Gene regulatory network reconfiguration in direct lineage reprogramming by Kenji Kamimoto, Mohd Tayyab Adil, Kunal Jindal, Christy M. Hoffmann, Wenjun Kong, Xue Yang, Samantha A. Morris

“…We previously developed CellOracle, a computational method to infer GRNs from single-cell transcriptome and epigenome data. Using inferred GRNs, CellOracle simulates gene expression changes in response to TF perturbation, enabling in silico interrogation of network reconfiguration. …”
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Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism by Mette Juul Jacobsen, Jakob H. Havgaard, Christian Anthon, Caroline M. Junker Mentzel, Susanna Cirera, Poula Maltha Krogh, Sachin Pundhir, Peter Karlskov-Mortensen, Camilla S. Bruun, Philippe Lesnik, Maryse Guerin, Jan Gorodkin, Claus B. Jørgensen, Merete Fredholm, Romain Barrès

“…Here, we used the pig, an animal model sharing many physiological and pathophysiological similarities with humans, to perform in-depth epigenomic and transcriptomic characterization of pure adipocyte fractions. …”
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3D Genome Plasticity in Normal and Diseased Neurodevelopment by Amara Plaza-Jennings, Aditi Valada, Schahram Akbarian

“…Furthermore, locus-specific structural DNA variations, such as micro-deletions, duplications, repeat expansions, and retroelement insertions carry the potential to disrupt the broader epigenomic and transcriptional landscape far beyond the boundaries of the site-specific variation, highlighting the critical importance of long-range intra- and inter-chromosomal contacts for neuronal and glial function.…”
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Arguments to Support a Viral Origin of Oral Squamous Cell Carcinoma in Non-Smoker and Non-Drinker Patients by Jean-Philippe Foy, Jean-Philippe Foy, Jean-Philippe Foy, Chloé Bertolus, David Boutolleau, David Boutolleau, Henri Agut, Henri Agut, Antoine Gessain, Zdenko Herceg, Pierre Saintigny, Pierre Saintigny, Pierre Saintigny

“…Because viral genome integration has not been detected in OSCC from NSND, a “hit and run” viral mechanism involving epigenome deregulation could therefore play a key role at early steps of oral carcinogenesis in this population of patients. …”
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Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs by Silvia F. Zanini, Philipp E. Bayer, Rachel Wells, Rod J. Snowdon, Jacqueline Batley, Rajeev K. Varshney, Henry T. Nguyen, David Edwards, Agnieszka A. Golicz

“…We conclude with a summary and outlook on innovative data structures representing the complete content of plant pangenomes including annotations of coding and noncoding elements and outcomes of transcriptomic and epigenomic experiments.…”
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Association of DNA Methylation at CPT1A Locus with Metabolic Syndrome in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study. by Mithun Das, Jin Sha, Bertha Hidalgo, Stella Aslibekyan, Anh N Do, Degui Zhi, Dianjianyi Sun, Tao Zhang, Shengxu Li, Wei Chen, Sathanur R Srinivasan, Hemant K Tiwari, Devin Absher, Jose M Ordovas, Gerald S Berenson, Donna K Arnett, Marguerite R Irvin

“…In this study, we conducted an epigenome-wide association study of metabolic syndrome (MetS) among 846 participants of European descent in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN). …”
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Chromatin Methylation Abnormalities in Autosomal Dominant Polycystic Kidney Disease by Jing Xu, Jing Xu, Cheng Xue, Xiaodong Wang, Xiaodong Wang, Lei Zhang, Lei Zhang, Lei Zhang, Changlin Mei, Zhiguo Mao

“…Considering the complexity of methylation abnormalities occurring in different regions and genes on the PKD epigenome, more specific therapy aiming to restore to the normal genome should lead to the development of epigenetic treatment.…”
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The New Era of Salivaomics in Dentistry: Frontiers and Facts in the Early Diagnosis and Prevention of Oral Diseases and Cancer by Flavia Papale, Simona Santonocito, Alessandro Polizzi, Antonino Lo Giudice, Saverio Capodiferro, Gianfranco Favia, Gaetano Isola

“…The growing realisation that saliva is an inexhaustible source of information has led to the coining of the term ‘Salivaomics’, which includes five “omics” in connection with the main constituents of saliva: genome and epigenome, transcriptomics, metabolomics, lipidomics, proteomics and microbiota. …”
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Tetraploidization of Immortalized Myoblasts Induced by Cell Fusion Drives Myogenic Sarcoma Development with <em>DMD</em> Deletion by Candice Merle, Noémie Thébault, Sophie LeGuellec, Jessica Baud, Gaëlle Pérot, Tom Lesluyes, Lucile Delespaul, Lydia Lartigue, Frédéric Chibon

“…Unlike processes based on duplication, cell fusion involves the merging of two different genomes, epigenomes and cellular states. Since it is involved in muscle differentiation, we hypothesized that it could play a role in the oncogenesis of myogenic cancers. …”
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Histone 3 Methyltransferases Alter Melanoma Initiation and Progression Through Discrete Mechanisms by Sara E. DiNapoli, Sara E. DiNapoli, Raúl Martinez-McFaline, Raúl Martinez-McFaline, Hao Shen, Hao Shen, Ashley S. Doane, Alexendar R. Perez, Akanksha Verma, Amanda Simon, Isabel Nelson, Isabel Nelson, Courtney A. Balgobin, Courtney A. Balgobin, Caitlin T. Bourque, Caitlin T. Bourque, Jun Yao, Jun Yao, Renuka Raman, Renuka Raman, Wendy Béguelin, Wendy Béguelin, Jonathan H. Zippin, Olivier Elemento, Ari M. Melnick, Ari M. Melnick, Yariv Houvras, Yariv Houvras, Yariv Houvras

“…Perturbations to the epigenome are known drivers of tumorigenesis. In melanoma, alterations in histone methyltransferases that catalyze methylation at histone 3 lysine 9 and histone 3 lysine 27—two sites of critical post-translational modification—have been reported. …”
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Oxidative Stress and Nuclear Reprogramming: A Pilot Study of the Effects of Reactive Oxygen Species on Architectural and Epigenetic Landscapes by Claudio Casali, Stella Siciliani, Luca Galgano, Marco Biggiogera

“…When assessing the stress-induced epigenome reprogramming, widely diffused biochemical and molecular approaches commonly fail to incorporate analyses such as architectural chromatin alterations and target molecules precise spatial localization. …”
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Regulation of the Immune System in Aging: Focus on Epigenetic Mechanisms by K. A. Aitbaev, I. T. Murkamilov, Zh. A. Murkamilova, I. O. Kudaibergenova, F. A. Yusupov

“…Under the influence of internal and external factors such as metabolic profile, hormones, nutrition, drugs, smoking and stress, epigenetic mechanisms are actively modulated and, in this sense, a lifestyle can significantly affect the epigenome, and consequently, the gene expression profile and function of cells. …”
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Nutriepigenomics in Environmental-Associated Oxidative Stress by Karla Rubio, Estefani Y. Hernández-Cruz, Diana G. Rogel-Ayala, Pouya Sarvari, Ciro Isidoro, Guillermo Barreto, José Pedraza-Chaverri

“…Understanding the mechanisms by which nutrients influence the epigenome, and thus global transcription, is crucial for future early diagnostic and therapeutic efforts in the field of environmental medicine.…”
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From the (Epi)Genome to Metabolism and Vice Versa; Examples from Hematologic Malignancy by Panagiota Karagianni, Stavroula Giannouli, Michael Voulgarelis

“…The aim is to illustrate the intricate interrelationship between the genome (and epigenome) and metabolism and its relevance to hematologic malignancy.…”
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Locus-Specific DNA Methylation Editing in Melanoma Cell Lines Using a CRISPR-Based System by Jim Smith, Rakesh Banerjee, Reema Waly, Arthur Urbano, Gregory Gimenez, Robert Day, Michael R. Eccles, Robert J. Weeks, Aniruddha Chatterjee

“…The advent of CRISPR-based technologies has provided a powerful toolkit for locus-specific manipulation of the epigenome. Here, we describe a comprehensive global workflow for the design and application of a dCas9-SunTag-based tool for editing the DNA methylation locus in human melanoma cells alongside protocols for downstream techniques used to evaluate subsequent methylation and gene expression changes in methylation-edited cells. …”
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The Role of Thymine DNA Glycosylase in Transcription, Active DNA Demethylation, and Cancer by Oladapo Onabote, Haider M. Hassan, Majdina Isovic, Joseph Torchia

“…TDG acts as a key player in transcriptional regulation through its interactions with various nuclear receptors and transcription factors, in addition to its involvement in classical BER and active DNA demethylation, which serve to protect the stability of the genome and epigenome, respectively. Recent animal studies have identified a connection between the loss of <i>Tdg</i> and the onset of tumorigenesis. …”
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Short-chain fatty acids activate acetyltransferase p300 by Sydney P Thomas, John M Denu

“…Here, we systematically investigate how SCFAs alter the epigenome. Using quantitative proteomics of histone modification states, we identified rapid and sustained increases in histone acetylation after the addition of butyrate or propionate, but not acetate. …”
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Chemical Synthesis of the PAX Protein Inhibitor EG1 and Its Ability to Slow the Growth of Human Colorectal Carcinoma Cells by Lorissa McDougall, Jui Thiang Brian Kueh, Jake Ward, Joel D. A. Tyndall, Joel D. A. Tyndall, Adele G. Woolley, Adele G. Woolley, Adele G. Woolley, Sunali Mehta, Sunali Mehta, Sunali Mehta, Cherie Stayner, David S. Larsen, Michael R. Eccles, Michael R. Eccles, Michael R. Eccles

“…The incidence rate has continued to increase over time, reflecting both demographic and lifestyle changes, which have resulted in genomic and epigenomic modifications. Many of the epigenetic modifications occur in genes known to be closely associated with embryonic development and cellular growth. …”
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Epigenetic Reprogramming for Targeting <i>IDH</i>-Mutant Malignant Gliomas by Jong-Whi Park, Şevin Turcan

“…Targeting the epigenome has been considered a compelling treatment modality for several cancers, including gliomas. …”
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Postnatal nutrition environment reprograms renal DNA methylation patterns in offspring of maternal protein-restricted stroke-prone spontaneously hypertensive rats by Chika Ando, Sihui Ma, Sihui Ma, Moe Miyoshi, Kyohei Furukawa, Kyohei Furukawa, Xuguang Li, Huijuan Jia, Hisanori Kato

“…Maternal malnutrition hampers the offspring health by manipulating the epigenome. Recent studies indicate that the changes in DNA methylation could be reversed by afterbirth nutrition supplementation. …”
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