Epigenetic regulation of the nuclear genome associated with mitochondrial dysfunction in Leber’s hereditary optic neuropathy (LHON) by Aswathy P. Nair, Ambika Selvakumar, Janani Gopalarethinam, B. Abishek Kumar, Balachandar Vellingiri, Mohana Devi Subramaniam

“…We isolated peripheral blood mononuclear cells (PBMCs) from LHON patients and healthy individuals and examined epigenetic modifications in ND4 mutant cells and control cells. Chromatin immunoprecipitation-qRT PCR (ChIP-qRT PCR) assays were performed to investigate the modifications of histones. …”
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12,13-diHOME Promotes Inflammatory Macrophages and Epigenetically Modifies Their Capacity to Respond to Microbes and Allergens by Din L. Lin, Kevin M. Magnaye, Cara E. Porsche, Sophia R. Levan, Elze Rackaityte, Mustafa Özçam, Susan V. Lynch

“…Exposure to 12,13-diHOME also induces macrophage chromatin remodeling, specifically diminishing access to interferon-stimulated response elements resulting in reduced interferon-regulated gene expression upon bacterial lipopolysaccharide stimulation. …”
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Clinical Factors Associated with Sperm DNA Fragmentation in Male Patients with Infertility by Akira Komiya, Tomonori Kato, Yoko Kawauchi, Akihiko Watanabe, Hideki Fuse

“…The SDF was evaluated using the sperm chromatin dispersion test (SCDt) to determine the SDF index (SDFI). …”
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The SIX1/LDHA Axis Promotes Lactate Accumulation and Leads to NK Cell Dysfunction in Pancreatic Cancer by Wanli Ge, Lingdong Meng, Shouji Cao, Chaoqun Hou, Xiaole Zhu, Dongya Huang, Qiang Li, Yunpeng Peng, Kuirong Jiang

“…PC cells and NK cells were cocultured to study the effect of SIX1 overexpression in PC cells on NK cell function. Chromatin immunoprecipitation (ChIP) assays were used to study the relationship between SIX1 and lactate dehydrogenase A (LDHA). …”
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Novel Pathogenic Variant in TGFBR2 Confirmed by Molecular Modeling Is a Rare Cause of Loeys-Dietz Syndrome by Michael T. Zimmermann, Raul A. Urrutia, Patrick R. Blackburn, Margot A. Cousin, Nicole J. Boczek, Eric W. Klee, Colleen Macmurdo, Paldeep S. Atwal

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Significance of Apoptosis in the Process of Tumorigenesis in Colorectal Mucosa and Adenomas in FAP Patients by Hildegard Weiß, Karl‐Heinz Jacobasch, Wolfgang Haensch, Brigitte Streller, Brigitte Hieke

“…In addition, transcriptional capacity was determined by chromatin in situ testing. For both, DNA flow cytometry was used. …”
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Identification of Genes Regulating Gene Targeting by a High-Throughput Screening Approach by Fabien Delacôte, Christophe Perez, Valérie Guyot, Catherine Mikonio, Pierrick Potrel, Jean-Pierre Cabaniols, Christophe Delenda, Frédéric Pâques, Philippe Duchateau

“…We showed that siRNAs directed against the ATF7IP gene, encoding a protein involved in chromatin remodeling, stimulated HGT by a factor of three to eight, at various loci and in different cell types. …”
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Reconstruction of gene regulatory networks from single cell transcriptomic data by M. A. Rybakov, N. A. Omelyanchuk, E. V. Zemlyanskaya

“…We pay specific attention to state-of-the-art methods for GRN reconstruction from single-cell transcriptomes recruiting other omics data, primarily transcription factor binding sites and open chromatin profiles (scATAC-seq), in order to increase inference accuracy. …”
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Phosphorylation of histone H3Ser10 in plant cell division by D. B. Loginova, O. G. Silkova

“…Histones, the major protein components of chromatin, undergo post-translational modifications, which particularly affect the structural and functional organization of chromosomes. …”
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Transcription Factor FXR Activates DHRS9 to Inhibit the Cell Oxidative Phosphorylation and Suppress Colon Cancer Progression by Jinlai Zhao, Yigang Wang, Yang Wang, Jianchao Gao, Haichao Yang, Xiaotang Wu, Hua Li

“…The binding relationship between FXR and its downstream gene dehydrogenase/reductase member 9 (DHRS9) was verified through luciferase reporter assay and chromatin immunoprecipitation assay. The changes of oxidative phosphorylation were detected by Western blot and oxygen consumption rate determination. …”
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Replication-IDentifier links epigenetic and metabolic pathways to the replication stress response by Sophie C. van der Horst, Leonie Kollenstart, Amandine Batté, Sander Keizer, Kees Vreeken, Praveen Pandey, Andrei Chabes, Haico van Attikum

“…During Repli-ID, the replicative polymerase epsilon (Pol ε) is tracked at a barcoded origin of replication by chromatin immunoprecipitation (ChIP) coupled to next-generation sequencing of the barcode in thousands of hydroxyurea-treated yeast mutants. …”
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Multi-Omics Insights into Regulatory Mechanisms Underlying Differential Deposition of Intramuscular and Abdominal Fat in Chickens by Yuxin Xing, Chenglin Ma, Hongbo Guan, Jianing Shen, Ying Shen, Guoxi Li, Guirong Sun, Yadong Tian, Xiangtao Kang, Xiaojun Liu, Hong Li, Weihua Tian

“…This review systematically summarizes the regulatory mechanisms underlying intramuscular and abdominal fat traits at chromatin, genomic, transcriptional, post-transcriptional, translational, and epigenetic-modification scales. …”
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Genome-Wide Expression of MicroRNAs Is Regulated by DNA Methylation in Hepatocarcinogenesis by Jing Shen, Shuang Wang, Abby B. Siegel, Helen Remotti, Qiao Wang, Iryna Sirosh, Regina M. Santella

“…Six miRNAs were validated in 56 additional paired HCC tissues, and significant inverse correlations were observed for miR-125b and miR-199a, which is consistent with the inactive chromatin pattern found in HepG2 cells. Conclusion. …”
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Senescence-Associated Molecular and Epigenetic Alterations in Mesenchymal Stem Cell Cultures from Amniotic Fluid of Normal and Fetus-Affected Pregnancy by Jūratė Savickienė, Sandra Baronaitė, Aistė Zentelytė, Gražina Treigytė, Rūta Navakauskienė

“…These differences correlated with changes in the level of chromatin modifiers (DNMT1 and HDAC1) and polycomb group proteins (EZH2, SUZ12, and BMI1) paralleling with changes in the expression of repressive histone marks (H3K9me3 and H3K27me3) and stemness markers (Oct4, Nanog, Sox2, and Rex1). …”
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Characterizing the regulatory effects of H2A.Z and SWR1-C on gene expression during hydroxyurea exposure in Saccharomyces cerevisiae. by Hilary T Brewis, Peter C Stirling, Michael S Kobor

“…Chromatin structure and DNA accessibility are partly modulated by the incorporation of histone variants. …”
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Epigenetic Induction of Definitive and Pancreatic Endoderm Cell Fate in Human Fibroblasts by Rangarajan Sambathkumar, Eric Kalo, Rob Van Rossom, Marijke M. Faas, Paul de Vos, Catherine M. Verfaillie

“…We demonstrated that histone deacetylase inhibitor (HDACi) Trichostatin A (TSA) combined with a chromatin remodeling medium (CRM) induced expression of a number of definitive endoderm and early and late pancreatic marker genes. …”
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R-loops acted on by RNase H1 influence DNA replication timing and genome stability in Leishmania by Jeziel D. Damasceno, Emma M. Briggs, Marija Krasilnikova, Catarina A. Marques, Craig Lapsley, Richard McCulloch

“…Furthermore, we demonstrate that such differential organisation of R-loops, RNase H1 and DNA replication timing across the parasite’s chromosomes correlates with size-dependent differences in chromatin accessibility, G quadruplex distribution and sequence content. …”
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Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells by Szabolcs Éliás, Angelika Schmidt, David Gomez-Cabrero, Jesper Tegnér

“…As a result, we provide a rich resource of integrated chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) data from these primary human CD4 T cell subsets and we show that the identified signatures are associated with human autoimmune diseases, especially multiple sclerosis. …”
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HIF-3α-Induced miR-630 Expression Promotes Cancer Hallmarks in Cervical Cancer Cells by Forming a Positive Feedback Loop by Qiaohui Gao, Zhenghua Ren, Shengyuan Jiao, Juan Guo, Xia Miao, Jin Wang, Junye Liu

“…We conducted RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) experiments to investigate the targets of HIF-3α or miR-630. …”
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Transcriptional Regulation of Fucosyltransferase 1 Gene Expression in Colon Cancer Cells by Fumiko Taniuchi, Koji Higai, Tomomi Tanaka, Yutaro Azuma, Kojiro Matsumoto

“…Furthermore, transfection of the dominant negative Elk-1 gene, and the chromatin immunoprecipitation (CHIp) assay, supported Elk-1-dependent transcriptional regulation of FUT1 gene expression in DLD-1 cells. …”
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