C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search by Divya Tej Sowpati, Surabhi Srivastava, Jyotsna Dhawan, Rakesh K Mishra

“…Abstract Background Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. …”
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Epi-mutations for spermatogenic defects by maternal exposure to di(2-ethylhexyl) phthalate by Yukiko Tando, Hitoshi Hiura, Asuka Takehara, Yumi Ito-Matsuoka, Takahiro Arima, Yasuhisa Matsui

“…Exposure to environmental factors during fetal development may lead to epigenomic modifications in fetal germ cells, altering gene expression and promoting diseases in successive generations. …”
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Consequences of 22q11.2 Microdeletion on the Genome, Individual and Population Levels by Małgorzata Karbarz

“…The rest of the genome, as well as epigenome and environmental factors, are not without influence on the variability of phenotypes. …”
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The PWWP domain and the evolution of unique DNA methylation toolkits in Hymenoptera by Robert Kucharski, Nancy Ellis, Tomasz P. Jurkowski, Paul J. Hurd, Ryszard Maleszka

“…We discuss our findings in the context of the crosstalk between DNA methylation and histone methylation, and the expanded potential of epigenomic modifications in Hymenoptera to drive evolutionary novelties.…”
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Sex chromosome complement and sex steroid signaling underlie sex differences in immunity to respiratory virus infection by Reegan A. J. Miller, Reegan A. J. Miller, Abigael P. Williams, Abigael P. Williams, Susan Kovats, Susan Kovats

“…Emerging research shows intrinsic sex differences in immune cell transcriptomes, epigenomes, and proteomes that may regulate human immunity when challenged by viral infection. …”
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Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis by Keren Cheng, I-Chung Chen, Ching-Hsun Eric Cheng, Kazadi Mutoji, Benjamin J. Hale, Brian P. Hermann, Christopher B. Geyer, Jon M. Oatley, John R. McCarrey

“…Here we provide the first multiparametric integrative analysis of mammalian germ cell epigenomes comparable with that done for >100 somatic cell types by the ENCODE Project. …”
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Integrated transcriptome and proteome analysis reveals posttranscriptional regulation of ribosomal genes in human brain organoids by Jaydeep Sidhaye, Philipp Trepte, Natalie Sepke, Maria Novatchkova, Michael Schutzbier, Gerhard Dürnberger, Karl Mechtler, Jürgen A Knoblich

“…Investigations of the transcriptome and epigenome have revealed important gene regulatory networks underlying this crucial developmental event. …”
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Hepatocyte SREBP signaling mediates clock communication within the liver by Dongyin Guan, Hosung Bae, Dishu Zhou, Ying Chen, Chunjie Jiang, Cam Mong La, Yang Xiao, Kun Zhu, Wenxiang Hu, Trang Minh Trinh, Panpan Liu, Ying Xiong, Bishuang Cai, Cholsoon Jang, Mitchell A. Lazar

“…Here, we report that in fatty liver caused by diet-induced obesity (DIO), hepatocyte SREBP cleavage–activating protein (SCAP) was required for Reverb-hDKO–induced diurnal rhythmic remodeling and epigenomic reprogramming in liver macrophages (LMs). …”
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The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses by Christian K. Ramsoomair, Michele Ceccarelli, John D. Heiss, Ashish H. Shah

“…To date, numerous clinical trials have been developed to target the proteome and epigenome of high-grade gliomas with promising results. …”
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MGMIN: A Normalization Method for Correcting Probe Design Bias in Illumina Infinium HumanMethylation450 BeadChips by Zhenxing Wang, Yongzhuang Liu, Yadong Wang

“…The Illumina Infinium HumanMethylation450 Beadchips have been widely utilized in epigenome-wide association studies (EWAS). However, the existing two types of probes (type I and type II), with the distribution of measurements of probes and dynamic range different, may bias downstream analyses. …”
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Changes in the Coding and Non-coding Transcriptome and DNA Methylome that Define the Schwann Cell Repair Phenotype after Nerve Injury by Peter J. Arthur-Farraj, Claire C. Morgan, Martyna Adamowicz, Jose A. Gomez-Sanchez, Shaline V. Fazal, Anthony Beucher, Bonnie Razzaghi, Rhona Mirsky, Kristjan R. Jessen, Timothy J. Aitman

“…Surprisingly, unlike during development, changes in CpG methylation are limited in injury, restricted to specific locations, such as enhancer regions of Schwann cell-specific genes (e.g., Nedd4l), and close to local enrichment of AP-1 motifs. These genetic and epigenomic changes broaden our mechanistic understanding of the formation of repair Schwann cell during peripheral nervous system tissue repair.…”
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Lactic acid induces transcriptional repression of macrophage inflammatory response via histone acetylation by Weiwei Shi, Tiffany J. Cassmann, Aditya Vijay Bhagwate, Taro Hitosugi, W.K. Eddie Ip

“…In the present study, we examined how lactic acid integrates cellular metabolism to shape the epigenome of macrophages during pro-inflammatory response. …”
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Insights from the Applications of Single-Cell Transcriptomic Analysis in Germ Cell Development and Reproductive Medicine by Hyeonwoo La, Hyunjin Yoo, Eun Joo Lee, Nguyen Xuan Thang, Hee Jin Choi, Jeongheon Oh, Ji Hyun Park, Kwonho Hong

“…Conventional genome-scale approaches cannot delineate the landscape of genomic, transcriptomic, and epigenomic diversity or heterogeneity in the differentiating germ cells of gonads. …”
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Activation of Lineage Regulators and Transposable Elements across a Pluripotent Spectrum by Jamie A. Hackett, Toshihiro Kobayashi, Sabine Dietmann, M. Azim Surani

“…Thus, extrinsic cues establish a spectrum of pluripotent states, in part by modulating sub-populations, as well as directing the transcriptome, epigenome, and TE.…”
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Molecular Landscapes and Models of Acute Erythroleukemia by Alexandre Fagnan, Maria-Riera Piqué-Borràs, Samantha Tauchmann, Thomas Mercher, Juerg Schwaller

“…More recently, genetic roadmaps have fueled efforts to establish models that are based on the epigenomic lesions observed in patients with erythroid malignancies. …”
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Mechanism and Therapeutic Opportunities of Histone Modifications in Chronic Liver Disease by Qiuyu Cai, Qiuyu Cai, Can Gan, Can Gan, Chengwei Tang, Chengwei Tang, Hao Wu, Jinhang Gao, Jinhang Gao

“…Chronic liver disease (CLD) represents a global health problem, accounting for the heavy burden of disability and increased health care utilization. Epigenome alterations play an important role in the occurrence and progression of CLD. …”
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Large-Scale “OMICS” Studies to Explore the Physiopatholgy of HIV-1 Infection by Sigrid Le Clerc, Sophie Limou, Sophie Limou, Sophie Limou, Jean-François Zagury

“…These “omics” studies are based on several technologies including genotyping, RNA interference, and transcriptome or epigenome analysis. Due to the direct connection with disease evolution, there has been a large focus on genotyping cohorts of well-characterized patients through genome-wide association studies (GWASs), but there have also been several invitro studies such as small interfering RNA (siRNA) interference or transcriptome analyses of HIV-1–infected cells. …”
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Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium. by Reo Maruyama, Sibgat Choudhury, Adam Kowalczyk, Marina Bessarabova, Bryan Beresford-Smith, Thomas Conway, Antony Kaspi, Zhenhua Wu, Tatiana Nikolskaya, Vanessa F Merino, Pang-Kuo Lo, X Shirley Liu, Yuri Nikolsky, Saraswati Sukumar, Izhak Haviv, Kornelia Polyak

“…The technologies we developed and the epigenetically regulated genes we identified will accelerate the characterization of primary cell epigenomes and the dissection of human mammary epithelial lineage-commitment and luminal differentiation.…”
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HOTAIR interacts with PRC2 complex regulating the regional preadipocyte transcriptome and human fat distribution by Feng-Chih Kuo, Matt J. Neville, Rugivan Sabaratnam, Agata Wesolowska-Andersen, Daniel Phillips, Laura B.L. Wittemans, Andrea D. van Dam, Nellie Y. Loh, Marijana Todorčević, Nathan Denton, Katherine A. Kentistou, Peter K. Joshi, Constantinos Christodoulides, Claudia Langenberg, Philippe Collas, Fredrik Karpe, Katherine E. Pinnick

“…These data identify HOTAIR as a dynamic regulator of the gluteal adipocyte transcriptome and epigenome with functional importance for human regional AT development.…”
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Gene Editing by Extracellular Vesicles by Dmitry Kostyushev, Anastasiya Kostyusheva, Sergey Brezgin, Valery Smirnov, Elena Volchkova, Alexander Lukashev, Vladimir Chulanov

“…Many different systems with new properties have been characterized and a plethora of hybrid CRISPR/Cas systems able to modify the epigenome, regulate transcription, and correct mutations in DNA and RNA have been devised. …”
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