Article
Multidisciplinary Sciences
Zhaozhong Zhu, Yijun Li, Robert J. Freishtat, Juan C. Celedon, Janice A. Espinola, Brennan Harmon, Andrea Hahn, Carlos A. Camargo, Liming Liang, Kohei Hasegawa
Summary: This study investigates the role of DNA methylation in the severity of bronchiolitis in infants. The authors analyze blood DNA methylation data from hospitalized infants and identify differentially methylated CpGs associated with disease severity. These CpGs are found to be differentially methylated in blood immune cells and enriched in various tissues, cells, and pathways. Additionally, they are also associated with respiratory and immune traits. The study highlights the importance of DNA methylation in understanding the pathobiology of bronchiolitis and its severity.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Wubin Ding, Diljeet Kaur, Steve Horvath, Wanding Zhou
Summary: Researchers have developed informatics infrastructure and methods for DNA methylation analysis in multiple species, including domesticated animals and laboratory mice. They have created a data-driven analysis pipeline for species inference, genome-specific data preprocessing, and regression modeling. Comparative analysis has revealed the dynamics of epigenome evolution in different genomic territories and tissue types, and specific methylation differences related to mouse strain phenotypes have been identified. These methods expand epigenome research to a wide range of species by streamlining DNA methylation array analysis for undesigned genomes.
BRIEFINGS IN BIOINFORMATICS
(2023)
Editorial Material
Biology
Brandon L. Pierce
Summary: This article introduces a new approach that helps assess the impact of accelerated epigenetic aging on the risk of cancer.
Article
Biology
Junying Wang, Wen Zhang, Xiaoqin Liu, Minjee Kim, Ke Zhang, Robert Y. L. Tsai
Summary: This study identified differentially methylated genomic regions (DMRs) in mouse livers that are co-regulated by aging and regeneration using whole-genome bisulfite sequencing (WGBS). The DMRs showed opposite methylation direction changes between 2 and 8 months and 8 and 16 months. Inverse-regulated DMRs by aging and regeneration were found in the promoter/gene regions of 12 genes. These findings provide insights into the epigenomic changes underlying the biology of aging on liver regeneration.
Article
Biochemistry & Molecular Biology
Yalan Yang, Xinhao Fan, Junyu Yan, Muya Chen, Min Zhu, Yijie Tang, Siyuan Liu, Zhonglin Tang
Summary: The study generated the first single-base resolution DNA methylome and transcriptome maps of porcine skeletal muscle across 27 developmental stages. The results showed a decrease in overall methylation level from embryo to adult, and identified over 40,000 developmentally differentially methylated CpGs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Endocrinology & Metabolism
Amanda L. Morin, Phyo W. Win, Angela Z. Lin, Christina A. Castellani
Summary: Bidirectional crosstalk between the nuclear and mitochondrial genomes is crucial for cell functioning. Mitochondrial DNA copy number and heteroplasmy can influence mitochondrial function, nuclear genome, and contribute to overall health and disease. Mitochondria act as environmental biosensors, conveying essential information about cell state to the nuclear genome. Cellular communication between mitochondrial variation and nuclear epigenome can occur through modifications of metabolites and intermediates, affecting epigenetic modifications.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Review
Plant Sciences
Dolores Rita Agius, Aliki Kapazoglou, Evangelia Avramidou, Miroslav Baranek, Elena Carneros, Elena Caro, Stefano Castiglione, Angela Cicatelli, Aleksandra Radanovic, Jean-Paul Ebejer, Daniel Gackowski, Francesco Guarino, Andrea Gulyas, Norbert Hidvegi, Hans Hoenicka, Vera Inacio, Frank Johannes, Erna Karalija, Michal Lieberman-Lazarovich, Federico Martinelli, Stephane Maury, Velimir Mladenov, Leonor Morais-Cecilio, Ales Pecinka, Eleni Tani, Pilar S. Testillano, Dimitar Todorov, Luis Valledor, Valya Vassileva
Summary: Epigenetic modifications, particularly DNA methylation, play a crucial role in preserving genome integrity and regulating gene expression, impacting growth, development, and stress response in plants. Detecting DNA methylation marks is essential for understanding these processes and enhancing crop productivity and stress resistance. This review provides an overview of different methods for detecting plant DNA methylation and compares their efficacy between model and crop plants. It also highlights the strengths and limitations of each method and emphasizes the importance of considering technical and biological factors. Overall, this review will assist scientists in selecting an appropriate DNA methylation profiling method.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Geriatrics & Gerontology
Elie Antoun, Emma S. Garratt, Andrea Taddei, Mark A. Burton, Sheila J. Barton, Phil Titcombe, Leo D. Westbury, Alicia Baczynska, Eugenia Migliavacca, Jerome N. Feige, Holly E. Sydall, Elaine Dennison, Richard Dodds, Helen C. Roberts, Peter Richardson, Avan A. Sayer, Sarah Shaw, Cyrus Cooper, Joanna D. Holbrook, Harnish P. Patel, Keith M. Godfrey, Karen A. Lillycrop
Summary: This study found that differences in muscle methylome are associated with sarcopenia and individual measures of muscle mass, strength, and function in older individuals, suggesting that changes in epigenetic regulation of genes may contribute to impaired muscle function in later life.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2022)
Article
Multidisciplinary Sciences
Kira M. Veley, Kiona Elliott, Greg Jensen, Zhenhui Zhong, Suhua Feng, Marisa Yoder, Kerrigan B. Gilbert, Jeffrey C. Berry, Zuh-Jyh Daniel Lin, Basudev Ghoshal, Javier Gallego-Bartolome, Joanna Norton, Sharon Motomura-Wages, James C. Carrington, Steven E. Jacobsen, Rebecca S. Bart
Summary: The targeted methylation at the TAL20 effector binding element of the cassava SWEET10a gene leads to resistance to Xanthomonas phaseoli. This study demonstrates that blocking access to host susceptibility (S) genes through targeted methylation can increase disease resistance.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Xuan Ma, Bingqian Wang, Zhe Li, Xingwang Ding, Ya Wen, Wenqi Shan, Weiyue Hu, Xinru Wang, Yankai Xia
Summary: The study found that GLA primarily affected the sperm epigenome and transcriptome in mice, but had little effect on fertility, testis histology, or semen quality. Further research is needed to understand the male reproductive toxicity of GLA using similar strategies in human sperm.
Article
Cell Biology
Priscila Chiavellini, Martina Canatelli-Mallat, Marianne Lehmann, Maria D. Gallardo, Claudia B. Herenu, Jose L. Cordeiro, James Clement, Rodolfo G. Goya
Summary: Advancements in biomedical sciences have led to a changing view on aging, with a focus on the epigenome and DNA methylation as key factors in the aging process. The discovery of the Horvath clock algorithm has provided a highly accurate biomarker of age based on specific CpG sites. Epigenetic rejuvenation may hold the key to halting or reversing organismal aging.
Review
Cell Biology
Muneaki Nakamura, Yuchen Gao, Antonia A. Dominguez, Lei S. Qi
Summary: The review discusses CRISPR-based epigenome engineering technologies for modulating histone and DNA modifications, perturbing DNA and RNA regulatory elements, and chromatin organization. The epigenome involves complex cellular processes governing genomic activity. Repurposing prokaryotic CRISPR systems has enabled the development of diverse technologies in epigenome engineering.
NATURE CELL BIOLOGY
(2021)
Review
Oncology
Irfete S. Fetahu, Sabine Taschner-Mandl
Summary: Neuroblastoma is a common solid tumor in infants, with genetic and epigenetic alterations playing a key role in its pathogenesis. Aberrant DNA methylation, disrupted histone modification patterns, and abnormal expression of non-coding RNAs are major epigenetic changes associated with NB.
CANCER AND METASTASIS REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Archibold Mposhi, Lin Liang, Kevin P. Mennega, Dilemin Yildiz, Crista Kampert, Ingrid H. Hof, Pytrick G. Jellema, Tom J. de Koning, Klaas Nico Faber, Marcel H. J. Ruiters, Klary E. Niezen-Koning, Marianne G. Rots
Summary: Mutations in mitochondrial DNA or nuclear genes encoding mitochondrial proteins can lead to dysfunctional mitochondria and mitochondrial diseases. This study investigated the role of mtDNA methylation in explaining impaired mitochondrial function in myopathy patients without known genetic mutations. Enhanced mtDNA methylation was observed in muscle biopsies of myopathy patients compared to healthy controls, but no disease-associated difference in mtDNA methylation was found in fibroblast samples. The study also discovered increased expression of SLC25A26 and enhanced mtDNA copy numbers in myopathy fibroblasts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Nutrition & Dietetics
Paola Ungaro, Immacolata Cristina Nettore, Fabiana Franchini, Giuseppe Palatucci, Giovanna Muscogiuri, Annamaria Colao, Paolo Emidio Macchia
Summary: Ketogenic diets are effective in the treatment of obesity, metabolic diseases, and other conditions. However, limited data is available on the epigenetic changes associated with these diets.
Article
Agronomy
Kenji Fujino, Mari Obara, Toshiaki Shimizu, Kanako O. Koyanagi, Tomohito Ikegaya
Article
Virology
Gabriel Gonzalez, Kanako O. Koyanagi, Koki Aoki, Hidemi Watanabe
JOURNAL OF VIROLOGY
(2015)
Article
Biology
Marcin Jakalski, Kazutaka Takeshita, Mathieu Deblieck, Kanako O. Koyanagi, Izabela Makalowska, Hidemi Watanabe, Wojciech Makalowski
Article
Genetics & Heredity
Atsuko Yamada, Kanako O. Koyanagi, Hidemi Watanabe
Article
Genetics & Heredity
Gabriel Gonzalez, Kanako O. Koyanagi, Koki Aoki, Nobuyoshi Kitaichi, Shigeaki Ohno, Hisatoshi Kaneko, Susumu Ishida, Hidemi Watanabe
Correction
Infectious Diseases
Tsuguto Fujimoto, Shotaro Yamane, Tomoko Ogawa, Nozomu Hanaoka, Atsushi Ogura, Chiemi Hotta, Takeshi Niwa, Yakou Chiba, Gabriel Gonzalez, Koki Aoki, Kanako Ono Koyanagi, Hidemi Watanabe
JAPANESE JOURNAL OF INFECTIOUS DISEASES
(2014)
Article
Infectious Diseases
Tsuguto Fujimoto, Shotaro Yamane, Tomoko Ogawa, Nozomu Hanaoka, Atsushi Ogura, Chiemi Hotta, Takeshi Niwa, Yakou Chiba, Gabriel Gonzalez, Koki Aoki, Kanako Ono Koyanagi, Hidemi Watanabe
JAPANESE JOURNAL OF INFECTIOUS DISEASES
(2014)
Article
Microbiology
Hisatoshi Kaneko, Koki Aoki, Shigeaki Ohno, Hiroaki Ishiko, Tsuguto Fujimoto, Masayuki Kikuchi, Seiya Harada, Gabriel Gonzalez, Kanako O. Koyanagi, Hidemi Watanabe, Tatsuo Suzutani
JOURNAL OF CLINICAL MICROBIOLOGY
(2011)
Article
Biotechnology & Applied Microbiology
Hisatoshi Kaneko, Koki Aoki, Susumu Ishida, Shigeaki Ohno, Nobuyoshi Kitaichi, Hiroaki Ishiko, Tsuguto Fujimoto, Yoshifumi Ikeda, Masako Nakamura, Gabriel Gonzalez, Kanako O. Koyanagi, Hidemi Watanabe, Tatsuo Suzutani
JOURNAL OF GENERAL VIROLOGY
(2011)
Letter
Virology
Shotaro Yamane, Amanda Wei Ling Lee, Nozomu Hanaoka, Gabriel Gonzalez, Hisatoshi Kaneko, Susumu Ishida, Nobuyoshi Kitaichi, Shigeaki Ohno, Kanako O. Koyanagi, Koki Aoki, Tsuguto Fujimoto, Nobuyo Yawata, Hidemi Watanabe
JOURNAL OF VIROLOGY
(2013)
Article
Plant Sciences
Ruifang Liu, Kanako O. Koyanagi, Sunlu Chen, Yuji Kishima
Article
Plant Sciences
Tsuyoshi Tanaka, Kanako O. Koyanagi, Takeshi Itoh
Article
Virology
Sunlu Chen, Ruifang Liu, Kanako O. Koyanagi, Yuji Kishima
Meeting Abstract
Biotechnology & Applied Microbiology
Takatoshi Abe, Hidemi Watanabe, Kanako O. Koyanagi, Botaro Inoue