Article
Immunology
Qi An, Chenyan Sun, Ruidi Li, Shuhui Chen, Xinpei Gu, Shuhong An, Zhaojin Wang
Summary: The study reveals that CGRP is involved in the pathogenesis of neuropathic pain by regulating microglial activation through EZH2-mediated H3K27me3 in the spinal dorsal horn. The findings demonstrate that CGRP treatment and chronic constriction injury lead to increased expressions of key mediators of microglial activation in the spinal dorsal horn and cultured microglial cells.
JOURNAL OF NEUROINFLAMMATION
(2021)
Article
Biochemistry & Molecular Biology
Shuhui Chen, Xinpei Gu, Ruidi Li, Shuhong An, Zhaojin Wang
Summary: In this study, the authors used chromatin immunoprecipitation sequencing (ChIP-seq) to investigate the alteration of H3K27me3 in the development of neuropathic pain. They found that chronic constriction injury (CCI) increased the enrichment of H3K27me3 in the sciatic nerve of rats and identified key genes involved in neuropathic pain. Further analysis revealed that these modified genes were associated with cellular processes and pathways related to neuropathic pain. Importantly, the authors demonstrated that inhibition of EZH2, the enzyme responsible for H3K27me3, reversed the pain-related changes and relieved behavioral symptoms in CCI rats.
NEUROCHEMICAL RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Veronica Uribe-Etxebarria, Jose Ramon Pineda, Patricia Garcia-Gallastegi, Alice Agliano, Fernando Unda, Gaskon Ibarretxe
Summary: The dental pulp of permanent human teeth contains stem cells known as Dental Pulp Stem Cells (DPSCs), which have the ability to differentiate into multiple cell lineages. The pluripotency core factors expressed by these cells, as well as the involvement of signaling pathways like Notch and Wnt, contribute to their stemness maintenance. Utilizing recombinant proteins, pharmacological modulators, serum-free media, and appropriate scaffolds, researchers can optimize the potency of DPSCs without genetic modification. This review highlights the mechanisms and regulatory pathways responsible for maintaining stemness in DPSCs, drawing interesting parallels with pluripotent stem cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yuan Fang, Yin Tang, Yanjun Zhang, Yixin Pan, Junqi Jia, Zhongxing Sun, Weiwu Zeng, Jiaqi Chen, Ying Yuan, Dong Fang
Summary: Epigenetics, especially histone marks, plays a crucial role in regulating gene expression beyond DNA sequences. NSD1 depletion leads to both up- and down-regulation of gene expression, with an increase in H3K27ac correlating with the decrease of H3K36me2. NSD1 acts as a 'safeguard' by depositing H3K36me2 and recruiting HDAC1 at active enhancers to prevent further activation of active enhancer-associated genes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Liangbing Yuan, Xin Song, Lu Zhang, Yaoguang Yu, Zhenwei Liang, Yawen Lei, Jiuxiao Ruan, Bin Tan, Jun Liu, Chenlong Li
Summary: The study reveals that the transcriptional repressors VAL1 and VAL2 recruit PRC2 to target loci in Arabidopsis thaliana. They physically interact with PRC2 catalytic subunits SWN and CLF, colocalize at target loci, and regulate H3K27me3 levels, affecting transcription.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
John R. Horton, Jujun Zhou, Qin Chen, Xing Zhang, Mark T. Bedford, Xiaodong Cheng
Summary: The N-terminal half of PHF2 contains a PHD and a Jumonji domain, which can recognize H3 trimethylated at lysine 4 and VRK1. The Jumonji domain can erase dimethylation mark from H3K9me2 at select promoters. The N-terminal half of PHF2 binds to H3 and VRK1 peptides containing K4me3 with higher affinities than the isolated PHD domain.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Dermatology
Shu-Hao Li, Chien-Chun Chiou, Chien-Chin Chen
Summary: This study investigated the expression of histone H3 trimethylation at lysine 27 (H3K27me3) in primary cutaneous mucinous carcinoma (PCMC) using immunohistochemistry. The results showed a loss of H3K27me3 expression in PCMC cells, indicating its potential role in the pathogenesis of PCMC.
DERMATOLOGICA SINICA
(2023)
Article
Parasitology
Ruolin Lin, Xiaopeng Wang, Caiya Ni, Chunxue Fu, Chun Yang, Dan Dong, Xiangwei Wu, Xueling Chen, Lianghai Wang, Jun Hou
Summary: Our study reveals that EgCF inhibits the expression of KDM6B and H3K27me3 demethylation, leading to the transcriptional inhibition of NLRP3 and IL-1 beta. These findings provide new insights into the immune evasion mechanisms of E. granulosus.
PARASITES & VECTORS
(2023)
Article
Plant Sciences
Hasan Mehraj, Satoshi Takahashi, Naomi Miyaji, Ayasha Akter, Yutaka Suzuki, Motoaki Seki, Elizabeth S. Dennis, Ryo Fujimoto
Summary: Covalent modifications of histone proteins, such as H3K4me3 and H3K36me3, are found to regulate gene expression in Brassica rapa L. Two lines of this species showed enrichment of these histone marks at transcription start sites, with gene expression levels being influenced by them. Genes with both H3K4me3 and H3K36me3 typically showed constitutive high expression levels. Additionally, bivalent active and repressive histone modifications were observed in some genes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Medicinal
Isabelle A. Engelberg, Jiuyang Liu, Jacqueline L. Norris-Drouin, Stephanie H. Cholensky, Samantha A. Ottavi, Stephen Frye, Tatiana G. Kutateladze, Lindsey James
Summary: PHF1, an accessory component of polycomb repressive complex 2, recognizes the active chromatin mark H3K36me3 for transcriptional regulation. UNC6641 is a peptidomimetic antagonist of PHF1 Tudor domain, capable of binding both PHF1 and PHF19 with high potency, providing insights into the binding mechanism through crystal structure and other data. Additionally, UNC6641 facilitates the development of a high-throughput assay for identifying small molecule binders of PHF1.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biology
Madeline M. Keenen, David Brown, Lucy D. Brennan, Roman Renger, Harrison Khoo, Christopher R. Carlson, Bo Huang, Stephan W. Grill, Geeta J. Narlikar, Sy Redding
Summary: Studies have found that HP1 proteins form liquid phase-separated droplets, with HP1α exhibiting dynamic liquid characteristics, while DNA molecules are constrained within local territories. These condensates are resistant but can be dissolved by HP1β, and the differences in properties among HP1 paralogs arise from their respective disordered regions.
Review
Plant Sciences
Huihui Fang, Yuke Shao, Gang Wu
Summary: This review discusses the reprogramming of histone H3 methylation during plant sexual reproduction, highlighting its importance in cell specification and establishment of pluripotency. Despite advancements in understanding this process, challenges remain in this area and future breakthroughs in cell-specific epigenomic profiling are expected to provide a solution.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Developmental Biology
Junghyun Kim, Yogendra Bordiya, Yanpeng Xi, Bo Zhao, Dong-Hwan Kim, Youngjae Pyo, Wei Zong, William A. Ricci, Sibum Sung
Summary: Changes in ambient temperature greatly affect developmental programs in many species. Plants adapt to high ambient growth temperature through the involvement of VIL1, which leads to genome-wide accumulation of H3K27me3. VIL1 is necessary for thermo-morphogenesis and loss of function results in hypo-responsiveness to warm ambient temperature.
Article
Biochemistry & Molecular Biology
Masaki Kikuchi, Satoshi Morita, Mie Goto, Masatoshi Wakamori, Kazushige Katsura, Kazuharu Hanada, Mikako Shirouzu, Takashi Umehara
Summary: In this study, the researchers established a nucleosome core particle (NCP) array containing histones with specific acetylated residues and compared the Kac-binding preferences of human YEATS domains. They found that the Kac-binding affinity of AF9-YEATS increased with the number of acetylated residues in the histone tail.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Masaki Kikuchi, Satoshi Morita, Mie Goto, Masatoshi Wakamori, Kazushige Katsura, Kazuharu Hanada, Mikako Shirouzu, Takashi Umehara
Summary: In this study, AF9-YEATS was found to have differential binding preferences for specific Kac positions and multiple Kac in histone H3. Crystal structures revealed that the aromatic cage of AF9-YEATS recognized the acetylated K8 residue, while E57 and D103 outside of the aromatic cage interacted with acetylated K5 and K12. Additionally, mutating E57 to alanine reduced the binding affinity of AF9-YEATS for multiacetylated H4.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Genetics & Heredity
Na Chen, Sen Zhao, Angad Jolly, Lianlei Wang, Hongxin Pan, Jian Yuan, Shaoke Chen, Andre Koch, Congcong Ma, Weijie Tian, Ziqi Jia, Jia Kang, Lina Zhao, Chenglu Qin, Xin Fan, Katharina Rall, Zeynep Coban-Akdemir, Zefu Chen, Shalini Jhangiani, Ze Liang, Yuchen Niu, Xiaoxin Li, Zihui Yan, Yong Wu, Shuangshuang Dong, Chengcheng Song, Guixing Qiu, Shuyang Zhang, Pengfei Liu, Jennifer E. Posey, Feng Zhang, Guangnan Luo, Zhihong Wu, Jianzhong Su, Jianguo Zhang, Eugenia Y. Chen, Konstantinos Rouskas, Stavros Glentis, Flora Bacopoulou, Efthymios Deligeoroglou, George Chrousos, Stanislas Lyonnet, Michel Polak, Carla Rosenberg, Irene Dingeldein, Ximena Bonilla, Christelle Borel, Richard A. Gibbs, Jennifer E. Dietrich, Antigone S. Dimas, Stylianos E. Antonarakis, Sara Y. Brucker, James R. Lupski, Nan Wu, Lan Zhu
Summary: This study identified 12 likely gene-disrupting variants in 7 genes that are essential for Mullerian/Wolffian ducts development in individuals with MRKHS, and these variants were not found in control samples. Interestingly, there was a sex-limited penetrance with paternal inheritance in multiple families. Furthermore, a syndromic condition characterized by congenital hypothyroidism and MRKHS was identified in one individual from a PAX8-associated cohort.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Biochemical Research Methods
Ping Hou, Siqi Bao, Dandan Fan, Congcong Yan, Jianzhong Su, Jia Qu, Meng Zhou
Summary: The study identified 40 methylation-driven prognostic genes associated with the tumorigenesis and progression of uveal melanoma, and proposed a 10-gene DNA methylation-driven signature (10MeSig) for predicting patients' survival risk. The 10MeSig was validated in an independent cohort and shown to have similar prognostic value. It was found to be an independent predictive factor for the survival of uveal melanoma patients, improving clinical decisions and providing new insights into the pathogenesis of the disease.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Bo Ye, Dandan Fan, Weiwei Xiong, Min Li, Jian Yuan, Qi Jiang, Yuting Zhao, Jianxiang Lin, Jie Liu, Yilv Lv, Xiongjun Wang, Zhigang Li, Jianzhong Su, Yunbo Qiao
Summary: The study identified numerous gained or lost enhancers in ESCC and LNC, contributing to transcriptomic aberrations and revealing putative driver onco-transcription factors. Inhibitors targeting the gained super-enhancers predicted HSP90AA1 and PDE4B as potential therapeutic targets for ESCC. Epigenomic profiling provides insights into reprogrammed cis-regulatory elements during ESCC carcinogenesis and metastasis, offering promising targets for cancer treatment.
NATURE COMMUNICATIONS
(2021)
Correction
Genetics & Heredity
Jian Yuan, Qi Jiang, Tongyang Gong, Dandan Fan, Ji Zhang, Fukun Chen, Xiaolin Zhu, Xinyu Wang, Yunbo Qiao, Hongyan Chen, Zhihua Liu, Jianzhong Su
NPJ GENOMIC MEDICINE
(2021)
Article
Ophthalmology
Liangde Xu, Youyuan Zhuang, Guosi Zhang, Yunlong Ma, Jian Yuan, Changseng Tu, MiaoMiao Li, Wencan Wang, Yaru Zhang, Xiaoyan Lu, Jing Li, Xinting Liu, Zhengbo Xue, Meng Zhou, Jie Sun, Jinhua Bao, Ming Li, Fan Lu, Hong Wang, Jianzhong Su, Jia Qu
Summary: The CAMS project successfully conducted a myopia survey on a million children and adolescents in Wenzhou, China, revealing high rates of myopia and high myopia among elementary, middle, and high school students. The project utilized an efficient screening model and demonstrated significant reductions in staff, cost, and time compared with previous surveys. The findings provide valuable insights for public health intervention and myopia prevention.
Article
Medicine, General & Internal
Zhengbo Xue, Jian Yuan, Fukun Chen, Yinghao Yao, Shilai Xing, Xiangyi Yu, Kai Li, Chenxiao Wang, Jinhua Bao, Jia Qu, Jianzhong Su, Hao Chen
Summary: This study aimed to investigate the shared genetic etiology among age-related macular degeneration (AMD), diabetic retinopathy (DR), glaucoma, retinal detachment (RD), and myopia. The analysis of genome-wide association identified meaningful genetic correlations between these ocular diseases. Cross-trait meta-analysis revealed 23 shared loci associated with at least two ocular diseases and 14 loci unique to individual disorders.
Article
Oncology
Xue Qing David Wang, Dandan Fan, Qinyu Han, Yiman Liu, Hongzhi Miao, Xinyu Wang, Qinglan Li, Dong Chen, Haley Gore, Pamela Himadewi, Gerd P. Pfeifer, Tomasz Cierpicki, Jolanta Grembecka, Jianzhong Su, Shasha Chong, Liling Wan, Xiaotian Zhang
Summary: Nucleophosmin (NPM1) is a nucleolar protein with various functions, and its mutation is commonly found in acute myeloid leukemia (AML). This study shows that mutant NPM1 directly binds to active chromatin regions and controls the transcription of AML-driving genes. These findings provide insights into the mechanism behind AML caused by NPM1 mutation and suggest potential therapeutic interventions.
Article
Genetics & Heredity
Jian Yuan, Fukun Chen, Dandan Fan, Qi Jiang, Zhengbo Xue, Ji Zhang, Xiangyi Yu, Kai Li, Jia Qu, Jianzhong Su
Summary: Eye diseases are common and diverse, with omics technology providing large datasets, but efficient analysis is lacking. The EyeDiseases database integrates multi-omics data of human eye diseases, revealing genes associated with SARS-CoV-2 infection and AMD.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Article
Ophthalmology
Jian Yuan, Dandan Fan, Zhengbo Xue, Jia Qu, Jianzhong Su
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2020)