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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Role of CTCF protein in regulating FMR1 locus transcription. by Stella Lanni, Martina Goracci, Loredana Borrelli, Giorgia Mancano, Pietro Chiurazzi, Umberto Moscato, Fabrizio Ferrè, Manuela Helmer-Citterich, Elisabetta Tabolacci, Giovanni Neri

“…We conclude that CTCF has a complex role in regulating FMR1 expression, probably through the organization of chromatin loops between sense/antisense transcriptional regulatory regions, as suggested by bioinformatics analysis.…”
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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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Construction of a 12-gene prognostic model for colorectal cancer based on heat shock protein-related genes by Qin Tong, Junchao Zhou

“…The efficacy and precision of this model were validated utilizing TCGA and Gene Expression Omnibus (GEO) datasets, demonstrating its reliability in CRC prognosis prediction. gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed significant disparities between high- and low-risk groups in chromatin remodeling biological functions and neutrophil extracellular trap formation pathways. …”
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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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Epigenetic regulation of the nuclear genome associated with mitochondrial dysfunction in Leber’s hereditary optic neuropathy (LHON) by Aswathy P. Nair, Ambika Selvakumar, Janani Gopalarethinam, B. Abishek Kumar, Balachandar Vellingiri, Mohana Devi Subramaniam

“…We isolated peripheral blood mononuclear cells (PBMCs) from LHON patients and healthy individuals and examined epigenetic modifications in ND4 mutant cells and control cells. Chromatin immunoprecipitation-qRT PCR (ChIP-qRT PCR) assays were performed to investigate the modifications of histones. …”
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12,13-diHOME Promotes Inflammatory Macrophages and Epigenetically Modifies Their Capacity to Respond to Microbes and Allergens by Din L. Lin, Kevin M. Magnaye, Cara E. Porsche, Sophia R. Levan, Elze Rackaityte, Mustafa Özçam, Susan V. Lynch

“…Exposure to 12,13-diHOME also induces macrophage chromatin remodeling, specifically diminishing access to interferon-stimulated response elements resulting in reduced interferon-regulated gene expression upon bacterial lipopolysaccharide stimulation. …”
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ENL mutation and AML: a new model that reveals oncogenic condensate's function in leukemogenesis by Zhong Fan, Yanan Jiang, Xiaotian Zhang

“…This mutant ENL forms condensates in hematopoietic stem/progenitor cells at the genomic loci of key leukemogenic genes, including Meis1 and Hoxa cluster genes, and disrupting condensate formation via mutagenesis impairs its chromatin and oncogenic function. Furthermore, they show that small‐molecule inhibition of the acetyl‐binding activity displaces ENL mutant condensates from oncogenic target loci, and this inhibitor significantly impairs the onset and progression of AML driven by mutant ENL in vivo.…”
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Clinical Factors Associated with Sperm DNA Fragmentation in Male Patients with Infertility by Akira Komiya, Tomonori Kato, Yoko Kawauchi, Akihiko Watanabe, Hideki Fuse

“…The SDF was evaluated using the sperm chromatin dispersion test (SCDt) to determine the SDF index (SDFI). …”
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Targeting the epigenome with advanced delivery strategies for epigenetic modulators by Sonia Guha, Yogeswaran Jagadeesan, Murali Monohar Pandey, Anupama Mittal, Deepak Chitkara

“…Abstract Epigenetics mechanisms play a significant role in human diseases by altering DNA methylation status, chromatin structure, and/or modifying histone proteins. …”
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