Results 71 to 80 of about 186,580 (246)

Epigenetic heterogeneity and plasticity in therapy‐induced tumor states through single‐cell multi‐omics

Molecular Oncology, EarlyView.
Single‐cell multi‐omics reveals epigenetic heterogeneity across therapy‐adaptive tumor states, including quiescent/dormant, drug‐tolerant persister, and EMT‐like phenotypes. By linking regulatory features with state‐associated biomarkers, these approaches inform biomarker‐guided therapeutic strategies for evolving tumors.
Hee Jung Kim, Hwiyeong Lee, Jin Hong, Daechan Park   +3 more
wiley   +1 more source

ATAC-seq with unique molecular identifiers improves quantification and footprinting [PDF]

Communications Biology, 2020
Abstract ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints.
Tao Zhu, Keyan Liao, Rongfang Zhou, Chunjiao Xia, Weibo Xie   +4 more
openaire   +2 more sources

ATACAmp: a tool for detecting ecDNA/HSRs from bulk and single-cell ATAC-seq data

BMC Genomics, 2023
Background High oncogene expression in cancer cells is a major cause of rapid tumor progression and drug resistance. Recent cancer genome research has shown that oncogenes as well as regulatory elements can be amplified in the form of extrachromosomal ...
Hansen Cheng, Wenhao Ma, Kun Wang, Han Chu, Guangchao Bao, Yu Liao, Yawen Yuan, Yixiong Gou, Liting Dong, Jian Yang, Haoyang Cai   +10 more
doaj   +1 more source

Paternal Circadian Disruption Impairs Offspring Cognition via Sperm microRNAs

Advanced Science, EarlyView.
Paternal circadian disruption remodels the sperm small RNA payload, elevating miR‐92a‐3p/miR‐25‐3p levels and perturbing early embryonic gene regulatory programs. Microinjection experiments and single‐embryo transcriptomics reveal sex‐specific developmental vulnerabilities, ultimately impairing offspring hippocampal synaptic plasticity and cognition ...
Kexin Zou, Sisi Luo, Binliang Tang, Zhiqiang Liu, Yuchuan Zhou, Yicong Meng, Zhengmu Wu, Zheng Sun, Weihui Shi, Jianzhong Sheng, Chuanjin Yu, Zhenhua Li, Siyi Wei, Mo Zhang, Yujie Luo, Jing Yan, Xueyun Qin, Jiahang Mo, Chengliang Zhou, Jinsong Li, Hefeng Huang, Yifu Ding, Guolian Ding   +22 more
wiley   +1 more source

Assessment of computational methods for the analysis of single-cell ATAC-seq data

Genome Biology, 2019
Recent innovations in single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands of individual cells.
Huidong Chen, C. Lareau, Tommaso Andreani, Michael E. Vinyard, Sara P. Garcia, Kendell Clement, Miguel Andrade, Jason D. Buenrostro, Luca Pinello   +8 more
semanticscholar   +1 more source

Harnessing changes in open chromatin determined by ATAC-seq to generate insulin-responsive reporter constructs

BMC Genomics, 2022
Background Gene regulation is critical for proper cellular function. Next-generation sequencing technology has revealed the presence of regulatory networks that regulate gene expression and essential cellular functions.
Collin B. Merrill, Austin B. Montgomery, Miguel A. Pabon, Andrey A. Shabalin, Aylin R. Rodan, Adrian Rothenfluh   +5 more
doaj   +1 more source

Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue

STAR Protocols, 2023
Summary: The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function.
Noga Korenfeld, Nicolaj I. Toft, Trine V. Dam, Meital Charni-Natan, Lars Grøntved, Ido Goldstein   +5 more
doaj   +1 more source

Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data

Oncogenesis, 2023
In cancer, extrachromosomal circular DNA (ecDNA), or megabase-pair amplified circular DNA, plays an essential role in intercellular heterogeneity and tumor cell revolution because of its non-Mendelian inheritance.
Manqiu Yang, Shufan Zhang, Rong Jiang, Shaomu Chen, Moli Huang   +4 more
semanticscholar   +1 more source

Self‐Assembling Hybrid Hydrogel Reprograms the Stromal Vascular Fraction to Treat Osteoarthritis

Advanced Science, EarlyView.
This study presents a bioinspired injectable hydrogel that enhances the therapeutic potential of stem cell‐rich stromal vascular fraction for treating osteoarthritis. By reprogramming cell behavior through epigenetic modulation, the hydrogel promotes cartilage regeneration and reduces joint damage in a rat model, offering a promising new approach for ...
Waifang Hou, Yongfeng Chen, Longyou Xiao, Wei Qi, Tianshu Du, Qiang Sun, Borui Xue, Qinghe Zhao, Pengfei Xie, Zi Ye, Fei Han, Lingli Guo, Yang Jiao, Ranran Zhang, Hong Jia, Xiao Huang, Jianwei Guo, Peng Wang, Huayi Wang, Yuanrui Wang, Wenjing Chen, Haining Wu, Liumin He, Dawei Zhang   +23 more
wiley   +1 more source

Activation of ERBB4 Pathway Inhibits Pathological Transdifferentiation of Lung Epithelial Progenitors into CD66c+ Basal Cells in Severe Lung Injury

Advanced Science, EarlyView.
In fibrotic distal lung regions, CD66c+ basal cells emerge as a pathological state. Using human distal lung organoids, this study identifies CD66c+ basal cells as a pro‐fibrotic state arising through transdifferentiation from secretory, AT2, and basal cells.
Kaijun Lin, Xinran Deng, Haonan Wang, Yamei Jiang, Jian Sun, Hailin Ding, Ming Ye, Xiaoting Wang, Yu Wang, Li Yuan, Zhenju Song, Xinhua Lin, Shenfei Sun, Ning Jiang   +13 more
wiley   +1 more source