Profiling Chromatin Accessibility at Single-cell Resolution by Sarthak Sinha, Ansuman T. Satpathy, Weiqiang Zhou, Hongkai Ji, Jo A. Stratton, Arzina Jaffer, Nizar Bahlis, Sorana Morrissy, Jeff A. Biernaskie

“…One key regulator is the cell’s epigenome state that drives distinct transcriptional programs by regulating chromatin accessibility. …”
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Histone H2A ubiquitination resulting from Brap loss of function connects multiple aging hallmarks and accelerates neurodegeneration by Yan Guo, Alison.A. Chomiak, Ye Hong, Clara C. Lowe, Caroline A. Kopsidas, Wen-Ching Chan, Jorge Andrade, Hongna Pan, Xiaoming Zhou, Edwin S. Monuki, Yuanyi Feng

“…Summary: Aging is an intricate process characterized by multiple hallmarks including stem cell exhaustion, genome instability, epigenome alteration, impaired proteostasis, and cellular senescence. …”
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糖尿病的发育起源:环境表观基因组学和新模式 by Hong Zhu, Guolian Ding, Xinmei Liu, Hefeng Huang

“…This review first summarizes the epigenetic targets, including metastable epialleles and imprinting genes, by which the environmental factors can modify the epigenome. Then we review the epigenetics changes in response to environmental challenge during critical developmental windows, gametogenesis, embryogenesis, and fetal and postnatal period, with the specific example of diabetic susceptibility. …”
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Dimethyl itaconate induces long-term innate immune responses and confers protection against infection by Anaísa V. Ferreira, Sarantos Kostidis, Laszlo A. Groh, Valerie A.C.M. Koeken, Mariolina Bruno, Ilayda Baydemir, Gizem Kilic, Özlem Bulut, Theano Andriopoulou, Victoria Spanou, Kalliopi D. Synodinou, Theologia Gkavogianni, Simone J.C.F.M. Moorlag, L. Charlotte de Bree, Vera P. Mourits, Vasiliki Matzaraki, Werner J.H. Koopman, Frank L. van de Veerdonk, Georgios Renieris, Martin Giera, Evangelos J. Giamarellos-Bourboulis, Boris Novakovic, Jorge Domínguez-Andrés

“…We show that dimethyl itaconate, a derivative of itaconate previously linked to suppression of inflammation and widely employed as an alternative to the endogenous metabolite, can induce long-term transcriptional, epigenomic, and metabolic changes, characteristic of trained immunity. …”
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Biochemical and Physiological Plant Processes Affected by Seed Treatment with Non-Thermal Plasma by Vida Mildaziene, Anatolii Ivankov, Bozena Sera, Danas Baniulis

“…Wide-scale changes evolving at the epigenomic, transcriptomic, proteomic and metabolic levels are triggered by seed irradiation with NTP and contribute to changes in germination, early seedling growth, phytohormone amounts, metabolic and defense enzyme activity, secondary metabolism, photosynthesis, adaptability to biotic and abiotic stress, microbiome composition, and increased plant fitness, productivity and growth on a longer time scale. …”
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Looking Beyond the Glioblastoma Mask: Is Genomics the Right Path? by Liliana Montella, Nunzio Del Gaudio, Guglielmo Bove, Mariella Cuomo, Mariella Cuomo, Michela Buonaiuto, Michela Buonaiuto, Davide Costabile, Davide Costabile, Roberta Visconti, Roberta Visconti, Gaetano Facchini, Lucia Altucci, Lucia Altucci, Lorenzo Chiariotti, Lorenzo Chiariotti, Rosa Della Monica, Rosa Della Monica

“…Recently, genetic analyses have been integrated with epigenetic investigations, strongly implementing typing and subtyping of brain tumors, including GBMs, and leading to the new WHO 2021 classification. GBM genomic and epigenomic profile influences evolution, resistance, and therapeutic responses. …”
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ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3 by Wei Wei, Qiongyi Zhao, Ziqi Wang, Wei-Siang Liau, Dean Basic, Haobin Ren, Paul R. Marshall, Esmi L. Zajaczkowski, Laura J. Leighton, Sachithrani U. Madugalle, Mason Musgrove, Ambika Periyakaruppiah, Jichun Shi, Jianjian Zhang, John S. Mattick, Timothy R. Mercer, Robert C. Spitale, Xiang Li, Timothy W. Bredy

“…This study expands the lexicon of experience-dependent lncRNA activity in the brain and highlights enhancer-derived RNAs (eRNAs) as key players in the epigenomic regulation of gene expression associated with the formation of fear extinction memory.…”
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Epigenetics and Early Development by Gokul Gopinathan, Thomas G. H. Diekwisch

“…The epigenome controls all aspect of eukaryotic development as the packaging of DNA greatly affects gene expression. …”
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Exploring the Potential of Drug Response Assays for Precision Medicine in Ovarian Cancer by Tanya Singh, Adam S. Neal, Neda A. Moatamed, Sanaz Memarzadeh

“…These differential responses may, in part, be due to a diverse range of genomic, epigenomic, proteomic, and metabolic alterations among individuals suffering from the same type of cancer. …”
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Effects of Thermal Manipulation on mRNA Regulation of Response Genes Regarding Improvement of Thermotolerance Adaptation in Chickens during Embryogenesis by Suriya Kumari Ramiah, Krishnan Nair Balakrishnan, Yashini Subramaniam, Oluwaseun Serah Iyasere, Zulkifli Idrus

“…There has been little investigation into the vulnerability of the epigenome involving TM during embryogenesis, although the cellular pathways activated by HS have been explored in chickens. …”
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Sonogenetic control of multiplexed genome regulation and base editing by Pei Liu, Josquin Foiret, Yinglin Situ, Nisi Zhang, Aris J. Kare, Bo Wu, Marina N. Raie, Katherine W. Ferrara, Lei S. Qi

“…Our work underscores the potential of ultrasound as a clinically viable approach to enhance cell and gene-based therapies via precision genome and epigenome engineering.…”
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Parenting stress and DNA methylation among African Americans in the InterGEN Study by Michelle L. Wright, Yunfeng Huang, Qin Hui, Kevin Newhall, Cindy Crusto, Yan V. Sun, Jacquelyn Y. Taylor

“…The purpose of this study was to examine the relationship between maternal parenting stress and DNA methylation among African Ancestry mother-child dyads.MethodsWe evaluated epigenome-wide DNA methylation relative to parenting stress in 74 mother-child dyads using linear mixed models.ResultsSignificant variation in maternal DNA methylation at 95 CpG sites was associated with level of parenting stress. …”
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Deconvoluting gene and environment interactions to develop an “epigenetic score meter” of disease by Alessio Butera, Lena Smirnova, Elisa Ferrando‐May, Thomas Hartung, Thomas Brunner, Marcel Leist, Ivano Amelio

“…Our argument converges on the concept that the GxE is recorded in the cellular epigenome, which might represent the key to deconvolute these multidimensional intricated layers of regulation. …”
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Building the Border: Development of the Chordate Neural Plate Border Region and Its Derivatives by Ankita Thawani, Andrew K. Groves, Andrew K. Groves

“…We review these studies and discuss the potential of recent advances in spatio-temporal transcriptomic and epigenomic analyses that would allow a mechanistic understanding of how these signaling pathways and their downstream transcriptional cascades regulate the formation of the neural plate border region.…”
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Identification of Cancer Driver Genes by Integrating Multiomics Data with Graph Neural Networks by Hongzhi Song, Chaoyi Yin, Zhuopeng Li, Ke Feng, Yangkun Cao, Yujie Gu, Huiyan Sun

“…In this paper, we first generate comprehensive instructive features for each gene from genomic, epigenomic, transcriptomic levels together with protein–protein interaction (PPI)-networks-derived attributes and then propose a novel semisupervised deep graph learning framework GGraphSAGE to predict cancer driver genes according to the impact of the alterations on a biological system. …”
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Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes by Tara N. Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A. Rosenfeld, Jennifer VanOudenhove, Daryl A. Scott, Elizabeth J. Leslie, Justin Cotney

“…Combining transcriptomic and epigenomic data we identified 539 genes likely to contribute to craniofacial disorders. …”
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Stem Cell Theory of Cancer: Implications for Translational Research from Bedside to Bench by Shi-Ming Tu, Sunny R. Singh, Konstantinos Arnaoutakis, Sindhu Malapati, Sajjad A. Bhatti, Aron Y. Joon, Omar T. Atiq, Louis L. Pisters

“…It is a unified theory of cancer that unites the genome with the epigenome, links the intracellular with the extracellular, and connects the cellular constituents and compartments with the microenvironment. …”
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Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas by Odessica Hughes, Amy R. Bentley, Charles E. Breeze, Francois Aguet, Xiaoguang Xu, Girish Nadkarni, Quan Sun, Bridget M. Lin, Thomas Gilliland, Mariah C. Meyer, Jiawen Du, Laura M. Raffield, Holly Kramer, Robert W. Morton, Mateus H. Gouveia, Elizabeth G. Atkinson, Adan Valladares-Salgado, Niels Wacher-Rodarte, Nicole D. Dueker, Xiuqing Guo, Yang Hai, Adebowale Adeyemo, Lyle G. Best, Jianwen Cai, Guanjie Chen, Michael Chong, Ayo Doumatey, James Eales, Mark O. Goodarzi, Eli Ipp, Marguerite Ryan Irvin, Minzhi Jiang, Alana C. Jones, Charles Kooperberg, Jose E. Krieger, Ethan M. Lange, Matthew B. Lanktree, James P. Lash, Paulo A. Lotufo, Ruth J.F. Loos, Vy Thi Ha My, Jesús Peralta-Romero, Lihong Qi, Leslie J. Raffel, Stephen S. Rich, Erik J. Rodriquez, Eduardo Tarazona-Santos, Kent D. Taylor, Jason G. Umans, Jia Wen, Bessie A. Young, Zhi Yu, Ying Zhang, Yii-Der Ida Chen, Tanja Rundek, Jerome I. Rotter, Miguel Cruz, Myriam Fornage, Maria Fernanda Lima-Costa, Alexandre C. Pereira, Guillaume Paré, Pradeep Natarajan, Shelley A. Cole, April P. Carson, Leslie A. Lange, Yun Li, Eliseo J. Perez-Stable, Ron Do, Fadi J. Charchar, Maciej Tomaszewski, Josyf C. Mychaleckyj, Charles Rotimi, Andrew P. Morris, Nora Franceschini

“…We integrated fine-mapped loci with epigenomic and transcriptomic resources to highlight potential effector genes relevant to kidney physiology and disease, and reveal key regulatory elements and pathways involved in renal function and development. …”
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Transcriptional Control of Subcutaneous Adipose Tissue by the Transcription Factor CTCF Modulates Heterogeneity in Fat Distribution in Women by Edina Erdos, Katalin Sandor, Crystal L. Young-Erdos, Laszlo Halasz, Steven R. Smith, Timothy F. Osborne, Adeline Divoux

“…We used functional genomics tools to profile the epigenomic landscape to help infer the differential transcriptional potential of apple- and pear-shaped women’s subcutaneous adipose-derived stem cells (ADSCs). …”
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Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes by Qiang Zhang, Sai Ma, Zhengzhi Liu, Bohan Zhu, Zirui Zhou, Gaoshan Li, J. Javier Meana, Javier González-Maeso, Chang Lu

“…Abstract The genome-wide DNA methylation profile, or DNA methylome, is a critical component of the overall epigenomic landscape that modulates gene activities and cell fate. …”
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