Results 111 to 120 of about 47,990 (270)

HiCeekR: A Novel Shiny App for Hi-C Data Analysis

Frontiers in Genetics, 2019
The High-throughput Chromosome Conformation Capture (Hi-C) technique combines the power of the Next Generation Sequencing technologies with chromosome conformation capture approach to study the 3D chromatin organization at the genome-wide scale. Although
Lucio Di Filippo, Dario Righelli, Miriam Gagliardi, Miriam Gagliardi, Maria Rosaria Matarazzo, Claudia Angelini   +5 more
doaj   +1 more source

Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix

, 2017
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other
A Laio, A Rich, AV Vologodskii, AV Vologodskii, AV Vologodskii, C Matek, CJ Benham, FC Oberstrass, H Meng, J SantaLucia, JA Gebe, JF Marko, JF Marko, JW Alexander, K Klenin, K Klenin, M Manghi, M Newman, M Thanbichler, MC Lagomarsino, MY Sheinin, N Blot, N Metropolis, P Carrivain, PG Wu, R Vlijm, SM Mirkin, T Lepage, T Strick, TR Strick, VV Rybenkov, Z Bryant, Z Liu   +32 more
core   +1 more source

eQTL Meta‐Analysis Reveals Conserved and Population‐Specific Regulatory Variation Underlying Nutritional Trait Evolution and Domestication in Tomato

Advanced Science, EarlyView.
A comprehensive meta‐analysis of expression quantitative trait loci (eQTLs) across five diverse tomato populations reveals a high‐resolution atlas of transcriptional regulation and uncovers conserved and population‐specific regulatory architectures underlying fruit nutritional quality traits, including flavonoids, sugars, organic acids, carotenoids ...
Jiantao Zhao, Xin Wang, Jing Zhang, Ryan McQuinn, Je Min Lee, Itay Gonda, Ari Feder, Yimin Xu, Baike Wang, Qinghui Yu, Denise M. Tieman, Sanwen Huang, Harry Klee, James J. Giovannoni, Zhangjun Fei   +14 more
wiley   +1 more source

A rapid simple approach to quantify chromosome conformation capture

Nucleic Acids Research, 2009
Chromosome conformation capture (3C) is a powerful tool to study DNA looping. The procedure generates chimeric DNA templates after ligation of restriction enzyme fragments juxtaposed in vivo by looping. These unique ligation products (ULPs) are typically quantified by gel-based methods, which are practically inefficient.
Abou El Hassan, M., Bremner, R.
openaire   +2 more sources

Tumor‐Derived Alpha‐1 Antitrypsin Promotes Liver Metastasis of Colorectal Cancer Through the Neutrophil Extracellular Traps–CCDC25 Pathway

Advanced Science, EarlyView.
ABSTRACT Liver metastasis is a leading cause of mortality in colorectal cancer (CRC), where the inflammatory tumor microenvironment, specifically neutrophil infiltration, significantly promotes metastatic colonization. This study reveals a pro‐metastatic role for alpha‐1 antitrypsin (A1AT) in CRC liver metastasis via a dual mechanism involving ...
Qian Fei, Chunning Li, Lei Zhan, Xiaoyan Li, Yan Hui, Yue Jin, Jing Zhang, Lu Yang, Xin Sun, Xiaoxi Li, Qian Dong, Jingdong Zhang   +11 more
wiley   +1 more source

Large-scale 3D chromatin reconstruction from chromosomal contacts

BMC Genomics, 2019
Background Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible interactions between these loci ...
Yanlin Zhang, Weiwei Liu, Yu Lin, Yen Kaow Ng, Shuaicheng Li   +4 more
doaj   +1 more source

T Cell Exhaustion in Cancer Immunotherapy: Heterogeneity, Mechanisms, and Therapeutic Opportunities

Advanced Science, EarlyView.
T cell exhaustion limits immunotherapy efficacy. This article delineates its progression from stem‐like to terminally exhausted states, governed by persistent antigen, transcription factors, epigenetics, and metabolism. It maps the exhaustion landscape in the TME and proposes integrated reversal strategies, providing a translational roadmap to overcome
Yang Yu, Xiaoyu Yao, Qingyang Wang, Mengrui Yang, Runze Li, Jiangjiang Qin, Jing Zhuang, Changgang Sun   +7 more
wiley   +1 more source

3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations

Nature Communications, 2017
Chromosome conformation capture techniques enable the study of genome organization in cancer cells. Here, the authors use Hi-C, WGS, and RNA-seq to study the 3D genome of multiple myeloma and find that genome disorganization is associated with copy ...
Pengze Wu, Tingting Li, Ruifeng Li, Lumeng Jia, Ping Zhu, Yifang Liu, Qing Chen, Daiwei Tang, Yuezhou Yu, Cheng Li   +9 more
doaj   +1 more source

The Rabl configuration limits topological entanglement of chromosomes in budding yeast. [PDF]

, 2019
The three dimensional organization of genomes remains mostly unknown due to their high degree of condensation. Biophysical studies predict that condensation promotes the topological entanglement of chromatin fibers and the inhibition of function.
Arsuaga, Javier, Burgess, Sean, Cruz, Brian, Pouokam, Maxime, Segal, Mark R, Vazquez, Mariel   +5 more
core  

FASLG Derived from Fibroblasts in Hydroxyapatite‐Rich Microenvironment Induces Urothelial Anoikis to Trigger Randall's Plaque Exposure

Advanced Science, EarlyView.
Randall's plaques (RP) serve as the nidus for calcium oxalate (CaOx) kidney stones. The current study reveals that hydroxyapatite (HAP) crystals activate the THY1–GSK3α/β–β‐catenin axis in renal interstitial fibroblasts (hRIFs), inducing FASLG secretion.
Minghui Liu, Maolan Wu, Meng Gao, Yongchao Li, Miao Yuan, Zhangcheng Liao, Zhi Liu, Yizhou Wang, Yu Cui, Jinbo Chen, Cheng He, Zhiyong Chen, Feng Zeng, Hequn Chen, Zewu Zhu   +14 more
wiley   +1 more source