Modelling Cell Origami via a Tensegrity Model of the Cytoskeleton in Adherent Cells by Lili Wang, Weiyi Chen

“…Adherent cell models contain a cytoskeleton (CSK), which is primarily composed of microtubules (MTs), microfilaments (MFs), intermediate filaments (IFs), and a nucleoskeleton (NSK), which is mainly made up of the nuclear lamina and chromatin. The microplate is assumed to be an isotropic linear-elastic solid material with a flexible joint that is connected to the cell tensegrity structure model by spring elements representing focal adhesion complexes (FACs). …”
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The Role of Plant DNA Methylation in Development, Stress Response, and Crop Breeding by Shuai Qiao, Wei Song, Wentao Hu, Fang Wang, Anzhong Liao, Wenfang Tan, Songtao Yang

“…We explore how these elements function within the broader epigenetic framework, focusing on their contributions to silencing transposable elements, modulating gene expression, and shaping chromatin architecture. The review also examines the significance of DNA methylation in plant development, particularly its role in adapting to biotic and abiotic stresses. …”
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Regulation of histone H4 acetylation in the CNS and defensive behavior command neurons of the mollusk Helix mediated by serotonin and neuropeptide FMRFamide by L. N. Grinkevich, T. G. Zachepilo

“…Presently, scientists’ attention is focused on changes in the levels of histone modifications (mainly acetylation and methylation) in the chromatin of CNS cells tested in various experimental models. …”
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Maternal asthma imprints fetal lung ILC2s via glucocorticoid signaling leading to worsened allergic airway inflammation in murine adult offspring by Tomoaki Takao, Ako Matsui, Chie Kikutake, Keiko Kan-o, Azusa Inoue, Mikita Suyama, Isamu Okamoto, Minako Ito

“…Furthermore, these offspring carry overlapping chromatin-accessible altered regions, including glucocorticoid receptor-binding regions in their lung ILC2s both at the fetal stage and adulthood, suggesting persistent prenatal epigenetic changes. …”
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System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach by Jihua Ran, Hui Li, Huiwu Li

“…The biology themes of clusters 1, 2, and 3 are chromatin modification, regulation of gene expression by transcription factor complex, and control of cell cycle, respectively. …”
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Integrated Bioinformatics and Experimental Approaches Identified the Role of NPPA in the Proliferation and the Malignant Behavior of Breast Cancer by Aijun Sun, Xiaonan Sheng, Jinhai Tang, Zhenfeng Yu, Jian Zhang

“…And we further validated the binding of MZF1 to the -318 bp~-452 bp region of the NPPA promoter with chromatin immunoprecipitation and dual luciferase assay. …”
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Impact of frequent ARID1A mutations on protein stability provides insights into cancer pathogenesis by Rajen K. Goutam, Gangtong Huang, Exequiel Medina, Feng Ding, William J. Edenfield, Hugo Sanabria

“…Abstract The ARID1A gene, frequently mutated in cancer, encodes the AT-rich interactive domain-containing protein 1 A, a key component of the chromatin remodeling SWI/SNF complex. The ARID1A protein features a conserved DNA-binding domain (ARID domain) of approximately 100 residues crucial for its function. …”
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FGFRL1 Promotes Ovarian Cancer Progression by Crosstalk with Hedgehog Signaling by Haiyan Tai, Zhiyong Wu, Su’an Sun, Zhigang Zhang, Congjian Xu

“…Loss of function of FGFRL1 significantly influenced cell proliferation, apoptosis, and migration of OC cells in vitro and tumor growth in vivo. Chromatin immunoprecipitation PCR analysis and microarray hybridization were performed to uncover the mechanism. …”
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Replication timing in Drosophila and its peculiarities in polytene chromosomes by T. D. Kolesnikova, O. V. Antonenko, I. V. Makunin

“…High-throughput methods allowed analysis of DNA replication on a genome scale, as well as its correlation with chromatin structure and gene activi ty. Precise mapping of the cytological structures of polytene chromosomes to the genome assembly allowed comparison of replication between polytene chromosomes and chromosomes of diploid cells. …”
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Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry by Lydia Freddolino, Jamie Yang, Amir Momen-Roknabadi, Saeed Tavazoie

“…Stochastic tuning operates locally at individual gene promoters, and its efficacy is modulated by perturbations to chromatin modification machinery.…”
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Deep Learning-Based Robust Automated System for Predicting Human Sperm DNA Fragmentation Index by Roopini Sathiasai Kumar, Swapnil Sharma, Arunima Halder, Vipin Gupta

“…Background: Determining the DNA fragmentation index (DFI) by the sperm chromatin dispersion (SCD) test involves manual counting of stained sperms with halo and no halo. …”
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Structure and evolution of metapolycentromeres by E. O. Grishko, P. M. Borodin

“…Metapolycentromeres consist of multiple sequential domains of centromeric chromatin associated with a centromere-specific variant of histone H3 (CENP-A), functioning collectively as a single centromere. …”
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Identification of CHD1L as an Important Regulator for Spermatogonial Stem Cell Survival and Self-Renewal by Shan-Shan Liu, Yin-Shan Bai, Li Feng, Wen-Wei Dong, Yang Li, Li-Ping Xu, Ning-Fang Ma

“…Chromodomain helicase/ATPase DNA binding protein 1-like gene (Chd1l) participates in chromatin-dependent processes, including transcriptional activation and DNA repair. …”
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Genomic landscape and comparative analysis of tissue and liquid-based NGS in Taiwanese anaplastic thyroid carcinoma by Chun-Nan Yeh, Shu-Fu Lin, Chia-Ling Wu, Miaw-Jene Liou, I-Wen Chen, Chiao-Ping Chen, Ching-Fu Chang, Qi‑An Wang, Chiao-En Wu

“…Genetic alterations showed highly heterogeneity, including mutations in RAS/RAF/MEK/ERK, PI3K/AKT/mTOR, cell cycle regulation, other receptor tyrosine kinases, DNA damage response, mismatch repair, and chromatin remodeling. TP53 (65.4%) and BRAF (30.8%) were the most frequently mutated genes in tissue NGS. …”
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Identifying RBBP7 as a Promising Diagnostic Biomarker for BK Virus-Associated Nephropathy by Yicun Wang, Yuxuan Wang, Di Zhang, Hao Zhang, Wei Wang, Xiaopeng Hu

“…RBBP7 (retinoblastoma binding protein 7) serves as component of serval complexes that regulate chromatin metabolism and functions in affecting DNA replication and controlling cell proliferation. …”
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Berberine decorated zinc oxide loaded chitosan nanoparticles a potent anti cancer agent against breast cancer by Fatemeh Esnaashari, Hojjatolah Zamani, Hossein Zahmatkesh, Mojtaba Soleimani, Golnesa Amirian Dashtaki, Behnam Rasti

“…Apoptosis induction in NP-treated cells was confirmed by Annexin V/PI staining, accompanied by the observation of condensed chromatin and fragmented DNA. Moreover, the pro-apoptotic potential of NPs was evidenced by significant increases in caspases-8 and 9 activity and a decreased Bcl-2/Bax ratio. …”
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Computational problems of analysis of short next generation sequencing reads by R. te Boekhorst, F. M. Naumenko, N. G. Orlova, E. R. Galieva, A. M. Spitsina, I. V. Chadaeva, Y. L. Orlov, I. I. Abnizova

“…Short read next generation sequencing (NGS) has significant impacts on modern genomics, genetics, cell biology and medicine, especially on meta-genomics, comparative genomics, polymorphism detection, mutation screening, transcriptome profiling, methylation profiling, chromatin remodelling and many more applications. However, NGS are prone for errors which complicate scientific conclusions. …”
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Brd7 loss reawakens dormant metastasis initiating cells in lung by forging an immunosuppressive niche by Jayanta Mondal, Junfeng Zhang, Feng Qing, Shunping Li, Dhiraj Kumar, Jason T. Huse, Filippo G. Giancotti

“…Using an in vivo screen, we demonstrate that several subunits of the polybromo-associated BAF (PBAF) chromatin remodeling complex, particularly Brd7, are required for maintaining breast cancer metastatic dormancy in the lungs of female mice. …”
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Regulatory Role of the RUNX2 Transcription Factor in Lung Cancer Apoptosis by Camila Bernal, Andrea Otalora, Alejandra Cañas, Alfonso Barreto, Karol Prieto, Martin Montecino, Adriana Rojas

“…Furthermore, to confirm whether the regulatory role of RUNX2 in the expression of these genes is related to its binding to the promoter region, we performed chromatin immunoprecipitation (ChIP) assays. Here, we report that overexpression of the RUNX2 gene in lung cancer may be related to the inhibition of the intrinsic apoptosis pathway, specifically, through direct transcriptional regulation of the antiapoptotic gene BCL2 and indirect regulation of BCL-XL and MCL1.…”
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Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding by Duyen Huynh, Philipp Hoffmeister, Tobias Friedrich, Kefan Zhang, Marek Bartkuhn, Francesca Ferrante, Benedetto Daniele Giaimo, Rhett A. Kovall, Tilman Borggrefe, Franz Oswald, J. Christof M. Gebhardt

“…We determine the binding kinetics, transcriptional activity, and genome-wide chromatin occupation of RBPJ and mutant variants by live-cell single-molecule tracking, reporter assays, and ChIP-Seq. …”
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