphering Tissue Heterogeneity From Spatial Multi‐Modal and Multi‐Omics With STransformer

Advanced Science, EarlyView.
STransformer is a unified deep learning framework designed to seamlessly accommodate a comprehensive landscape of spatial data. By simultaneously capturing short‐range cellular interactions and tissue‐wide semantic patterns, it extracts robust representations to accurately dissect complex tissue heterogeneity.
Xingyi Li, Jialuo Xu, Gaoyuan Du, Xiangting Jia, Dongmin Zhao, Chunyan Zhou, Kexin Xiao, Jia Gu, Junnan Zhu, Xuequn Shang   +9 more
wiley   +1 more source

Cholesterol‐Mediated Metabolic‐mechanotransductive Crosstalk Orchestrates Castration Resistance in Prostate Cancer

Advanced Science, EarlyView.
Full androgen deprivation (FAD) induces paracrine cholesterol in prostate cancer that drives the polarization of cancer‐associated fibroblasts (CAFs) and subsequent elevated matrix stiffness. Matrix stiffness in turn potentiates tumor cell survival under FAD pressure via dual mechanotransductive activation of the IRE1α‐XBP1s stress‐response axis ...
Shaojie Liu, Chao Xu, Jun Jiang, Limin He, Yike Zhou, Zhengxuan Li, Yu Li, Keying Zhang, Fa Yang, Tong Lu, Hongtao Song, Hai Zhu, Zhihao Hu, Xiaolong Zhao, Kai Gan, Hongji Li, Bo Yang, Rui Zhang, Weihong Wen, Donghui Han, Weijun Qin   +20 more
wiley   +1 more source

Targeting Lactate‐Driven Stromal Autophagy via MCT1 Disrupts the Immunosuppressive Niche and Sensitizes Pancreatic Cancer to PD‐1 Blockade

Advanced Science, EarlyView.
Tumor‐derived lactate activates PSCs through MCT1‐mediated Vps34 lactylation and autophagy. These activated PSCs secrete CXCL9/10, upregulating PD‐1 on CD8+ T cells via the CXCR3/STAT3 axis to foster immunosuppression. Disrupting this metabolic crosstalk by targeting MCT1 effectively sensitizes pancreatic cancer to PD‐1 blockade, presenting a promising
Wenfeng Zhuo, Rong Hu, Yuhang Hu, Ping Hu, Shengbo Han, Guozheng Lv, Zhu Zeng, Yong Zhao, Yang Li, Yan Huang, Yingsong Zhao, Hongda Wang, Guangyu Zhao, Eryang Zhao, Gang Zhao   +14 more
wiley   +1 more source

Allosteric Inhibition of Polycomb Repressive Complex 2 by an EZH2‐Selective Small Molecule Inhibitor

Advanced Science, EarlyView.
The study characterizes C36, a highly selective EZH2/PRC2 inhibitor that acts via a novel allosteric mechanism. Unlike previous inhibitors, C36 inhibits EZH2/PRC2 by disrupting the allosteric communication between EZH2 and EED in a SAM‐noncompetitive manner.
Ting Cao, Dongdong Liu, Haishan Gao, Chenyang Qin, Wen Zhang, Ziyun Lu, Dongxia Tan, Yuxiu Qu, Yusong Liu, Zhiran Zou, Hongtao Yu, Wei Qi   +11 more
wiley   +1 more source

p300 Degradation by the p53‐SIAH1 Axis Relieves TBK1 Acetylation to Enhance Innate Antiviral Immunity

Advanced Science, EarlyView.
This study identifies p300 as the acetyltransferase that acetylates TBK1 and inhibits its phosphorylation. Activation of the p53‐SIAH1 axis by immune response downregulates p300 expression to sustain innate antiviral immunity. Conditional p300 knockout in alveolar epithelial cells in vivo promotes antiviral responses and suppresses virus replication ...
Huidi Yu, Zhihao Zhan, Xiaoxiang Pan, Xinyue Zhang, Penggang Liu, Jing Sun, Xiulong Xu   +6 more
wiley   +1 more source

Tandem Duplication‐Driven Neofunctionalization of UDP‐Glycosyltransferases Shapes the Diversification of Triterpenoid Saponins in the Cucurbitaceae

Advanced Science, EarlyView.
We present a chromosome‐level genome assembly of Siraitia grosvenorii and, through comparative genomics, uncover a conserved UGT73 tandem array driving triterpenoid saponin diversification in Cucurbitaceae. Crystalized SgUGT73AM30 further reveals the regioselectivity mechanism underlying its catalytic activity.
Guangyi Wang, Mengmeng Li, Xuehui Dai, Yanchen Zhang, Yuhan Wu, Zhaotao Yan, Chenfei Tian, Hongkai Fan, Haili Liu, Xiaowei Zhang, Yiming Yang, Jiayu Lu, Yuwei Sun, Yong Wang   +13 more
wiley   +1 more source