Neurotoxic Effect of Myricitrin in Copper-Induced Oxidative Stress Is Mediated by Increased Intracellular Ca²⁺ Levels and ROS/p53/p38 Axis by Ignacija Vlašić, Antonio Krstačić-Galić, Anđela Horvat, Nada Oršolić, Anja Sadžak, Lucija Mandić, Suzana Šegota, Maja Jazvinšćak Jembrek

“…In combination with copper, myricitrin also activated caspase-3/7, promoted nuclear chromatin changes, and compromised membrane integrity. …”
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IL-7 promotes integrated glucose and amino acid sensing during homeostatic CD4+ T cell proliferation by Seema Bachoo, Nancy Gudgeon, Rebecca Mann, Victoria Stavrou, Emma L. Bishop, Audrey Kelly, Alejandro Huerta Uribe, Jordan Loeliger, Corina Frick, Oliver D.K. Maddocks, Paul Lavender, Christoph Hess, Sarah Dimeloe

“…In agreement, IL-7 promotes glucose-dependent histone acetylation and chromatin accessibility, notable at the loci of the amino acid-sensing Ragulator complex. …”
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Effects of L-carnitine and pentoxifylline on long-term preservation of the human sperms: An experimental study by Elham Aliabadi, Zohre Nateghian, Mohammad Hossein Nasr-Esfahani, Marziyeh Tavalaee, Tahereh Talaei-Khozani

“…The percentages of the sperms with double-stranded DNA, apoptotic, and acrosomal interacted sperms were evaluated by sperm chromatin structure assay, AnnexinV-PI staining, and peanut agglutinin, respectively. …”
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Overcoming the Silencing of Doxycycline-Inducible Promoters in hiPSC-derived Cardiomyocytes [version 1; peer review: 1 approved, 2 approved with reservations] by Michelle Guichardaz, Elisa Balmas, Alessandro Bertero, Sveva Bottini

“…We compared two promoters, TRE3VG and T11, for activity and stability, and investigated the addition of a Ubiquitous Chromatin Opening Element (UCOE) to reduce silencing. …”
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Disease-associated genetic variants in the regulatory regions of human genes: mechanisms of action on transcription and genomic resources for dissecting these mechanisms by E. V. Ignatieva, E. A. Matrosova

“…The review provides a brief description of a number of the most well-known public genomic information resources containing data obtained using omics technologies, including (1) resources that accumulate data on the chromatin states and the regions of transcription factor binding derived from ChIP-seq experiments; (2) resources containing data on genomic loci, for which allele-specific transcription factor binding was revealed based on ChIP-seq technology; (3) resources containing in silico predicted data on the potential impact of genetic variants on the transcription factor binding sites.…”
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Histone Arginine Methylation-Mediated Epigenetic Regulation of Discoidin Domain Receptor 2 Controls the Senescence of Human Bone Marrow Mesenchymal Stem Cells by Zhenyu Xu, Wenming Wu, Fang Shen, Yue Yu, Yue Wang, Charlie Xiang

“…Further, we found through knockdown and overexpression approaches that coactivator-associated arginine methyltransferase 1 (CARM1) regulated the expression level of DDR2 and the senescence of hBM-MSCs. Finally, chromatin immunoprecipitation analysis confirmed direct binding of CARM1 to the DDR2 promoter region with a high level of H3R17 methylation in early-passage hBM-MSCs, and inhibition of CARM1-mediated histone arginine methylation decreased DDR2 expression and led to cellular senescence. …”
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Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation. by Constance Ciaudo, Nicolas Servant, Valérie Cognat, Alexis Sarazin, Emmanuelle Kieffer, Stéphane Viville, Vincent Colot, Emmanuel Barillot, Edith Heard, Olivier Voinnet

“…Accordingly, a miR-302 representative was strongly enriched in embryonic germ cells derived from primordial germ cells of male but not female mouse embryos. Identifying the chromatin remodelling and E2F-dependent transcription repressors Ari4a and Arid4b as additional targets of miR-302 and miR-290 supports and possibly expands a model integrating possible overlapping functions of the two miRNA families in mouse cell totipotency during early development. …”
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Topography of Genetic Loci in Tissue Samples: Towards New Diagnostic Tool Using Interphase FISH and High-Resolution Image Analysis Techniques by I. Koutná, S. Kozubek, J. Žaloudík, M. Kozubek, E. Lukášová, P. A. Matula, E. Bártová, M. Skalníková, A. Cafourková, P. Jirsová

“…In order to validate high‐resolution cytometry for oncology, further investigations should include more precise parameters reflecting the state of chromatin in the neighbourhood of critical oncogenes or tumour suppresser genes.…”
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Synergistic Activations of REG Iα and REG Iβ Promoters by IL-6 and Glucocorticoids through JAK/STAT Pathway in Human Pancreatic β Cells by Akiyo Yamauchi, Asako Itaya-Hironaka, Sumiyo Sakuramoto-Tsuchida, Maiko Takeda, Kiyomi Yoshimoto, Tomoko Miyaoka, Takanori Fujimura, Hiroki Tsujinaka, Chikatsugu Tsuchida, Hiroyo Ota, Shin Takasawa

“…Electrophoretic mobility shift assay and chromatin immunoprecipitation revealed that IL-6+Dx stimulation increased STAT3 binding to the REG Iα promoter. …”
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Assessing cell lines with inducible depletion of cohesin and condensins components through analysis of metaphase chromosome morphology by A. M. Yunusova, A. V. Smirnov, I. E. Pristyazhnuk, T. A. Shnaider, E. K. Maltseva, S. D.  Afonnikova, O. A. Gusev, N.  R. Battulin

“…To select clones induced by depletion of the architectural chromatin proteins RAD21 (a component of the cohesin complex) and SMC2 (a component of the condensin complex), we propose to use the morphology of metaphase chromosomes as a convenient functional test. …”
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Regulatory factor X‐5/SCL/TAL1 interruption site axis promotes aerobic glycolysis and hepatocellular carcinoma cell stemness by Zhi‐Zhong Zhang, Zi‐Ming Wang, Hao‐Wen Zhang, Yan‐Xin Gong, Hao‐Ran Sun, Wei Zhang

“…Lactate production, oxygen consumption rate, and extracellular acidification rate were measured to assess the glycolytic capacity of HCC cells. Chromatin immunoprecipitation and dual‐luciferase experiments were performed to validate the connection between RFX5 and STIL. …”
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SIRT5‐mediated HOXA5 desuccinylation inhibits ferroptosis to alleviate sepsis induced‐lung injury by Lei Wang, Heng Fan, Min Sun, Ji‐Hui Ye

“…HOXA5, ferroptosis suppressor protein 1 (FSP1), sirtuin 5 (SIRT5), and glutathione peroxidase 4 (GPX4) expressions were measured using western blotting and Real‐Time Quantitative Polymerase Chain Reaction (RT‐qPCR. Chromatin immunoprecipitation and luciferase reporter assays were performed to validate HOXA5 binding to the FSP1/GPX4 promoter, and regulation of SIRT5 on HOXA5 desuccinylation was confirmed through co‐immunoprecipitation. …”
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Preliminary Evidence of a Horizontal Transfer of Paramutation Phenomenon at the <i>pl1</i> Gene in Maize (<i>Zea mays</i> L.) by Roberto Pilu, Martina Ghidoli, Alessia Follador, Alessandro Passera, Paola Casati, Ervane Laure Cheyep Dinzeu, Elena Cassani, Michela Landoni

“…Despite extensive research, the molecular mechanisms underlying paramutation are still not fully understood, although numerous studies suggest the involvement of RNA-mediated changes in DNA methylation and in the chromatin structure of silenced genes. In this paper, we report preliminary evidence regarding horizontal paramutation transfer at the <i>pl1</i> (<i>purple plant1</i>) regulatory gene involved in the accumulation of anthocyanin in several plant tissues such as tassel, kernel, and cob. …”
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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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p53-loss induced prostatic epithelial cell plasticity and invasion is driven by a crosstalk with the tumor microenvironment by Darya Yanushko, Beatriz German Falcon, Rana El Bizri, Despoina Pervizou, Robin Dolgos, Céline Keime, Tao Ye, Christelle Thibault-Carpentier, Clementine Le Magnen, Sandrine Henri, Gilles Laverny, Daniel Metzger

“…Importantly, our single-cell transcriptomic and chromatin accessibility analyses combined with histological examinations uncovered an epithelial cell population characterized by an induction of Jak/Stat3 signaling and displaying mesenchymal features. …”
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Aberrant heterochromatin silences immune response genes in chronic lymphocytic leukemia by Olivia M. Depies, Qianqian Guo, Yuan Gao, Sutapa Sinha, Zhenqing Ye, Weiguo Han, Kari G. Rabe, Mingma S. Hoel, Heather C. Darby, Chuanhe Yu, Esteban Braggio, Sameer A. Parikh, Susan L. Slager, Neil E. Kay, Zhiquan Wang

“…We further found that this aberrant chromatin signature also exists in the CLL precursor stage monoclonal B-cell lymphocytosis (MBL) cells, implicating the importance of epigenetic silencing in CLL evolution. …”
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Here and there: the double-side transgene localization by P. A. Salnikov, A. A. Khabarova, G. S. Koksharova, R. V. Mungalov, P. S. Belokopytova, I. E. Pristyazhnuk, A. R. Nurislamov, P. Somatich, M. M. Gridina, V. S. Fishman

“…These techniques have already been used for functional gene annotation by transposon-insertion sequencing, for identification of transcription factor binding sites and regulatory sequences, and for dissecting chromatin position effects. Precise localization of transgenes and accurate artifact filtration are essential for this type of method. …”
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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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High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4 by Kraege, Anton, Chavarro-Carrero, Edgar A., Guiglielmoni, Nadège, Schnell, Eva, Kirangwa, Joseph, Heilmann-Heimbach, Stefanie, Becker, Kerstin, Köhrer, Karl, Schiffer, Philipp, Thomma, Bart P. H. J., Rovenich, Hanna

“…Using long-read PacBio HiFi and Oxford Nanopore Technologies in combination with chromatin conformation capture (Hi-C) sequencing, we assembled the genome into 21 scaffolds with a total length of 50.9 Mb, an N50 of 2.7 Mb and a BUSCO score of 98.6%. …”
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NCAPD3‐mediated AKT activation regulates prostate cancer progression by Yi Zhang, Wanlin Xie, Xicui Zong, Yuanyuan Fang, Jia Ren, Zuolei Jing, Yong Wei, Shan Lu, Qingyi Zhu, Ping Liu

“…Clinical samples and cell lines were used to measure the expression of genes by quantitative real‐time RT‐PCR (qRT‐PCR), Western‐blot assay (WB), immunohistochemistry (IHC), and immunofluorescence (IF). Chromatin immunoprecipitation quantitative PCR (ChIP‐qPCR) and dual‐luciferase reporter assays were examined to explore the interplays between molecules. …”
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