Results 101 to 110 of about 186,580 (246)

TAMC: A deep-learning approach to predict motif-centric transcriptional factor binding activity based on ATAC-seq profile.

PLoS Computational Biology, 2022
Determining transcriptional factor binding sites (TFBSs) is critical for understanding the molecular mechanisms regulating gene expression in different biological conditions.
Tianqi Yang, Ricardo Henao
doaj   +1 more source

Introgressed Variation in TaMYB7‐A1 Drives Graded Dormancy and Climate‐Adaptive Pre‐Harvest Sprouting Resistance in Wheat

Advanced Science, EarlyView.
TaMYB7‐A1 directly activates TaABI5 to enhance ABA signaling and regulate ABA‐GA homeostasis, enforcing seed dormancy. Its superior allele, derived from wild einkorn introgression, harbors a MITE insertion that elevates expression and two amino acid substitutions that enhance transcriptional activity, collectively generating graded PHS resistance for ...
Hao Wang, Dongzhi Wang, Yafei Guo, Qi Zheng, Min Zhang, James Simmonds, Jian Hou, Xuemei Liu, Xuelei Lin, Xiaomin Bie, Xiansheng Zhang, Xiaohui Li, Yuan Chen, Xueyong Zhang, Cristobal Uauy, Fei Lu, Chengcai Chu, Zhixi Tian, Jun Xiao   +18 more
wiley   +1 more source

ACLY‐Driven Metabolic Reprogramming Promotes Histone Acetylation and Inflammation‐Associated Fibrosis in Chronic Kidney Disease

Advanced Science, EarlyView.
This study reveals a citrate–ACLY–H3K27ac metabolic–epigenetic axis driving inflammatory gene activation and kidney fibrosis, highlighting ACLY inhibition as a potential therapeutic strategy for chronic kidney disease (CKD). ABSTRACT The mechanisms by which metabolic stress drives epigenetic dysregulation and fibrosis in chronic kidney disease (CKD ...
Chunxiu Du, Dhanunjay Mukhi, Lingzhi Li, Chenyu Li, Siyu Pan, Bernhard Dumoulin, Eunji Ha, Lakshmi P Kolligundla, Yanjuan Hou, Jonathan Levinsohn, Chaelin Kang, Konstantin Adrian Klötzer, Junnan Wu, Samer Mohandes, Kathryn E Wellen, Katalin Susztak   +15 more
wiley   +1 more source

A simple ATAC-seq protocol for population epigenetics

Wellcome Open Research, 2020
We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions.
Ronaldo de Carvalho Augusto, Aki Minoda, Christoph Grunau   +2 more
openaire   +1 more source

Integrated ATAC‐seq and RNA‐seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa

Molecular plant pathology
Animal studies have shown that virus infection causes changes in host chromatin accessibility, but little is known about changes in chromatin accessibility of plants infected by viruses and its potential impact.
Miaomiao Li, Jing Li, Yan Zhang, Yushan Zhai, Yi Chen, Lin Lin, Jiejun Peng, Hongying Zheng, Jianping Chen, Fei Yan, Yuwen Lu   +10 more
semanticscholar   +1 more source

A Viscous DES‐AAV‐Foxo1 Delivery System With High Transfection Efficiency for the Treatment of Corneal Endothelial Dysfunction by Restoring Mitochondria‐ER Contacts

Advanced Science, EarlyView.
High glucose triggers corneal endothelial dysfunction by impairing FOXO1‐mediated ITPR1 transcription, leading to disrupted mitochondria‐associated membrane (MAM) integrity and defective ER‐to‐mitochondria Ca2+ transfer. This study develops an innovative viscous DES‐AAV‐Foxo1 delivery system with enhanced transfection efficiency. This non‐invasive gene
Hongran Zhao, Xiaoyu Li, Hongwei Wang, Zongyi Li, Qun Wang, Yangyang Zhang, Xu Jing, Xia Qi, Qingjun Zhou, Shengqian Dou, Lixin Xie   +10 more
wiley   +1 more source

High-Resolution ATAC-Seq Analysis of Frozen Clinical Tissues

, 2022
The ATAC-seq method enables the genome-wide analysis of accessible chromatin revealing transcriptionally active and poised regulatory elements. The ATAC-seq analysis of clinical specimens at a single-cell resolution reveals the cellular composition of the tissue contributing to the understanding of intra-tissue heterogeneity.
Cejas, Paloma, Long, Henry W
openaire   +3 more sources

quaqc: efficient and quick ATAC-seq quality control and filtering. [PDF]

Bioinformatics
Abstract Summary “quaqc” allows for ATAC-seq-specific quality control and read filtering of NGS data with minimal processing time and extremely low memory overhead. An efficient scaling implementation allows for a wide range of use cases, from processing individual samples processed on personal ...
Tremblay BJM, Qüesta JI.
europepmc   +5 more sources

Integrated Single‐Cell RNA‐seq and ATAC‐seq Reveals Heterogeneous Differentiation of CD4+ Naive T Cell Subsets is Associated with Response to Antidepressant Treatment in Major Depressive Disorder

Advancement of science
The mechanism involved in major depressive disorder (MDD) is well‐studied but the mechanistic origin of the heterogeneous antidepressant effect remains largely unknown. Single‐cell RNA‐sequencing (scRNA‐seq) and assay for transposase‐accessible chromatin
Zuoli Sun, Bowen Zhang, Jingjing Zhou, Yanting Luo, Xuequan Zhu, Yaping Wang, Yi He, Peng Zheng, Ling Zhang, Jian Yang, Gang Wang   +10 more
semanticscholar   +1 more source

SpaMode: A Broadly Applicable Framework for Deciphering Spatial Multi‐Omics Using Multimodal Mixture of Disentangled Experts

Advanced Science, EarlyView.
SpaMode introduces a versatile framework for spatial multi‐omics integration across vertical, horizontal, and mosaic scenarios. By disentangling modality‐invariant and variant features through a mixture‐of‐experts mechanism, it adaptively reconfigures spatially heterogeneous signals.
Xubin Zheng, Xinlei Huang, Xiang Zhou, Dian Meng, Ziyue Qiao, Zhiyuan Yuan, Lixin Cheng   +6 more
wiley   +1 more source