Transcriptomic analysis of Medicago truncatula calli with MtWOX9-1 overexpression by V. E. Tvorogova, E. Y. Krasnoperova, A. A. Kudriashov, K. A. Kuznetsova, E. A. Potsenkovskaya, Y. A. Fedorova, L. A. Lutova

“…Enriched GO pathways included  several groups  related to histone  methyltransferase activity as well as DNA methylation and chromatin binding,  suggesting major epigenetic changes that  occur in call overexpressing MtWOX9-1. …”
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Comprehensive guide for epigenetics and transcriptomics data quality control by Arianna Comendul, Frederique Ruf-Zamojski, Colby T. Ford, Pankaj Agarwal, Elena Zaslavsky, German Nudelman, Manoj Hariharan, Aliza Rubenstein, Hanna Pincas, Venugopalan D. Nair, Adam M. Michaleas, Philip D. Fremont-Smith, Darrell O. Ricke, Stuart C. Sealfon, Christopher W. Woods, Kajal T. Claypool, Rafael Jaimes, III

“…Improved signature discovery, including the identification of the agent and timing of exposure, has been enabled by advancements in assaying techniques to detect RNA expression, DNA base modifications, histone modifications, and chromatin accessibility. The interrogation of the epigenome and transcriptome cascade requires analyzing disparate datasets from multiple assay types, often at single-cell resolution, derived from the same biospecimen. …”
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Computational model for mammalian circadian oscillator: interacting with NAD+/SIRT1 pathway and age-related changes in gene expression of circadian oscillator by N. L. Podkolodnyy, N. N. Tverdokhleb, O. A. Podkolodnaya

“…In particular, the effects of SIRT1 in circadian oscillator are the gain of degradation of protein Per2, increasing of the gene Bmal1 transcription, deacetylation of chromatin in regulatory regions of circadian oscillator genes in the E-boxes area with subsequent suppression of transcription. …”
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Androgen Receptor-Target Genes in African American Prostate Cancer Disparities by Bi-Dar Wang, Qi Yang, Kristin Ceniccola, Fernando Bianco, Ramez Andrawis, Thomas Jarrett, Harold Frazier, Steven R. Patierno, Norman H. Lee

“…Gene promoter analysis revealed that 382 out of 1,188 genes contained cis-acting AR-binding sequences. Chromatin immunoprecipitation confirmed STAT1, RHOA, ITGB5, MAPKAPK2, CSNK2A,1 and PIK3CB genes as novel AR targets in PCa disparities. …”
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Complex immunotoxic effects of T-2 Toxin on the murine spleen and thymus: Oxidative damage, inflammasomes, apoptosis, and immunosuppression by Mingyan Chen, Yanfang Zhang, Yangbo Zhao, Kewei Cao, Ruiyan Niu, Dongguang Guo, Zilong Sun

“…We observed mitochondrial swelling, chromatin condensation, and nuclear structure disruptions in these organs. …”
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The Use of Trichostatin A during Pluripotent Stem Cell Generation Does Not Affect MHC Expression Level by Sara Farahi, Sara Hosseini, Hossein Ghanbarian, Seyed Mahmoud Hashemi, Mohammad Salehi, Samaneh Hosseini

“…Highly efficient generation of PSCs through chromatin modulators such as trichostatin A (TSA) might change their MHC molecule expression profile. …”
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High mobility group box 1 (HMGB1) mediates nicotine-induced podocyte injury by Sayantap Datta, Mohammad Atiqur Rahman, Saisudha Koka, Krishna M. Boini

“…High mobility group box 1(HMGB1) is a highly conserved non-histone chromatin associated protein that largely contributes to the pathogenesis of chronic inflammatory and autoimmune diseases such as sepsis, atherosclerosis, and chronic kidney diseases. …”
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Evidence for Decreased Nucleolar PARP-1 as an Early Marker of Cognitive Impairment by Matthew Regier, Jiancong Liang, Alexander Choi, Kavita Verma, Jenny Libien, A. Iván Hernández

“…Poly(ADP-ribose) polymerase-1 (PARP-1) is a nuclear protein that regulates gene expression through poly(ADP)-ribosylation, resulting in the loosening of chromatin structure. PARP-1 enzymatic activity has been shown to be necessary for the expression of several genes required for memory formation and consolidation. …”
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All-Trans Retinoic Acid Inhibits Bone Marrow Mesenchymal Stem Cell Commitment to Adipocytes via Upregulating FRA1 Signaling by Linjun Xie, Liying Zou, Jie Chen, Youxue Liu

“…However, compared with si-fra1, si-fra1 + atRA significantly inhibited adipogenic differentiation. Chromatin immunoprecipitation showed that RARG directly regulates Fra1 and FRA1 directly regulates Pparg2 and Cebpa. …”
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Modulation of biological activities in adipose derived stem cells by histone deacetylation by Sallam Abdallah, Mouna Tabebi, Sawsan Qanadilo, Neserin Ali, Jing Wang, Pádraig D’Arcy, Wen Zhong, Folke Sjoberg, Moustafa Elmasry, Ahmed El-Serafi

“…Pathway enrichment analysis showed cell cycle, ATP-dependent chromatin remodeling and DNA processes were among the affected pathways. …”
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Ellagic Acid Alleviates Rheumatoid Arthritis in Rats through Inhibiting MTA1/HDAC1-Mediated Nur77 Deacetylation by Huanjin Song, Hao Wu, Jun Dong, Sihua Huang, Jintao Ye, Ruoxi Liu

“…MTA1 knockdown inhibited proliferation, inflammation, and oxidative stress and promoted apoptosis in MH7A cells, while HDAC1 overexpression reversed these effects. Moreover, chromatin immunoprecipitation assay indicated that EA inhibited HDAC1-mediated Nur77 deacetylation. …”
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Epigenetic Alterations and an Increased Frequency of Micronuclei in Women with Fibromyalgia by Victoria Menzies, Debra E. Lyon, Kellie J. Archer, Qing Zhou, Jenni Brumelle, Kimberly H. Jones, G. Gao, Timothy P. York, Colleen Jackson-Cook

“…The DM sites included significant biological clusters involved in neuron differentiation/nervous system development, skeletal/organ system development, and chromatin compaction. Genes associated with DM sites whose function has particular relevance to FM included BDNF, NAT15, HDAC4, PRKCA, RTN1, and PRKG1. …”
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Plant diversity and transcriptional variability assessed by retrotransposon-based molecular markers by R. N. Kalendar, K. S. Aizharkyn, O. N. Khapilina, A. A. Amenov, D. S. Tagimanova

“…Retrotransposon activity can occur during development, cell differentiation and stress, and a source of chromatin instability and genomic rearrangements. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. …”
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Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations. by Chenxing Liu, Myoung Keun Lee, Sahin Naqvi, Hanne Hoskens, Dongjing Liu, Julie D White, Karlijne Indencleef, Harold Matthews, Ryan J Eller, Jiarui Li, Jaaved Mohammed, Tomek Swigut, Stephen Richmond, Mange Manyama, Benedikt Hallgrímsson, Richard A Spritz, Eleanor Feingold, Mary L Marazita, Joanna Wysocka, Susan Walsh, Mark D Shriver, Peter Claes, Seth M Weinberg, John R Shaffer

“…Genome scans of these multivariate shape phenotypes revealed significant (p < 2.5 × 10-8) signals at 20 loci, which were enriched for active chromatin elements in human cranial neural crest cells and embryonic craniofacial tissue, consistent with an early developmental origin of the facial variation. …”
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Effects of Antipsychotic Drugs on the Epigenetic Modification of Brain-Derived Neurotrophic Factor Gene Expression in the Hippocampi of Chronic Restraint Stress Rats by Mi Kyoung Seo, Young Hoon Kim, Roger S. McIntyre, Rodrigo B. Mansur, Yena Lee, Nicole E. Carmona, Ah Jeong Choi, Gyung-Mee Kim, Jung Goo Lee, Sung Woo Park

“…The levels of histone H3 acetylation and MeCP2 binding at BDNF promoter IV were assessed with chromatin immunoprecipitation assays. The mRNA levels of total BDNF with exon IV, HDAC5, DNMT1, and DNMT3a were assessed with a quantitative RT-PCR procedure. …”
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scRNA seq of an F1 cross of Marek’s disease resistant and susceptible chickens identifies allele specific expression signatures enriched in transcription modulators by Deborah Velez-Irizarry, Hans Cheng, Cari Hearn

“…We identified 22 SNPs with ASE in response to MDV infection mapped to gene rich regions surrounding 59 genes of critical importance for chromatin remodeling and transcriptional regulation. …”
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Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament by Emmajay Sutherland, Christopher J. Harding, Tancrède du Monceau de Bergendal, Gordon J. Florence, Katrin Ackermann, Bela E. Bode, Silvia Synowsky, Ramasubramanian Sundaramoorthy, Clarissa Melo Czekster

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High glucose reduces Nrf2-dependent cRAGE release and enhances inflammasome-dependent IL-1β production in monocytes: the modulatory effects of EGCG by Chi-Hao Wu, Yin-Hsuan Chang, Chin-Lin Hsu, Sheng-Yi Chen, Gow-Chin Yen

“…Mechanistically, the HG effects were counteracted by siRAGE and exacerbated by siNrf2. Chromatin immunoprecipitation results showed that Nrf2 binding to the ADAM10 promoter and HG interfered with this binding. …”
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Utilizing liquid-liquid biopolymer regulators to predict the prognosis and drug sensitivity of hepatocellular carcinoma by Jianhao Li, Han Chen, Lang Bai, Hong Tang

“…Abstract Background Liquid-liquid phase separation (LLPS) is essential for the formation of membraneless organelles and significantly influences cellular compartmentalization, chromatin remodeling, and gene regulation. Previous research has highlighted the critical function of liquid-liquid biopolymers in the development of hepatocellular carcinoma (HCC). …”
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Decreased SynMuv B gene activity in response to viral infection leads to activation of the antiviral RNAi pathway in C. elegans. by Ashwin Seetharaman, Himani Galagali, Elizabeth Linarte, Mona H X Liu, Jennifer D Cohen, Kashish Chetal, Ruslan Sadreyev, Alex J Tate, Taiowa A Montgomery, Gary Ruvkun

“…Many synMuv B genes encode dREAM complex chromatin-regulatory proteins found in nearly all animals and plants. …”
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