Results 31 to 40 of about 69,491 (204)

Accurate prediction of inducible transcription factor binding intensities in vivo. [PDF]

PLoS Genetics, 2012
DNA sequence and local chromatin landscape act jointly to determine transcription factor (TF) binding intensity profiles. To disentangle these influences, we developed an experimental approach, called protein/DNA binding followed by high-throughput ...
Michael J Guertin, André L Martins, Adam Siepel, John T Lis   +3 more
doaj   +1 more source

Databases and prospects of dynamic gene regulation in eukaryotes: A mini review

Computational and Structural Biotechnology Journal, 2023
In eukaryotes, dynamic regulation enables DNA polymerases to catalyze a variety of RNA products in spatial and temporal patterns. Dynamic gene expression is regulated by transcription factors (TFs) and epigenetics (DNA methylation and histone ...
Chi-Nga Chow, Chien-Wen Yang, Wen-Chi Chang   +2 more
doaj   +1 more source

EDNRB‐dependent endothelin signaling reduces proliferation and promotes proneural‐to‐mesenchymal transition in gliomas

Molecular Oncology, EarlyView.
Glioma cells mainly express the endothelin receptor EDNRB, while EDNRA is restricted to a perivascular tumor subpopulation. Endothelin signaling reduces glioma cell proliferation while promoting migration and a proneural‐to‐mesenchymal transition associated with poor prognosis. This pathway activates Ca2+, K+, ERK, and STAT3 signalings and is regulated
Donovan Pineau, Leonor Garcia, Hugo Arnold, Antonija Hanžek, Maialen Arrieta, Laurent R Gauthier, Christine Granotier‐Beckers, François D Boussin, Amaury Herbet, Marie Hautière, Valentin Asei‐Ceschino, Clémentin Jacques, Laura Brard, Thomas Harnois, Valérie Coronas, Bruno Constantin, Aurélien Chatelier, Jean Chemin, Serge Urbach, Martial Seveno, Szimonetta Hideg, Chantal Ripoll, Kasandra Aguilar‐Cázarez, Min Zheng, Guo‐Hao Huang, Sheng‐Qing Lv, Lei Zhang, Philippe Rondard, Laurent Prezeau, Jean‐Philippe Pin, Hugues Duffau, Luc Bauchet, Valérie Rigau, Franck Denat, Charles Truillet, Didier Boquet, Jean‐Philippe Hugnot   +36 more
wiley   +1 more source

Exploring the relationship between intron retention and chromatin accessibility in plants

BMC Genomics, 2018
Background Intron retention (IR) is the most prevalent form of alternative splicing in plants. IR, like other forms of alternative splicing, has an important role in increasing gene product diversity and regulating transcript functionality.
Fahad Ullah, Michael Hamilton, Anireddy S.N. Reddy, Asa Ben-Hur   +3 more
doaj   +1 more source

CCDC80 suppresses high‐grade serous ovarian cancer migration via negative regulation of B7‐H3

Molecular Oncology, EarlyView.
PAX8 is a lineage‐specific master regulator of transcription in high‐grade serous ovarian cancer (HGSC) progression. We show for the first time that PAX8 facilitates proliferation and metastasis by repressing the cell autonomous tumor suppressor CCDC80 and inducing B7‐H3 expression.
Aya Saleh, Nitzan Medina‐Itzhaki, Milena Chekov, Eden Gal‐Swisa, Roba Gabesh‐Wahabi, Inbar Savyon, Inna Naroditsky, Hilary A. Kenny, Basem Fares, Lina Korsensky, Einav Girsh, Liron Berger, Ruth Perets   +12 more
wiley   +1 more source

Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness

Scientific Reports, 2017
Light, as the energy source in photosynthesis, is essential for plant growth and development. Extended darkness causes dramatic gene expression changes.
Yue Liu, Wenli Zhang, Kang Zhang, Qi You, Hengyu Yan, Yuannian Jiao, Jiming Jiang, Wenying Xu, Zhen Su   +8 more
doaj   +1 more source

CD47 promotes mitogen‐activated protein kinase and epithelial‐to‐mesenchymal transition molecular programs to drive prometastatic phenotypes in non‐small cell lung cancer

Molecular Oncology, EarlyView.
Beyond its role in immune evasion, this study identified that CD47 drives tumor‐intrinsic signaling in non‐small cell lung cancer (NSCLC). Transcriptomic profiling and functional studies revealed that CD47 regulates cell adhesion, migration, and metastasis through an ERK–EMT signaling axis.
Asa P.Y. Lau, Lilian G. Zhai, Ryunosuke Hoshi, Zackary Rousseau, Abraam Zakhary, Yin Fang Wu, Rola M. Saleeb, Heyu Ni, Kelsie L. Thu   +8 more
wiley   +1 more source

OCRFinder: a noise-tolerance machine learning method for accurately estimating open chromatin regions

Frontiers in Genetics, 2023
Open chromatin regions are the genomic regions associated with basic cellular physiological activities, while chromatin accessibility is reported to affect gene expressions and functions.
Jiayi Ren, Jiayi Ren, Yuqian Liu, Yuqian Liu, Xiaoyan Zhu, Xiaoyan Zhu, Xuwen Wang, Xuwen Wang, Yifei Li, Yifei Li, Yuxin Liu, Yuxin Liu, Wenqing Hu, Wenqing Hu, Xuanping Zhang, Xuanping Zhang, Jiayin Wang, Jiayin Wang   +17 more
doaj   +1 more source

Decellularized Extracellular Matrix (dECM) in Tendon Regeneration: A Comprehensive Review

Advanced Healthcare Materials, EarlyView.
Decellularized Extracellular Matrix (dECM) offers a promising solution by replicating the native tendon microenvironment and promoting regeneration. This review highlights advances in the decellularization methods, as well as their integration with emerging technologies and translational progress in tendon tissue engineering.
Kumaresan Sakthiabirami, Yeonwoo Park, Seong Kyeong Jo, Min Hee Kim, Jae Hwang Song   +4 more
wiley   +1 more source

Correcting nucleotide-specific biases in high-throughput sequencing data

BMC Bioinformatics, 2017
Background High-throughput sequence (HTS) data exhibit position-specific nucleotide biases that obscure the intended signal and reduce the effectiveness of these data for downstream analyses.
Jeremy R. Wang, Bryan Quach, Terrence S. Furey   +2 more
doaj   +1 more source