SAHA inhibits lung fibroblast activation by increasing p66Shc expression epigenetically by Yiheng Dong, Jieting Peng, Xiangyu Zhang, Qiong Wang, Xing Lyu

“…However, silencing of p66Shc significantly reversed the aforementioned effects of SAHA on MRC‐5 cells. Furthermore, chromatin immunoprecipitation (ChIP) assays demonstrated that SAHA enhanced active histone markers, H3K9Ac and H3K4Me3, in the p66Shc gene region. …”
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A cell atlas of the human fallopian tube throughout the menstrual cycle and menopause by Melanie Weigert, Yan Li, Lisha Zhu, Heather Eckart, Preety Bajwa, Rahul Krishnan, Sarah Ackroyd, Ricardo Lastra, Agnes Bilecz, Anindita Basu, Ernst Lengyel, Mengjie Chen

“…Postmenopausal fallopian tubes show high chromatin accessibility in transcription factors associated with aging such as Jun, Fos, and BACH1/2, while hormone receptors were generally downregulated, a small proportion of secretory epithelial cells had high expression of ESR2, IGF1R, and LEPR. …”
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Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq by Shintaro Funasaki, Yuri Miyamura, Shunsuke Kamei, Akhinur Rahman, Masaya Yamazaki, Shingo Usuki, Keiichiro Yasunaga, Yorifumi Satou, Hiroto Ohguchi, Takashi Minami

“…We then detail procedures for library preparation for single-cell RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq), and data analysis. …”
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PARP inhibition-associated heterochromatin confers increased DNA replication stress and vulnerability to ATR inhibition in SMARCA4-deficient cells by Kimiyoshi Yano, Megumi Kato, Syoju Endo, Taichi Igarashi, Ryoga Wada, Takashi Kohno, Astrid Zimmermann, Heike Dahmen, Frank T. Zenke, Bunsyo Shiotani

“…PARP inhibition triggers chromatin changes, namely elevated histone H3 at lysine 9 di-methylation (H3K9me2), a hallmark of facultative heterochromatin, increasing dependence on ATR activity for replication fork progression and cell survival. …”
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Hypermethylation at 45S rDNA promoter in cancers. by Trang Thi Quynh Tran, Trang Hien Do, Tung The Pham, Phương Thi Thu Luu, Oanh Minh Pham, Uyen Quynh Nguyen, Linh Dieu Vuong, Quang Ngoc Nguyen, Tuan Van Mai, Son Van Ho, Than Thi Nguyen, Lan Thi Thuong Vo

“…In cancer cells, upregulation of ribosome biogenesis has been recognized as a hallmark feature, thus, the reduced methylation of rDNA promoter has been thought to support conformational changes of chromatin accessibility and the subsequent increase in rDNA transcription. …”
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Structural basis of SIRT7 nucleosome engagement and substrate specificity by Carlos Moreno-Yruela, Babatunde E. Ekundayo, Polina N. Foteva, Dongchun Ni, Esther Calvino-Sanles, Henning Stahlberg, Beat Fierz

“…Abstract Chromatin-modifying enzymes target distinct residues within histones to finetune gene expression profiles. …”
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Thrombin Induces COX-2 and PGE2 Expression via PAR1/PKCalpha/MAPK-Dependent NF-kappaB Activation in Human Tracheal Smooth Muscle Cells by Chien-Chung Yang, Li-Der Hsiao, Ya-Fang Shih, Chih-Kai Hsu, Chia-Yu Hu, Chuen-Mao Yang

“…The role of NF-κB was assessed by a chromatin immunoprecipitation (ChIP) assay, immunofluorescent staining, as well as Western blot. …”
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Why is it so difficult to understand why we don’t understand human systemic lupus erythematosus? Contemplating facts, conflicts, and impact of “the causality cascade paradigm”... by Ole Petter Rekvig, Ole Petter Rekvig

“…Likewise, inconclusive dogmatic data indicate that different glomerular ligands are recognized by nephritogenic anti-dsDNA antibodies—exposed chromatin fragments or inherent membrane ligands. These incongruent models have not been comparatively and systematically investigated. …”
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Myogenesis gone awry: the role of developmental pathways in rhabdomyosarcoma by Annika L. Gustafson, Annika L. Gustafson, Annika L. Gustafson, Adam D. Durbin, Kristin B. Artinger, Heide L. Ford, Heide L. Ford, Heide L. Ford

“…In FP-RMS, the PAX3/7-FOXO1 chromosomal translocation results in restructured chromatin, altering the binding of many MRFs and driving an oncogenic state. …”
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MetArea: a software package for analysis of the mutually exclusive occurrence in pairs of motifs of transcription factor binding sites based on ChIP-seq data by V. G. Levitsky, A. V. Tsukanov, T. I. Merkulova

“…ChIP-seq technology, which is based on chromatin immunoprecipitation (ChIP), allows mapping a set of genomic loci (peaks) containing binding sites (BS) for the investigated (target) transcription factor (TF). …”
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The Kat in the HAT: The Histone Acetyl Transferase Kat6b (MYST4) Is Downregulated in Murine Macrophages in Response to LPS by Smita Shukla, Carly Levine, Roopa Payanur Sripathi, Genie Elson, Carol Susan Lutz, Samuel Joseph Leibovich

“…As Kat6B is a HAT that has the potential to modulate gene expression by its effects on chromatin accessibility, we are continuing our studies into the potential roles of this epigenetic modulator in macrophage activation pathways.…”
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Long non-coding RNA CAR10 promotes angiogenesis of lung adenocarcinoma by mediating nuclear LDHA to epigenetically regulate VEGFA/C by Xiaolu Ge, Chao Du, Li Fang, Wei Xu, Juanjuan Xiang, Jiheng Liu, Ming Zhou, Yuejun Chen, Ziyao Wang, Zheng Li

“…Here we show lncRNA chromatin-associated RNA 10 (CAR10) was upregulated in the tumor tissue of patients with LUAD and enhanced tumor metastasis. …”
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Romidepsin Promotes Osteogenic and Adipocytic Differentiation of Human Mesenchymal Stem Cells through Inhibition of Histondeacetylase Activity by Dalia Ali, Elna P. Chalisserry, Muthurangan Manikandan, Rimi Hamam, Musaad Alfayez, Moustapha Kassem, Abdullah Aldahmash, Nehad M. Alajez

“…Pharmacological inhibition of FAK signaling during adipogenesis or inhibition of FAK or TGFβ signaling during osteogenesis diminished the biological effects of romidepsin on BMSCs. The results of chromatin immunoprecipitation combined with quantitative polymerase chain reaction indicated a significant increase in H3K9Ac epigenetic markers in the promoter regions of peroxisome proliferator-activated receptor gamma (PPARγ) and KLF15 (related to adipogenesis) or SP7 (Osterix) and alkaline phosphatase (ALP) (related to osteogenesis) in romidepsin-treated BMSCs. …”
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Sorbitol Destroyed Intestinal Microfold Cells (M Cells) Development through Inhibition of PDE4-Mediated RANKL Expression by Li Xiang, Wenxu Pan, Huan Chen, Wenjun Du, Shuping Xie, Xinhua Liang, Fangying Yang, Rongwei Niu, Canxin Huang, Minan Luo, Yuxin Xu, Lanlan Geng, Sitang Gong, Wanfu Xu, Junhong Zhao

“…Real-time polymerase chain reaction, immunofluorescence, and western blotting were performed to analyze the effect of sorbitol-regulated M-cell differentiation in vivo and in vitro, and luciferase and chromatin Immunoprecipitation were used to reveal the mechanism through which sorbitol-modulated M-cell differentiation. …”
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Activation of PAR4 Upregulates p16 through Inhibition of DNMT1 and HDAC2 Expression via MAPK Signals in Esophageal Squamous Cell Carcinoma Cells by Ming Wang, Shuhong An, Diyi Wang, Haizhen Ji, Xingjing Guo, Zhaojin Wang

“…PAR4 activation could suppress DNMT1 and HDAC2, as well as increase p16 expressions, whereas silencing PAR4 dramatically increased HDAC2 and DNMT1, as well as reduced p16 expressions. Importantly, the chromatin immunoprecipitation-PCR (ChIP-PCR) data indicated that treatment of ESCC cells with PAR4-AP remarkably suppressed DNMT1 and HDAC2 enrichments on the p16 promoter. …”
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Mutational Analysis of Extranodal NK/T-Cell Lymphoma Using Targeted Sequencing with a Comprehensive Cancer Panel by Seungkyu Choi, Jai Hyang Go, Eun Kyung Kim, Hojung Lee, Won Mi Lee, Chun-Sung Cho, Kyudong Han

“…Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. …”
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YBX1 alleviates ferroptosis in osteoporosis via the ATF4/FSP1 axis in an m5C manner by Lei Tong, Yanbo Chen, Yan Gao, Xiaoming Gao, Yanming Hao

“…Ferroptosis suppressor protein 1 (FSP1), activating transcription factor 4 (ATF4), and Y-box binding protein 1 (YBX1) knockdown MC3T3-E1 cells were generated, and their effects on ferroptosis were verified by measuring lipid reactive oxygen species levels and cellular Fe2+. Chromatin immunoprecipitation and luciferase assays were performed to confirm the binding of ATF4 to the FSP1 promoter. …”
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ATRX loss inhibits DDR to strengthen radio-sensitization in p53-deficent HCT116 cells by Lijing Qin, Geng Tang, Ruirui Gui, Yanming Yang, Li Wang, Weiqiang Xu, Hongyuan Tian, Lei Yu, Xiangshan Yang, Zhicheng Wang

“…Alpha-thalassemia/mental retardation X-linked (ATRX), a member of the SWI/SNF-like chromatin remodeling protein family, functions in the maintenance of genomic integrity and the regulation of apoptosis and senescence. …”
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Hepatitis B virus hijacks MRE11-RAD50-NBS1 complex to form its minichromosome. by Kaitao Zhao, Jingjing Wang, Zichen Wang, Mengfei Wang, Chen Li, Zaichao Xu, Qiong Zhan, Fangteng Guo, Xiaoming Cheng, Yuchen Xia

“…Transiently or stably knockdown of MRE11, RAD50 or NBS1 in hepatocytes before HBV infection significantly decreased viral markers, including cccDNA, while reconstitution reversed the effect. Chromatin immunoprecipitation assay further validated the interaction of MRN complex and HBV DNA. …”
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Association of a non-synonymous substitution in the condensin NCAPG gene with traits of eggs in laying hens by O. Yu. Barkova, M. G. Smaragdov

“…The results obtained are discussed in connection with the role of the canonical condensin complex in the compaction of chromatin and segregation of chromosomes.…”
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