Editorial: Epigenetics and genomic causality in development and chromatin research by Ellen V. Rothenberg, Ute Deichmann

Subjects: “…chromatin modification and accessibility…”
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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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Transcriptome and chromatin accessibility landscape of ovarian development at different egg-laying stages in taihe black-bone silky fowls by Jingyi Zhang, Yong Cui, Jiming Ruan, Haiyan Zhu, Haiping Liang, Ji Cao, Qing Wei, Jianzhen Huang

“…This study aims to explore the ovarian development status, as well as the changes in the transcriptome and chromatin accessibility landscape at different egg-laying stages of SF, in order to reveal the epigenetic regulatory mechanisms underlying ovarian development in laying hens. …”
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Editorial: Current insights in Epigenetics and Epigenomics by Steven Henikoff, Steven Henikoff, Sharon Y. R. Dent, Sharon Y. R. Dent, Raul Mostoslavsky, Raul Mostoslavsky, Ting Wang, Luca Comai

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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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Hairy transcriptional repression targets and cofactor recruitment in Drosophila. by Daniella Bianchi-Frias, Amir Orian, Jeffrey J Delrow, Julio Vazquez, Alicia E Rosales-Nieves, Susan M Parkhurst

“…The majority of Hairy targets are associated with the presence of a combination of dCtBP and dSir2. Thus, the DamID chromatin profiling technique provides a systematic means of identifying transcriptional target genes and of obtaining a global view of cofactor recruitment requirements during development.…”
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Integration of unpaired single cell omics data by deep transfer graph convolutional network. by Yulong Kan, Yunjing Qi, Zhongxiao Zhang, Xikeng Liang, Weihao Wang, Shuilin Jin

“…The rapid advance of large-scale atlas-level single cell RNA sequences and single-cell chromatin accessibility data provide extraordinary avenues to broad and deep insight into complex biological mechanism. …”
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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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