Longitudinal analysis of influenza vaccination implicates regulation of RIG-I signaling by DNA methylation by Hongxiang Fu, Harry Pickering, Liudmilla Rubbi, Ted M. Ross, Elaine F. Reed, Matteo Pellegrini

“…However, less is known about the effect of the influenza vaccine on the epigenome. We utilized a targeted DNA methylation approach to study the longitudinal effects (day 0 pre-vaccination and day 28 post-vaccination) on influenza vaccination responses in peripheral blood mononuclear cells. …”
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Histone lysine methacrylation is a dynamic post-translational modification regulated by HAT1 and SIRT2 by Kyle Delaney, Minjia Tan, Zhesi Zhu, Jinjun Gao, Lunzhi Dai, Sunjoo Kim, Jun Ding, Maomao He, Levon Halabelian, Lu Yang, Prabakaran Nagarajan, Mark Robert Parthun, Sangkyu Lee, Saadi Khochbin, Yujun George Zheng, Yingming Zhao

“…Altogether, these investigations uncover a new type of enzyme-catalyzed histone modification and suggest that methacrylyl-CoA generating metabolism is part of a growing number of epigenome-associated metabolic pathways.…”
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Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells by Shelley, Brandon C., Mandefro, Berhan, Sareen, Dhruv, Svendsen, Clive N., Milani, Pamela, Escalante, Renan A., Patel-Murray, Natasha Leanna, Xin, Xiaofeng, Adam, Miriam, Fraenkel, Ernest

“…In recent years, the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) has become a fundamental tool of epigenomic research. However, it is difficult to perform this technique on frozen samples because freezing cells before extracting nuclei can impair nuclear integrity and alter chromatin structure, especially in fragile cells such as neurons. …”
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Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells by Shelley, Brandon C., Mandefro, Berhan, Sareen, Dhruv, Svendsen, Clive N., Milani, Pamela, Escalante, Renan A., Patel-Murray, Natasha Leanna, Xin, Xiaofeng, Adam, Miriam, Fraenkel, Ernest

“…In recent years, the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) has become a fundamental tool of epigenomic research. However, it is difficult to perform this technique on frozen samples because freezing cells before extracting nuclei can impair nuclear integrity and alter chromatin structure, especially in fragile cells such as neurons. …”
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Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. by Pasquali, L, Gaulton, K, Rodríguez-Seguí, SA, Mularoni, L, Miguel-Escalada, I, Akerman, I, Tena, J, Morán, I, Gómez-Marín, C, van de Bunt, M, Ponsa-Cobas, J, Castro, N, Nammo, T, Cebola, I, García-Hurtado, J, Maestro, M, Pattou, F, Piemonti, L, Berney, T, Gloyn, A, Ravassard, P, Gómez-Skarmeta, J, Müller, F, McCarthy, M, Ferrer, J

“…Our studies illustrate how islet transcription factors interact functionally with the epigenome and provide systematic evidence that the dysregulation of islet enhancers is relevant to the mechanisms underlying type 2 diabetes.…”

Single cell analysis of normal and leukemic hematopoiesis by Povinelli, B, Rodriguez-Meira, A, Mead, A

“…Recent advances in single cell techniques allow analysis of the genome, transcriptome, epigenome and proteome in single cells at an unprecedented scale. …”

Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications by Jinshou Yang, Bo Ren, Jie Ren, Gang Yang, Yuan Fang, Xing Wang, Feihan Zhou, Lei You, Yupei Zhao

“…Conclusions These findings revealed the critical role of the epigenome-metabolome interaction in regulating PDAC liver metastasis and suggested potential therapeutic strategies targeting GAA metabolism and epigenetic regulatory mechanisms.…”
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Transcriptional signature of islet neogenesis-associated protein peptide-treated rat pancreatic islets reveals induction of novel long non-coding RNAs by Agustín Romero, Agustín Romero, Ana C. Heidenreich, Ana C. Heidenreich, Carolina L. Román, Macarena Algañarás, Ezequiel Nazer, Juan J. Gagliardino, Bárbara Maiztegui, Luis E. Flores, Santiago A. Rodríguez-Seguí, Santiago A. Rodríguez-Seguí

“…The list of INGAP-PP-regulated genes was integrated with epigenomic data. Using the new gene annotation generated in this work, we quantified RNA-seq data profiled in INS-1 cells treated with IL1β, IL1β+Calcipotriol (a vitamin D agonist) or vehicle, and single-cell RNA-seq data profiled in rat pancreatic islets. …”
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Identification of New Helicobacter pylori Subpopulations in Native Americans and Mestizos From Peru by Andrés Julián Gutiérrez-Escobar, Billie Velapatiño, Billie Velapatiño, Victor Borda, Charles S. Rabkin, Eduardo Tarazona-Santos, Eduardo Tarazona-Santos, Lilia Cabrera, Jaime Cok, Catherine C. Hooper, Helena Jahuira-Arias, Phabiola Herrera, Mehwish Noureen, Mehwish Noureen, Difei Wang, Judith Romero-Gallo, Bao Tran, Richard M. Peek, Douglas E. Berg, Robert H. Gilman, M. Constanza Camargo

“…Phylogenetic profiling showed that Orthogroups in the indigenous strains seem to have evolved differentially toward epigenomic regulation and chromosome maintenance, whereas OGs in the modern mestizo (LIM) seem to have evolved toward virulence and adherence. …”
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Longitudinal Study of DNA Methylation and Epigenetic Clocks Prior to and Following Test-Confirmed COVID-19 and mRNA Vaccination by Alina P. S. Pang, Albert T. Higgins-Chen, Albert T. Higgins-Chen, Florence Comite, Florence Comite, Ioana Raica, Christopher Arboleda, Hannah Went, Tavis Mendez, Michael Schotsaert, Michael Schotsaert, Varun Dwaraka, Ryan Smith, Morgan E. Levine, Lishomwa C. Ndhlovu, Michael J. Corley

“…The host epigenetic landscape rapidly changes during SARS-CoV-2 infection, and evidence suggest that severe COVID-19 is associated with durable scars to the epigenome. Specifically, aberrant DNA methylation changes in immune cells and alterations to epigenetic clocks in blood relate to severe COVID-19. …”
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Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis by Marietta Armaka, Dimitris Konstantopoulos, Christos Tzaferis, Matthieu D. Lavigne, Maria Sakkou, Anastasios Liakos, Petros P. Sfikakis, Meletios A. Dimopoulos, Maria Fousteri, George Kollias

“…We integrated the transcriptomic and epigenomic data to infer gene regulatory networks using ArchR and custom-implemented algorithms. …”
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Neuronal-specific methylome and hydroxymethylome analysis reveal significant loci associated with alcohol use disorder by Diego E. Andrade-Brito, Diego E. Andrade-Brito, Diana L. Núñez-Ríos, Diana L. Núñez-Ríos, José Jaime Martínez-Magaña, José Jaime Martínez-Magaña, Sheila T. Nagamatsu, Sheila T. Nagamatsu, Gregory Rompala, Lea Zillich, Stephanie H. Witt, Shaunna L. Clark, Maria C. Lattig, Janitza L. Montalvo-Ortiz, Janitza L. Montalvo-Ortiz

“…Our findings provide new insights into the epigenomic dysregulation of AUD in the human brain.…”
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Targeting Host Cellular Factors as a Strategy of Therapeutic Intervention for Herpesvirus Infections by Kumari Asha, Neelam Sharma-Walia

“…These anti-herpesvirus therapeutics include inhibitors blocking viral life cycle events, engineered anticancer agents, epigenome influencing factors, immunomodulators, and therapeutic compounds from natural extracts.…”
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Genetics and epigenetics of gliomas by Mario Luca Suvà

“…In this review, we discuss recent discoveries in the genetics of adult and paediatric gliomas, and highlight how some of the founding genetic mutations reshape the cancer epigenome. These studies provide an in-depth view of the molecular routes leading to brain tumour development and will be key for refining classification systems and improving clinical care. …”
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Identification of critical base pairs required for CTCF binding in motif M1 and M2 by Wufeng Li, Liping Shang, Kaimeng Huang, Jiao Li, Zhibin Wang, Hongjie Yao

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Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat. by Ben P Williams, Daniela Pignatta, Steven Henikoff, Mary Gehring

“…We propose that the ROS1 locus functions as an epigenetic rheostat, tuning the level of demethylase activity in response to methylation alterations, thus ensuring epigenomic stability.…”
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Aberrant DNA methylation defines isoform usage in cancer, with functional implications. by Yun-Ching Chen, Laura Elnitski

“…These findings provide new insights into the functional impact of dysregulated DNA methylation in cancer and highlight the relationship between the epigenome and transcriptome.…”
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The enigma of memory T cells in viral infections (including SARS-CoV-2) by Sorin Buzinschi

“…An important role in these disorders is played by the host's genetic structure and epigenome. …”
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Epigenetic Mechanisms beyond Tumour–Stroma Crosstalk by Teresa Gagliano, Claudio Brancolini

“…An increasing number of studies have highlighted that the cancer epigenome can be influenced by tumour microenvironment and vice versa. …”
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Tertiary Epimutations - A Novel Aspect of Epigenetic Transgenerational Inheritance Promoting Genome Instability. by John R McCarrey, Jake D Lehle, Seetha S Raju, Yufeng Wang, Eric E Nilsson, Michael K Skinner

“…Exposure to environmental factors can induce the epigenetic transgenerational inheritance of disease. Alterations to the epigenome termed "epimutations" include "primary epimutations" which are epigenetic alterations in the absence of genetic change and "secondary epimutations" which form following an initial genetic change. …”
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