Chromatin remodeling (SWI/SNF) complexes, cancer, and response to immunotherapy by Razelle Kurzrock, Shumei Kato, Nithya Krishnamurthy, Scott Lippman

“…Chromatin regulation involves four subfamilies composed of ATP-dependent multifunctional protein complexes that remodel the way DNA is packaged. …”
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Mapping chromatin remodelling in glioblastoma identifies epigenetic regulation of key molecular pathways and novel druggable targets by Claire Vinel, James Boot, Weiwei Jin, Nicola Pomella, Alexandra Hadaway, Charles Mein, Nicolae Radu Zabet, Silvia Marino

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D-2-hydroxyglutarate impairs DNA repair through epigenetic reprogramming by Fengchao Lang, Karambir Kaur, Haiqing Fu, Javeria Zaheer, Diego Luis Ribeiro, Mirit I. Aladjem, Chunzhang Yang

“…Mechanistically, D-2-HG diminishes the chromatin interactions in the DNA damage regions via revoking CTCF binding. …”
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Deciphering the generation of heterogeneity in esophageal squamous cell carcinoma metastasis via single-cell multiomics analysis by Kaiwen Sheng, Jun Chen, Ruitang Xu, Haoqiang Sun, Ran Liu, Yongjie Wang, Wenwen Xu, Jiao Guo, Miao Zhang, Shuai Liu, Juan Lei, Yawen Sun, Yang Jia, Dianhao Guo

“…Abstract Background Chromatin accessibility plays a crucial role in mediating transcriptional dysregulation and heterogeneity in Esophageal Squamous Cell Carcinoma (ESCC). …”
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DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. by Chunhong Long, Hongqiong Liang, Biao Wan

“…This advancement in understanding the spontaneous formation of nucleosomes may offer insights into the complex dynamics of chromatin assembly and the fundamental mechanisms governing the structure and function of chromatin.…”
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Valproic acid targets IDH1 mutants through alteration of lipid metabolism by Lubayna S. Elahi, Michael C. Condro, Riki Kawaguchi, Yue Qin, Alvaro G. Alvarado, Brandon Gruender, Haocheng Qi, Tie Li, Albert Lai, Maria G. Castro, Pedro R. Lowenstein, Matthew C. Garrett, Harley I. Kornblum

“…Surprisingly, genes upregulated by VPA showed no enhanced chromatin accessibility at the promoter, but there was a correlation between VPA-downregulated genes and diminished promoter chromatin accessibility. …”
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A biallelically active embryonic enhancer dictates GNAS imprinting through allele-specific conformations by Yorihiro Iwasaki, Monica Reyes, Harald Jüppner, Murat Bastepe

“…Here, we show that the STX16-ICR forms different chromatin conformations with each GNAS parental allele and enhances two GNAS promoters in human embryonic stem cells. …”
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Anaerobic metabolism promotes breast cancer survival via Histone-3 Lysine-18 lactylation mediating PPARD axis by Ying Xu, Weiwei Meng, Yingqi Dai, Lin Xu, Ning Ding, Jinqing Zhang, Xuewei Zhuang

“…ATAC-seq analysis revealed that glycolysis in BC cells enhanced chromatin accessibility. Additionally, we confirmed that HDAC2 and HDAC3 act as “erasers” for H3 lysine lactylation. …”
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Tumor-initiating and metastasis-initiating cells of clear-cell renal cell carcinoma by Dinh-Xuan Pham, Tien Hsu

“…TICs likely originate from kidney tubule progenitor cells bearing VHL gene inactivation, including chromatin 3p loss. Recent studies also point to the importance of microenvironment reconstituted by the VHL-deficient kidney tubule cells in promoting ccRCC initiation and progression. …”
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Plasma membrane and nuclear phosphatidylinositol 4,5-bisphosphate signalling in cancer by Agnieszka Chytła, Stephanie Rattay, Baki Akgül, Martin Sztacho

“…Nuclear phosphoinositides, particularly PI(4,5)P2, are essential for regulating transcription factors and chromatin organisation, thereby shaping gene expression patterns. …”
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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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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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Replication-IDentifier links epigenetic and metabolic pathways to the replication stress response by Sophie C. van der Horst, Leonie Kollenstart, Amandine Batté, Sander Keizer, Kees Vreeken, Praveen Pandey, Andrei Chabes, Haico van Attikum

“…During Repli-ID, the replicative polymerase epsilon (Pol ε) is tracked at a barcoded origin of replication by chromatin immunoprecipitation (ChIP) coupled to next-generation sequencing of the barcode in thousands of hydroxyurea-treated yeast mutants. …”
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R-loops acted on by RNase H1 influence DNA replication timing and genome stability in Leishmania by Jeziel D. Damasceno, Emma M. Briggs, Marija Krasilnikova, Catarina A. Marques, Craig Lapsley, Richard McCulloch

“…Furthermore, we demonstrate that such differential organisation of R-loops, RNase H1 and DNA replication timing across the parasite’s chromosomes correlates with size-dependent differences in chromatin accessibility, G quadruplex distribution and sequence content. …”
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Novel histone deacetylase-5 inhibitor T2943 exerts an anti-depressive effect in mice by enhancing GRID1 expression by Juan Du, Ruyun Liu, Lin Ma, Yue Liu, Wei Wei, Ning Liu, Qiuhua Cao, Jianqiang Yu

“…This modification loosens the chromatin structure, allowing transcription factors to bind to the Grid1 promoter region and enhance its transcription and expression. …”
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Endometrial polyps with bizarre stromal cells: a Benign or a low-grade lesion? by Musen Wang, Fei Gao, Hongkai Zhang, Wenxin Zheng

“…Higher magnification revealed eosinophilic cytoplasm in the stromal cells, which exhibited both mono- and multinucleation, hyperchromasia with coarse chromatin, and an absence of conspicuous nucleoli and mitotic figures. …”
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Structural basis of SIRT7 nucleosome engagement and substrate specificity by Carlos Moreno-Yruela, Babatunde E. Ekundayo, Polina N. Foteva, Dongchun Ni, Esther Calvino-Sanles, Henning Stahlberg, Beat Fierz

“…Abstract Chromatin-modifying enzymes target distinct residues within histones to finetune gene expression profiles. …”
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LncRNA PVT1 links estrogen receptor alpha and the polycomb repressive complex 2 in suppression of pro-apoptotic genes in hormone-responsive breast cancer by Viola Melone, Domenico Palumbo, Luigi Palo, Noemi Brusco, Annamaria Salvati, Antonietta Tarallo, Giorgio Giurato, Francesca Rizzo, Giovanni Nassa, Alessandro Weisz, Roberta Tarallo

“…A set of lncRNAs was selected among ERα-associated RNAs in BC cell nuclei due to their roles in processes such as transcriptional regulation and epigenetic chromatin modifications. Native immunoprecipitation of nuclear ERα-interacting RNAs coupled to NGS (RIP-Seq) was performed in MCF-7 cells, leading to the identification of essential lncRNAs interacting with the receptor in multi-molecular regulatory complexes. …”
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Identification of selective SWI/SNF dependencies in enzalutamide-resistant prostate cancer by Bengul Gokbayrak, Umut Berkay Altintas, Shreyas Lingadahalli, Tunc Morova, Chia-Chi Flora Huang, Betul Ersoy Fazlioglu, Ivan Pak Lok Yu, Batuhan M. Kalkan, Paloma Cejas, Sonia H. Y. Kung, Ladan Fazli, Akane Kawamura, Henry W. Long, Ceyda Acilan, Tamer T. Onder, Tugba Bagci-Onder, James T. Lynch, Nathan A. Lack

“…From this, we identify and validate SMARCC2, a core component of the SWI/SNF complex, that is selectivity essential in enzalutamide-resistant models. We show that the chromatin occupancy of SMARCC2 and BRG1 is expanded in enzalutamide resistance at regions that overlap with CRPC-associated transcription factors that are accessible in CRPC clinical samples. …”
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Semen Parameters Can be Used as a Credible Marker with Doppler Ultrasonography in the Diagnosis of Subclinical Varicocele Cases by Tulay Irez, Bahar Sarikaya, Mine Erguven, Emre Salabas

“…Sperm mitochondria potential at the TG was lower than the CG (p<0.001, p<0.05). Sperm chromatin condensation at the TG was higher than the CG (p<0.001, p<0.05). …”
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