Review
Cell Biology
Chao Wan, Fengjie Zhang, Hanyu Yao, Haitao Li, Rocky S. Tuan
Summary: Histone modifications play a significant role in cartilage development, pathology, and regeneration. Targeting histone modifying proteins with candidate molecules or drugs shows promising therapeutic potential in treating cartilage lesions associated with joint degeneration.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Fabrizio Frasca, Matteo Matteucci, Michele Leone, Marco J. Morelli, Marco Masseroli
Summary: This study proposes a novel computational pipeline for accurately and interpretable modeling of gene transcriptional regulation through HM. By extracting insightful gene-specific regulative patterns and comparing with ChromHMM, the method has shown advantages in predicting gene transcriptional states.
BMC BIOINFORMATICS
(2022)
Article
Plant Sciences
Mohammad Reza Atighi, Bruno Verstraeten, Tim De Meyer, Tina Kyndt
Summary: Epigenetic processes, particularly histone modifications, play a crucial role in plant-nematode interactions, with a specific focus on H3K9 targeting plant defence-related genes.
MOLECULAR PLANT PATHOLOGY
(2021)
Article
Biochemical Research Methods
Rania Hamdy, Fahima A. Maghraby, Yasser M. K. Omar
Summary: This paper focuses on the histone modification mechanism in gene regulation and proposes the ConvChrome deep learning methodology for predicting gene expression behavior from histone modifications data. The results show significant improvement in gene expression classification prediction task.
CURRENT BIOINFORMATICS
(2022)
Review
Plant Sciences
Rocio Nunez-Vazquez, Benedicte Desvoyes, Crisanto Gutierrez
Summary: Plants have developed various mechanisms to adapt to abiotic stresses, which involve transcriptional regulation and chromatin modifications. Understanding and manipulating these regulatory networks are crucial for enhancing crop resilience and performance against stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Arijita Sarkar, Nancy Q. Q. Liu, Jenny Magallanes, Jade Tassey, Siyoung Lee, Ruzanna Shkhyan, Youngjoo Lee, Jinxiu Lu, Yuxin Ouyang, Hanhan Tang, Fangzhou Bian, Litao Tao, Neil Segil, Jason Ernst, Karen Lyons, Steve Horvath, Denis Evseenko
Summary: This study establishes an epigenetic clock based on DNA methylation profiling of human chondrocytes and reveals an association between CpG methylation and chondrocyte age. It also demonstrates the role of STAT3 in regulating DNA methylation in chondrocyte development and osteoarthritis. Furthermore, functional assessment shows that a subset of chondrocytes acquire a progenitor-like phenotype.
Review
Biochemistry & Molecular Biology
Yulei Shi, Wei Qi
Summary: Nonalcoholic fatty liver disease (NAFLD) is a progressive liver condition associated with high energy-density diets and sedentary lifestyles. It is closely linked to metabolic disorders like obesity and hyperlipidemia. The epigenetic regulation, particularly histone modifications, plays a crucial role in the initiation and progression of NAFLD, offering potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Qingyun Yang, Yingxiao Gao, Xia Liu, Yihang Xiao, Mingxuan Wu
Summary: A new method for editing the N-tail of histone H3 using sortase mediated metathesis (SMM) is reported. This method expands the application scope of sortase and offers a strategy for precise editing of PTMs of cellular histone H3.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Plant Sciences
Meng Ma, Wenying Zhong, Qing Zhang, Li Deng, Jing Wen, Bin Yi, Jinxing Tu, Tingdong Fu, Lun Zhao, Jinxiong Shen
Summary: This study compared the epigenome and transcriptome data of a hybrid and its parental lines in different tissues to explore their contribution to heterosis in allopolyploid B. napus. The study found that a small proportion of non-additive genes in the hybrid, as well as parental expression level dominance, had a significant effect on heterosis. Histone modification variations were observed between the parents and hybrid, with H3K4me3 variations positively correlated with gene expression differences. These findings provide valuable insights into the understanding of heterosis in allopolyploid crops.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Zihang Huang, Shuai Song, Xiaokai Zhang, Linqi Zeng, Aijun Sun, Junbo Ge
Summary: This review summarizes the impact of cardiac metabolism disorder on histone modifications and gene expression, as well as the dual role of metabolic substrates in regulating cardiac hypertrophy. The article suggests the therapeutic supplementation of metabolic substrates as a potential approach to restore histone modifications.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2023)
Article
Cell Biology
Yoshitaka Kubota, Hidekazu Nagano, Kentaro Kosaka, Hideyuki Ogata, Akitoshi Nakayama, Masataka Yokoyama, Kazutaka Murata, Shinsuke Akita, Motone Kuriyama, Nobutaka Furuyama, Masayuki Kuroda, Tomoaki Tanaka, Nobuyuki Mitsukawa
Summary: Ceiling culture-derived preadipocytes (ccdPAs) and adipose-derived stem cells (ASCs) were isolated from human subcutaneous fat tissue and showed differences in adipogenic potential due to variations in methylation and histone modification levels of adipogenesis-related genes, such as PPARc, fatty acid-binding protein 4, and leptin. Genomewide epigenetic analysis revealed distinct patterns in CpG methylation and H3K4me3 modification between ccdPAs and ASCs, suggesting epigenetic mechanisms underlying adipogenic differentiation capabilities of these cell types.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shang-Kun Dai, Ruo-Bing Hao, Fei Shen
Summary: This study systematically investigated the role of histone lysine crotonylation (Kcr) in neural differentiation and found its association with neural fate specification. The study also revealed the collaborative role of H3K9cr and H3K9ac in regulating gene expression changes.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
S. Pranav Adithya, K. Balagangadharan, N. Selvamurugan
Summary: In bone biology, epigenetics and histone modifications play a crucial role in the commitment and differentiation of mesenchymal stem cells towards osteoblasts. Understanding the importance of histone modifications in osteogenesis can lead to the development of epigenetic-based therapies for genetic bone disorders. This review highlights the significance of epigenetic modifications, including post-translational modifications of histones, in regulating gene expression during osteoblast differentiation and discusses future advancements in the field of epigenetics for orthopaedic therapeutics.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Biochemistry & Molecular Biology
Carmen Nunez-Carro, Margarita Blanco-Blanco, Tatiana Montoya, Karla M. Villagran-Andrade, Tamara Hermida-Gomez, Francisco J. Blanco, Maria C. de Andres
Summary: Osteoarthritis is a chronic disease that affects articular cartilage and leads to its degeneration. Recent research has shown the importance of the interplay between inflammatory processes and epigenetic regulation in the development of osteoarthritis. However, the lack of specific protocols to extract histones from human articular cartilage has hindered further investigation in this area.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Irina Bure, Marina Nemtsova, Ekaterina B. Kuznetsova
Summary: In recent years, scientists have increasingly suggested and confirmed that epigenetic regulators are closely linked and form a comprehensive network of regulatory pathways and feedback loops. This is particularly important for a better understanding of the development and progression of various diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)