Results 101 to 110 of about 540 (209)

Transformers significantly improve splice site prediction

Communications Biology
Mutations that affect RNA splicing significantly impact human diversity and disease. Here we present a method using transformers, a type of machine learning model, to detect splicing from raw 45,000-nucleotide sequences.
Benedikt A. Jónsson, Gísli H. Halldórsson, Steinþór Árdal, Sölvi Rögnvaldsson, Eyþór Einarsson, Patrick Sulem, Daníel F. Guðbjartsson, Páll Melsted, Kári Stefánsson, Magnús Ö. Úlfarsson   +9 more
doaj   +1 more source

Rbm3 deficiency leads to transcriptome-wide splicing alterations

RNA Biology
Rbm3 (RNA-binding motif protein 3) is a stress responsive gene, which maintains cellular homeostasis and promotes survival upon various harmful cellular stimuli.
Steffen Erkelenz, Marta Grzonka, Antonios Papadakis, Heiner Schaal, Jan H. J. Hoeijmakers, Ákos Gyenis   +5 more
doaj   +1 more source

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

UniSplicer: A deep-learning framework for accurate splice-site prediction and splice-altering mutation detection across diverse taxa

Plant Communications
RNA splicing removes non-coding introns from pre-mRNA to generate mature mRNA in eukaryotes, and accurate identification of splice sites is essential for understanding gene structure and regulation.
Conghao Hong, Wenzhen Cheng, Zhengyi Li, Jiajie Deng, Yiqiong Li, Youyi Zang, Hongbo Gao   +6 more
doaj   +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

Comprehensive profiling of cancer neoantigens from aberrant RNA splicing

Journal for ImmunoTherapy of Cancer
Background Cancer neoantigens arise from protein-altering somatic mutations in tumor and rank among the most promising next-generation immuno-oncology agents when used in combination with immune checkpoint inhibitors.
Yi Lin, Yan W Asmann, Barath Shreeder, Keith L Knutson, Erik Jessen, Daniel P Wickland, Colton McNinch, Brian Necela   +7 more
doaj   +1 more source

Targeting Dnmt3a/m5C/RelA Axis Attenuates Microglia Inflammatory Response and Improves Postoperative Recovery in Chronic Compressive Cervical Spinal Cord Injury

Advanced Science, EarlyView.
A pro‐inflammatory microglial subset persists after decompression in chronic compressive cervical spinal cord injury and shows enhanced Dnmt3a‐driven m5C signaling. By stabilizing RelA mRNA, this axis sustains NF‐κB activation and postoperative neuroinflammation.
Tianyu Qin, Yuan Jiang, Yongheng Xie, Huanwei Qu, Wenbin Yan, Jingle Chen, Yining Chen, Huayi Li, Naibo Feng, Jiajun Wu, Chao Zhang, Zhengqi Huang, Ming Shi, Zhihuai Deng, Guozhi Xiao, Houqing Long   +15 more
wiley   +1 more source

PRMT9 Aggravated Dopaminergic Neurodegeneration in Parkinson's Disease Model by Facilitating the Degradation of DUSP26 and Inducing Mitochondrial Dysfunction

Advanced Science, EarlyView.
In the pathological state of PD induced by MPP+, the upregulated PRMT9 in dopaminergic neurons translocates into mitochondrion and interacts with DUSP26 and catalyzes its arginine methylation, leading to the ubiquitin‐proteasomal degradation of DUSP26 mediated by Trim32.
Tengfei Liu, Xiaomeng Song, Xin Guo, Rui Xiao, Ru Sun, Qiuran Ji, Lu Yu, Yiquan Li, Qingyi Fu, Qidi Xue, Lingjun Kong, Lin Chen, Chengjiang Gao, Huiqing Liu   +13 more
wiley   +1 more source

The unusual gene architecture of polyubiquitin is created by dual-specific splice sites

Genome Biology
Background The removal of introns occurs through the splicing of a 5′ splice site (5′ss) with a 3′ splice site (3′ss). These two elements are recognized by distinct components of the spliceosome. However, introns in higher eukaryotes contain many matches
Chaorui Duan, Truman Mooney, Luke Buerer, Cory Bowers, Stephen Rong, Seong Won Kim, Alger M. Fredericks, Sean F. Monaghan, William G. Fairbrother   +8 more
doaj   +1 more source

Intrinsically Mitochondria‐Targeting Nanozyme via Coordination‐Assembly of Natural Quercetin for Cascade Antioxidant Therapy of Cerebral Ischemia‐Reperfusion Injury

Advanced Science, EarlyView.
This study uncovers that quercetin naturally targets mitochondria. By coordinating quercetin with Fe3+, we engineer an ultrasmall cascade nanozyme (MCN) with superoxide dismutase‐catalase activities. MCN crosses the damaged blood–brain barrier, scavenges mitochondrial ROS, prevents mitochondrial DNA leakage, and blocks the cGAS‐STING pathway, thereby ...
Wenxuan Zheng, Zhicheng Wang, Xin Zhou, Shuya Wang, Xiaojing Shi, Tingli Xiong, Ruishi Li, Yuting Lin, Zhen Chen, Jiawen Wei, Fei Li, Jinwen Ge, Kelong Ai, Chong Liu, Guiming Deng   +14 more
wiley   +1 more source