Article
Agronomy
Athanasios Dalakouras, Ioannis Ganopoulos
Summary: Exogenous RNA molecules can trigger RNA interference in plants, and high-pressure spraying of dsRNAs can induce de novo methylation of promoter sequences in plants.
Article
Cell Biology
Xubin Zheng, Qiong Wu, Haonan Wu, Kwong-Sak Leung, Man-Hon Wong, Xueyan Liu, Lixin Cheng
Summary: This study introduced the most prevalent methods for processing bisulfite sequencing data and evaluated the consistency of the data acquired from different measurements in liver cancer. Differential methylated genes measured by various bisulfite sequencing assays and 450 k beadchip were consistently hypo-methylated in liver cancer with high functional similarity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Oncology
Seungjae Lee, Ti-Cheng Chang, Patrick Schreiner, Yiping Fan, Neeraj Agarwal, Charles Owens, Reinhard Dummer, John M. Kirkwood, Raymond L. Barnhill, Dan Theodorescu, Gang Wu, Armita Bahrami
Summary: The study showed that in wild-type cancer cells, there were significant methylation differences in different regions of the TERT promoter between the two epialleles. Decitabine therapy was able to reduce methylation in the core and proximal regions of the promoter, leading to reactivation of the silent allele.
Article
Biochemistry & Molecular Biology
Dasa Jevsinek Skok, Nina Hauptman
Summary: This article investigates the CpG island methylator phenotype (CIMP) in colorectal cancer development, using unsupervised hierarchical clustering to identify four distinct subtypes. Through mapping methylated regions to Ensembl database, 253 genes were found to exhibit aberrant methylation in promoter regions, with bone morphogenic protein 4 (BMP4) being highlighted as the most prominent candidate. This finding highlights the potential role of BMP4 in colorectal cancer development and progression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Zhenyu Shao, Yang Han, Dan Zhou
Summary: Through comprehensive bioinformatic analyses, this study reveals that previous observations of extensive and strand-biased 5-methylcytosine (5mC) in mitochondrial DNA (mtDNA) are likely artifacts caused by a combination of factors including inefficient bisulfite conversion, low sequencing reads in the L strand, and interference from nuclear mitochondrial DNA sequences (NUMTs). By establishing an optimized procedure for library preparation and data analysis of bisulfite sequencing, the researchers demonstrate an even distribution of 5mC signals across mtDNA and an average methylation level similar to background noise.
Article
Biochemical Research Methods
Marco Morselli, Colin Farrell, Liudmilla Rubbi, Heather L. Fehling, Rebecca Henkhaus, Matteo Pellegrini
Summary: Cytosine methylation, a well-studied epigenetic modification, plays crucial roles in development and disease, with patterns varying among cells and changing with age. DNA methylation arrays have been developed to detect methylation status in a cost-effective way, while a Targeted Bisulfite Sequencing method offers a promising approach for biomarker discovery across different phenotypes.
Article
Medicine, General & Internal
Dae-Yeon Kim, Hee-Tae Cheong, Chang-Six Ra, Kazuhiro Kimura, Bae Dong Jung
Summary: The study revealed that inhibition of UCP2 expression in Hep3B cells was due to methylation of the promoter region, and treatment with 5-aza could increase UCP2 expression, which may have implications for cancer treatment.
INTERNATIONAL JOURNAL OF MEDICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Veronika N. Laine, Bernice Sepers, Melanie Lindner, Fleur Gawehns, Suvi Ruuskanen, Kees van Oers
Summary: The field of molecular biology is rapidly advancing and there is a growing interest in studying ecological epigenetics, particularly in wild vertebrates. This review provides a practical guide for researchers studying DNA methylation variation in wild vertebrates, discussing technical aspects, limitations, and data analysis methods.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Maximilian Schonung, Jana Hess, Pascal Bawidamann, Sina Stable, Joschka Hey, Jens Langstein, Yassen Assenov, Dieter Weichenhan, Pavlo Lutsik, Daniel B. Lipka
Summary: AmpliconDesign is a webserver that provides scalable and user-friendly platform for designing and analyzing targeted DNA methylation studies based on bisulfite-treated genomic DNA (BT-DNA). Core functionalities include high-throughput primer design and binding site validation, prediction of fragmentation patterns for EpiTYPER MassArray, interactive quality control, and a streamlined analysis workflow for deep amplicon bisulfite sequencing (ampBS-seq).
Article
Biochemistry & Molecular Biology
Antonella Sarnataro, Giulia De Riso, Sergio Cocozza, Antonio Pezone, Barbara Majello, Stefano Amente, Giovanni Scala
Summary: DNA methylation is an important epigenetic modification that influences gene regulation, genomic imprinting, and genome stability. EpiStatProfiler is an R package that allows the analysis of CpG and non-CpG epialleles based on bisulfite sequencing data, with additional features for genomic annotation and analysis. It is the first package to provide functionalities specifically for epiallele composition analysis from any type of bisulfite sequencing experiment.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Mauricio Penuela, Jenny Johana Gallo-Franco, Jorge Finke, Camilo Rocha, Anestis Gkanogiannis, Thaura Ghneim-Herrera, Mathias Lorieux
Summary: This study investigates the association between recombination rates and DNA methylation in two commercial rice varieties, revealing negative and positive correlations between them, as well as the significant impact of the centromere region. Furthermore, machine learning regression models are developed to predict recombination rates using methylated cytosines in the CHH context.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Fabio Coppede, Utsa Bhaduri, Andrea Stoccoro, Vanessa Nicoli, Eleonora Di Venere, Giuseppe Merla
Summary: The central objective of combining discovery science with biomedical applications is to benefit patients and reduce the global disease burden. The conversion of DNA methylation (DNAm) from a biological process to a diagnostic tool is a prime example of this transformation, which took nearly a century. In recent years, DNAm studies have been standardized in clinical applications more than ever before, offering great potential for diagnosing various diseases associated with epigenetic alterations. DNAm detection plays a role in noninvasive prenatal testing and indicates prenatal risk factors in very preterm infants. In the field of cancer, liquid biopsy-based DNAm profiling provides valuable epigenetic biomarkers for early-stage diagnosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Hossein Dehdari, Fatemeh Moradian, Ali Barzegar, Mohammed Ali Ebirahimzadeh
Summary: This study found that increased transcription of CYP1A1 in breast cancer is correlated with hypermethylation of a specific CpG block and upregulation of antiapoptotic protein BCL-2. The hypermethylation of this CpG block may serve as a potential biomarker for diagnosis and progression of breast cancer.
EXPERIMENTAL CELL RESEARCH
(2022)
Article
Genetics & Heredity
Julien Guemri, Morgane Pierre-Jean, Solene Brohard, Nouara Oussada, Caroline Horgues, Eric Bonnet, Florence Mauger, Jean-Francois Deleuze
Summary: This study developed a targeted sequencing protocol to identify potential noninvasive biomarkers of Alzheimer's disease (AD) based on methylated ccfDNA. The authors identified methylated CpGs that were consistent with previous AD studies, as well as potential novel sites. These findings suggest that methylated ccfDNA could be a useful noninvasive biomarker for AD.
Review
Oncology
Hyun Jin Shin, Junjie T. Hua, Haolong Li
Summary: Epigenetic modifications, particularly DNA methylation, are extensively studied in cancer and have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. Aberrant DNA methylation patterns, such as the CpG island hypermethylator phenotype (CIMP), are associated with aggressive subtypes, higher Gleason score, and overall worse prognosis in prostate cancer. DNA methylation alterations can serve as potential biomarkers for prostate cancer and have the potential for targeted treatment development.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Le Zhang, Tianming Lan, Chuyu Lin, Wenyuan Fu, Yaohua Yuan, Kaixiong Lin, Haimeng Li, Sunil Kumar Sahu, Zhaoyang Liu, Daqing Chen, Qunxiu Liu, Aishan Wang, Xiaohong Wang, Yue Ma, Shizhou Li, Yixin Zhu, Xingzhuo Wang, Xiaotong Ren, Haorong Lu, Yunting Huang, Jieyao Yu, Boyang Liu, Qing Wang, Shaofang Zhang, Xun Xu, Huanming Yang, Dan Liu, Huan Liu, Yanchun Xu
Summary: The South China tiger is critically endangered due to functional extinction in the wild and inbreeding depression among the captive population. This research assembled and characterized the genomes of the South China tiger and six other tiger subspecies, revealing the genomic signatures of inbreeding depression in the South China tiger. The study provides important information for genetic management policies for the South China tiger.
MOLECULAR ECOLOGY RESOURCES
(2023)
Correction
Multidisciplinary Sciences
Yilong Li, Nicola D. Roberts, Jeremiah A. Wala, Ofer Shapira, Steven E. Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O. Korbel, James E. Haber, Marcin Imielinski, Joachim Weischenfeldt, Rameen Beroukhim, Peter J. Campbell
Correction
Multidisciplinary Sciences
Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao, Henrik Hornshoj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andres Lanzos, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, Andre Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uuskuela-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jueri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Nuria Lopez-Bigas, Joachim Weischenfeldt, Rameen Beroukhim, Inigo Martincorena, Jakob Skou Pedersen, Gad Getz
Article
Biochemistry & Molecular Biology
Xin Jin, Yanqun Wang, Jinjin Xu, Yimin Li, Fanjun Cheng, Yuxue Luo, Haibo Zhou, Shanwen Lin, Fei Xiao, Lu Zhang, Yu Lin, Zhaoyong Zhang, Yan Jin, Fang Zheng, Wei Chen, Airu Zhu, Ye Tao, Jingxian Zhao, Tingyou Kuo, Yuming Li, Lingguo Li, Liyan Wen, Rijing Ou, Fang Li, Long Lin, Yanjun Zhang, Jing Sun, Hao Yuan, Zhen Zhuang, Haixi Sun, Zhao Chen, Jie Li, Jianfen Zhuo, Dongsheng Chen, Shengnan Zhang, Yuzhe Sun, Peilan Wei, Jinwei Yuan, Tian Xu, Huanming Yang, Jian Wang, Xun Xu, Nanshan Zhong, Yonghao Xu, Kun Sun, Jincun Zhao
Summary: This study investigates the potential of plasma cell-free DNA fragmentation patterns in assessing tissue injury and monitoring treatment effectiveness in COVID-19 patients. The findings show that these DNA fragmentation characteristics reflect patient-specific physiological changes during treatment, and reveal frequent tissue injuries in COVID-19 patients.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Multidisciplinary Sciences
Yang Dong, Shengchang Duan, Qiuju Xia, Zhenchang Liang, Xiao Dong, Kristine Margaryan, Mirza Musayev, Svitlana Goryslavets, Goran Zdunic, Pierre-Francois Bert, Thierry Lacombe, Erika Maul, Peter Nick, Kakha Bitskinashvili, Gyorgy Denes Bisztray, Elyashiv Drori, Gabriella De Lorenzis, Jorge Cunha, Carmen Florentina Popescu, Rosa Arroyo-Garcia, Claire Arnold, Ali Ergul, Yifan Zhu, Chao Ma, Shufen Wang, Siqi Liu, Liu Tang, Chunping Wang, Dawei Li, Yunbing Pan, Jingxian Li, Ling Yang, Xuzhen Li, Guisheng Xiang, Zijiang Yang, Baozheng Chen, Zhanwu Dai, Yi Wang, Arsen Arakelyan, Varis Kuliyev, Gennady Spotar, Nabil Girollet, Serge Delrot, Nathalie Ollat, Patrice This, Cecile Marchal, Gautier Sarah, Valerie Laucou, Roberto Bacilieri, Franco Roeckel, Pingyin Guan, Andreas Jung, Michael Riemann, Levan Ujmajuridze, Tekle Zakalashvili, David Maghradze, Maria Hohn, Gizella Jahnke, Erzsebet Kiss, Tamas Deak, Oshrit Rahimi, Sariel Hubner, Fabrizio Grassi, Francesco Mercati, Francesco Sunseri, Jose Eiras-Dias, Anamaria Mirabela Dumitru, David Carrasco, Alberto Rodriguez-Izquierdo, Gregorio Munoz, Tamer Uysal, Cengiz Ozer, Kemal Kazan, Meilong Xu, Yunyue Wang, Shusheng Zhu, Jiang Lu, Maoxiang Zhao, Lei Wang, Songtao Jiu, Ying Zhang, Lei Sun, Huanming Yang, Ehud Weiss, Shiping Wang, Youyong Zhu, Shaohua Li, Jun Sheng, Wei Chen
Summary: We investigate the evolution and domestication of grapevines by studying 3525 cultivated and wild varieties worldwide. Harsh climate in the Pleistocene led to the separation of wild grape ecotypes due to habitat fragmentation. Domestication occurred around 11,000 years ago in Western Asia and the Caucasus, giving rise to table and wine grapevines. The domesticates from Western Asia dispersed into Europe, hybridizing with ancient wild ecotypes and diversifying into muscat and unique western wine grape ancestries as human migration took place in the late Neolithic. Analysis of domestication traits also provides insights into the selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These findings demonstrate the significance of grapevines in the early development of agriculture across Eurasia.
Article
Multidisciplinary Sciences
Ziqi Gao, Chenran Jiang, Jiawen Zhang, Xiaosen Jiang, Lanqing Li, Peilin Zhao, Huanming Yang, Yong Huang, Jia Li
Summary: This article presents a new computational model, HIGH-PPI, for predicting protein-protein interactions (PPIs) and extrapolating molecular details. The model uses a double-viewed hierarchical graph learning approach, considering both the interactions between proteins and the structure-function relationship within proteins. Experimental results demonstrate that HIGH-PPI achieves high accuracy and robustness in PPI prediction.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Xiaoqian Lin, Tongyuan Hu, Jianwei Chen, Hewei Liang, Jianwei Zhou, Zhinan Wu, Chen Ye, Xin Jin, Xun Xu, Wenwei Zhang, Xiaohuan Jing, Tao Yang, Jian Wang, Huanming Yang, Karsten Kristiansen, Liang Xiao, Yuanqiang Zou
Summary: The authors present an expanded version of the Cultivated Genome Reference (CGR), termed CGR2, which includes 3324 high-quality draft genomes based on gut bacterial isolates from Chinese individuals. They classify 527 species from 8 phyla, including 179 previously unidentified species, and provide information on secondary metabolite biosynthetic gene clusters and gut phage-bacteria interactions.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Xiaomin Liu, Leying Zou, Chao Nie, Youwen Qin, Xin Tong, Jian Wang, Huanming Yang, Xun Xu, Xin Jin, Liang Xiao, Tao Zhang, Junxia Min, Yi Zeng, Huijue Jia, Yong Hou
Summary: Although the association between human microbiome, especially gut microbiota, and longevity has been revealed in recent studies, the causality between them is still unclear. This study used bidirectional two-sample Mendelian randomization (MR) analyses to assess the relationship between the human microbiome (gut and oral microbiota) and longevity. The findings suggest that certain disease-protected gut microbiota and probiotics are associated with increased odds of longevity, while other gut microbiota are negatively associated with longevity.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Xiangwei Hu, Kai Xia, Minhui Dai, Xiaofeng Han, Peng Yuan, Jia Liu, Shiwei Liu, Fuhuai Jia, Jiayu Chen, Fangfang Jiang, Jieyao Yu, Huanming Yang, Jian Wang, Xun Xu, Xin Jin, Karsten Kristiansen, Liang Xiao, Wei Chen, Mo Han, Shenglin Duan
Summary: Intermittent fasting is a promising weight loss method that modulates the gut microbiota. A three-week IF program resulted in an average weight loss of 3.67 kg and improved clinical parameters, regardless of initial BMI and gut microbiota status.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Ecology
Yang Zhou, Xiaoyu Zhan, Jiazheng Jin, Long Zhou, Juraj Bergman, Xuemei Li, Marjolaine Marie C. Rousselle, Meritxell Riera Belles, Lan Zhao, Miaoquan Fang, Jiawei Chen, Qi Fang, Lukas Kuderna, Tomas Marques-Bonet, Haruka Kitayama, Takashi Hayakawa, Yong-Gang Yao, Huanming Yang, David N. Cooper, Xiaoguang Qi, Dong-Dong Wu, Mikkel Heide Schierup, Guojie Zhang
Summary: A comparative analysis of Y chromosomes in 29 primate species reveals rapid evolution and different patterns of evolution in different regions. The Y chromosome plays a critical role in determining male sex and has unique sequence classes that have experienced distinct evolutionary trajectories. By generating and analyzing 19 new primate sex chromosome assemblies, along with 10 existing ones, this study reports the rapid evolution of the primate Y chromosome. Different primate lineages exhibit varying rates of gene loss, structural changes, and chromatin modifications on their Y chromosomes. The study also highlights the contribution of selection on Y-linked genes to the evolution of male traits across primates.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Xiaoying Zhao, Kunli Qu, Benedetta Curci, Huanming Yang, Lars Bolund, Lin Lin, Yonglun Luo
Summary: Recent progress in CRISPR gene editing tools has expanded the possibilities for treating devastating genetic diseases. In this study, three methods of gene editing (NHBEJ, HDR, and PE) were compared for correcting loss-of-function mutations in Duchenne Muscular Dystrophy. The highest efficiency was achieved with NHBEJ, followed by HDR and PE2. The correction efficiency was increased with the use of PE3. This study demonstrates the potential for highly efficient correction of DMD mutations using CRISPR gene editing.
Article
Chemistry, Multidisciplinary
Zhiming Li, Yanmei Ju, Jingjing Xia, Zhe Zhang, Hefu Zhen, Xin Tong, Yuzhe Sun, Haorong Lu, Yang Zong, Peishan Chen, Kaiye Cai, Zhen Wang, Huanming Yang, Jiucun Wang, Jian Wang, Yong Hou, Xin Jin, Tao Zhang, Wenwei Zhang, Xun Xu, Liang Xiao, Ruijin Guo, Chao Nie
Summary: This study used deep-shotgun sequencing to analyze 450 facial samples and 2069 publicly available skin metagenomic datasets, and constructed a Unified Human Skin Genome (UHSG) catalog containing 813 prokaryotic species. The core functions of the skin microbiome were described based on the UHSG, and differences in amino acid metabolism, carbohydrate metabolism, and drug resistance functions among different phyla were identified. Additionally, analysis of near-complete genomes revealed 1220 putative novel secondary metabolites. The UHSG provides a convenient reference database for studying the role of skin microorganisms in the skin.
Article
Biology
Xi Dai, Honglian Shao, Nianqin Sun, Baiquan Ci, Jun Wu, Chuanyu Liu, Liang Wu, Yue Yuan, Xiaoyu Wei, Huanming Yang, Longqi Liu, Weizhi Ji, Bing Bai, Zhouchun Shang, Tao Tan
Summary: This study applied scATAC-seq technology to investigate the chromatin status of in vitro cultured cynomolgus monkey embryos. The findings provide insights into the chromatin reorganization and transcriptional regulatory mechanisms during early post-implantation development in primates, including the identification of regulatory factors and lineage specification.
Article
Cell Biology
Chentao Yang, Yang Zhou, Yanni Song, Dongya Wu, Yan Zeng, Lei Nie, Panhong Liu, Shilong Zhang, Guangji Chen, Jinjin Xu, Hongling Zhou, Long Zhou, Xiaobo Qian, Chenlu Liu, Shangjin Tan, Chengran Zhou, Wei Dai, Mengyang Xu, Yanwei Qi, Xiaobo Wang, Lidong Guo, Guangyi Fan, Aijun Wang, Yuan Deng, Yong Zhang, Jiazheng Jin, Yunqiu He, Chunxue Guo, Guoji Guo, Qing Zhou, Xun Xu, Huanming Yang, Jian Wang, Shuhua Xu, Yafei Mao, Xin Jin, Jue Ruan, Guojie Zhang
Summary: Since the release of the complete human genome, efforts in human genomic study have shifted towards closing gaps in ethnic diversity. In this study, a fully phased diploid human genome from a Han Chinese male individual (CN1) was presented, achieving the telomere-to-telomere (T2T) level. Comparisons with the CHM13 haploid T2T genome revealed significant variations in the centromere and numerous novel structural variations outside the centromere. CN1 outperformed CHM13 as a reference genome for the East Asian population, impacting rare SNP calling and uncovering East Asian specific introgression sequences.
Article
Ophthalmology
Wei Li, Xiang-Dong He, Zheng-Tao Yang, Dong-Ming Han, Yan Sun, Yan-Xian Chen, Xiao-Tong Han, Si-Cheng Guo, Yu-Ting Ma, Xin Jin, Huan-Ming Yang, Ya Gao, Zhuo-Shi Wang, Jian-Kang Li, Wei He
Summary: The aim of this study was to investigate the genetic characteristics and genotype-phenotype associations in a trio-based cohort of inherited eye diseases (IEDs). Through retrospective analysis of a large cohort of Chinese proband-parent trios, the researchers identified 108 IED-causative genes and found that the top 24 genes explained two-thirds of the genetically solved trios. The study also revealed the significant role of de novo mutations (DNMs) in IEDs and its association with paternal age at reproduction.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2023)