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
Automation & Control Systems
Yinjing Liao, Hui Guo, Runyu Jing, Jiesi Luo, Menglong Li, Yizhou Li
Summary: Post-translational modifications of histone play a key role in gene expression regulation by controlling DNA accessibility and recruiting transcription factors. Developing computational methods to predict gene expression levels from histone modification data can enhance understanding of their function and contribute to the development of epigenetic drugs. Additionally, histone signals at the transcription termination site (TTS) provide valuable information to improve model performance, indicating potential regulatory mechanisms that need further exploration.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2021)
Article
Genetics & Heredity
Yajiao Wu, Wenqiang Bao, Jinjin Ren, Chutao Li, Mengting Chen, Dongcheng Zhang, An Zhu
Summary: This study investigated the relationship between AFB1-induced intestinal toxicity and N6-methyladenosine (m6A) RNA methylation. The results showed that the injury caused by AFB1 to HCT116 cells was related to the disruptions to the levels of m6A methylation modifications of target genes and the abnormal expression of m6A regulators.
Article
Biotechnology & Applied Microbiology
Fang-Hui-Zi Shang, Hai-Nan Liu, Yu-Tong Wan, Yi-He Yu, Da-Long Guo
Summary: This study identified and isolated eight genes related to H3K4 methyltransferase in the grape genome, which were divided into three categories based on phylogenetic relationship. Transcriptome data showed that VvH3K4-5 was up-regulated during fruit ripening and its expression level differed significantly between different grape varieties. The promoters of VvH3K4s contain cis-acting elements in response to stress, indicating their potential involvement in metabolic pathways regulated by ROS signaling. Subcellular localization and promoter activity experiments suggest that VvH3K4s may be regulated by H2O2. Additionally, treatment with H2O2 and Hypotaurine revealed opposite expression patterns for most genes and varied expression levels over time.
Article
Biochemistry & Molecular Biology
Ting Li, Changjie Lin, Yifan Zhu, Haojun Xu, Yiya Yin, Chaohao Wang, Xin Tang, Tongxing Song, Aizhen Guo, Yingyu Chen, Changmin Hu
Summary: This study investigated the role and mechanism of RNA m(6)A modification in mastitis treated with E. coli using MeRIP-seq technology, revealing the significant impact of m(6)A in mastitis and elucidating the interplay between gene expression and m(6)A modification, providing important insights for future research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Tao Huang, Wei-Jie He, Cheng Li, Jing-Bo Zhang, Yu-Cai Liao, Bo Song, Peng Yang
Summary: This study discovers the important role of N6-methyladenosine (m6A) in translation regulation in hexaploid wheat. The methylation extent of m6A is negatively correlated with mRNA expression levels, and m6A at different locations has different impacts on mRNA translation. m6a methylated genes are more conserved and enriched in genes with close expression levels. m6A-containing mRNAs are enriched in processes and pathways of translation and RNA transport.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Fisheries
Yaorong Wang, Zhiyuan Li, Yuwen Guo, Chuntai Nong, Charles Brighton Ndandala, Hao Yang, Hai Huang, Guangli Li, Huapu Chen
Summary: In this study, lncRNAs and mRNAs involved in IGF3-induced ovarian maturation were evaluated in spotted scat (Scatophagus argus). The results demonstrate that lncRNAs might be involved in the reproductive processes in S. argus.
AQUACULTURE REPORTS
(2022)
Article
Cell Biology
Yidan Tang, Changliang Liu, Tao Zhu, Hai Chen, Yalan Sun, Xueying Zhang, Qi Zhao, Jiahui Wu, Xuejie Fei, Shixin Ye, Chan Chen
Summary: Chronic neuropathic pain is often associated with memory loss, but the molecular processes and effective therapies are still unknown. In this study, a rat model of CCI-induced memory impairment was used to investigate the gene expression changes in the hippocampus. RNA-Seq and bioinformatics analysis revealed differentially expressed mRNAs and lncRNAs between the CCI-induced memory impairment model and the control. Pathway analysis identified genes and pathways involved in ferroptosis and memory impairment. Furthermore, a competing RNA network analysis was performed to investigate the regulatory link between lncRNAs and mRNAs. This study provides insights into the potential treatments for CCI-induced memory impairment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Engineering, Environmental
Zhuohang Yu, Zengrui Wu, Moran Zhou, Kangjia Cao, Weihua Li, Guixia Liu, Yun Tang
Summary: In this study, a novel strategy called EDC-Predictor was proposed to predict endocrine-disrupting chemicals (EDCs) using pharmacological and toxicological profiles. Different from conventional methods, EDC-Predictor considers more targets and utilizes computational target profiles for better prediction accuracy. The research demonstrates that EDC-Predictor outperforms other tools in predicting EDCs.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Cell Biology
Xinying Zhou, Yang Yang, Yuejun Li, Guojun Liang, Dawei Kang, Bing Zhou, Qingchu Li
Summary: The study revealed that METTL3 is upregulated in osteosarcoma and associated with poor clinical outcomes. Silencing METTL3 inhibited proliferation, migration, and invasion of osteosarcoma cells, potentially through regulating the stability of lncRNA DANCR. These findings suggest METTL3 as a promising therapeutic target for osteosarcoma treatment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Natsu Nakajima, Tomoatsu Hayashi, Katsunori Fujiki, Katsuhiko Shirahige, Tetsu Akiyama, Tatsuya Akutsu, Ryuichiro Nakato
Summary: This study proposed a method for detecting gene communities based on coexpression properties and developed an exclusively expressed index (EEI) to identify mutually exclusive gene pairs. Applying these methods to glioblastoma scRNA-seq data, it was found that gene communities were partially conserved after serum stimulation, and EEI improved the sensitivity of capturing cellular heterogeneity.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Jianheng Liu, Tao Huang, Wanying Chen, Chenhui Ding, Tianxuan Zhao, Xueni Zhao, Bing Cai, Yusen Zhang, Song Li, Ling Zhang, Maoguang Xue, Xiuju He, Wanzhong Ge, Canquan Zhou, Yanwen Xu, Rui Zhang
Summary: In this study, the authors identified massive methylation of maternal mRNAs mediated by NSUN2 and NSUN6 during animal development in 6 species. Using Drosophila as a model, they found that embryos lacking maternal mRNA m5C exhibited cell cycle delays and failure to initiate maternal-to-zygotic transition in a timely manner, highlighting the functional importance of maternal mRNA m5C. The research also revealed two waves of m5C regulatory innovations from invertebrates to humans. Overall, this study provides important insights into the role of mRNA m5C in biology and disease.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Xiaoming Fu, Heta P. Patel, Stefano Coppola, Libin Xu, Zhixing Cao, Tineke L. Lenstra, Ramon Grima, Anna Akhmanova
Summary: This study compares transcriptional parameters with and without correction for cell cycle phases and post-transcriptional noise in yeast cells using smFISH, finding that corrections can significantly reduce errors in parameter estimation. The study also outlines how to adjust for measurement noise in smFISH effectively.
Review
Horticulture
Saaya Shiraki, Kazumasa Fujiwara, Yoshiki Kamiya, Mst. Arjina Akter, Elizabeth S. Dennis, Ryo Fujimoto, Hasan Mehraj
Summary: Heterosis is an important phenomenon in high-yield crop breeding, but its molecular mechanism is not well understood in horticultural crops. This review summarizes the new genetic and epigenetic studies on heterosis in horticultural crops. Molecular approaches are being used to study the molecular basis of heterosis in horticultural crops due to the difficulty of predicting heterosis from parental genetic distance. Transcriptome analyses have identified photosynthesis-related genes and noncoding RNAs as important factors in heterosis. QTL analysis has revealed the association of specific loci with heterosis in vegetative and fruit tissues.
Article
Pharmacology & Pharmacy
Kartiga Natarajan, Arun Sundaramoorthy, Narkunaraja Shanmugam
Summary: This study reveals the post-transcriptional regulation of IP-10 mRNA in diabetes conditions and shows that S100b affects the stability of IP-10 mRNA by regulating the methylation of hnRNPK. These findings indicate the important role of hnRNPK in S100b-induced accumulation of IP-10 mRNA.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Guifen Liu, Wen Wang, Shengen Hu, Xiangxiu Wang, Yong Zhang
Article
Cell Biology
Ye Zhang, Jian-Feng Chang, Jin Sun, Lu Chen, Xiao-Mei Yang, Huan-Yin Tang, Yuan-Ya Jing, Xuan Kang, Zhi-Min He, Jun-Yu Wu, Hui-Min Wei, Da-Liang Wang, Rong-Gang Xu, Rui-Bao Zhu, Ying Shen, Shi-Yang Zeng, Chen Wang, Kui-Nan Liu, Yong Zhang, Zhi-Yong Mao, Ci-Zhong Jiang, Fang-Lin Sun
JOURNAL OF CELL SCIENCE
(2018)
Article
Cell Biology
Chenfei Wang, Xiaoyu Liu, Yawei Gao, Lei Yang, Chong Li, Wenqiang Liu, Chuan Chen, Xiaochen Kou, Yanhong Zhao, Jiayu Chen, Yixuan Wang, Rongrong Le, Hong Wang, Tao Duan, Yong Zhang, Shaorong Gao
NATURE CELL BIOLOGY
(2018)
Article
Cell & Tissue Engineering
Rui Gao, Chenfei Wang, Yawei Gao, Wenchao Xiu, Jiayu Chen, Xiaochen Kou, Yanhong Zhao, Yuhan Liao, Dandan Bai, Zhibin Qiao, Lei Yang, Mingzhu Wang, Ruge Zang, Xiaoyu Liu, Yanping Jia, Yanhe Li, Yalin Zhang, Jiqing Yin, Hong Wang, Xiaoping Wan, Wenqiang Liu, Yong Zhang, Shaorong Gao
Article
Hematology
Yanyan Ding, Wen Wang, Dongyuan Ma, Guixian Liang, Zhixin Kang, Yuanyuan Xue, Yifan Zhang, Lu Wang, Jian Heng, Yong Zhang, Feng Liu
Summary: The study examined the chromatin accessibility and transcriptional features of zebrafish nascent and fetal HSPCs, revealing dynamic changes during HSPC transition. The role of chromatin remodeler-mediated epigenetic programming, particularly Smarca5, in fetal HSPC development was highlighted. This research provides new insights into the generation of functional HSPCs both in vivo and in vitro.
Article
Biochemical Research Methods
Chengchen Zhao, Wenchao Xiu, Yuwei Hua, Naiqian Zhang, Yong Zhang
Summary: CStreet is a computed Cell State trajectory inference method for time-series scRNA-seq data that constructs k-nearest neighbor connections between cells and estimates the connection probabilities, visualizing the trajectory. Compared to other methods, CStreet demonstrates high accuracy and tolerance.
Article
Biochemical Research Methods
Shiyang Zeng, Yuwei Hua, Yong Zhang, Guifen Liu, Chengchen Zhao
Summary: GLEANER is a web server dedicated to the analysis and visualization of multiomics data related to the mammalian germline cycle, providing a comprehensive collection of transcriptome, DNA methylome, chromatin accessibility, and histone modification characteristics. It displays integrative analysis results for each input gene, genes with correlated transcriptional changes, and overall continuous dynamic trends in the germline cycle.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Xiaolan Chen, Hui Yang, Guifen Liu, Yong Zhang
Summary: The NUCOME database filters qualified nucleosome organization referenced landscapes in human and mouse based on QC metrics, providing standardized, qualified data source and informative nucleosome organization features at a whole-genome scale and on the level of individual loci.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Yanhui Xiao, Wenjing Li, Hui Yang, Lulu Pan, Liwei Zhang, Lu Lu, Jiwei Chen, Wei Wei, Jie Ye, Jiwen Li, Guohong Li, Yong Zhang, Minjia Tan, Jianping Ding, Jiemin Wong
Summary: Recent studies have found that HBO1 serves as a versatile histone acyltransferase, catalyzing various histone acylations in a scaffold protein-dependent manner. It is highly enriched at transcriptional start sites of active genes and associated with a subset of DNA replication origins, linking histone acylations to promoter acylations and selection of DNA replication origins.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Xiangxiu Wang, Wen Wang, Yiman Wang, Jia Chen, Guifen Liu, Yong Zhang
Summary: This study presents a modified CUT&RUN method, FitCUT&RUN, for profiling the occupancy of key transcription factors (TFs) during zygotic genome activation (ZGA) in early embryogenesis. The method uses an Fc fragment of immunoglobulin G for tagging and demonstrates its reliability and robustness even with a small number of cells. The authors applied FitCUT&RUN to zebrafish embryogenesis and generated occupancy profiles of three known activators of zebrafish ZGA, observing a gradual increase in the occupancy of Nanog and its importance for the activation of early transcribed genes.
Article
Cell Biology
Hui Yang, Dandan Bai, Yanhe Li, Zhaowei Yu, Chenfei Wang, Yifan Sheng, Wenqiang Liu, Shaorong Gao, Yong Zhang
Summary: This study comprehensively analyzed the association between DNA methylation and H3K9me3 reprogramming in mouse pre-implantation embryos and revealed that CpG-rich genomic loci with high H3K9me3 signal and DNA methylation level are hotspots of DNA methylation maintenance. The study also identified 1,279 allele-specific CHMs, including 19 known imprinting control regions, and suggested that 22 ICR-like regions may regulate allele-specific transcription similar to known ICRs, with five of them being important for mouse embryo development.
NATURE CELL BIOLOGY
(2022)
Article
Biology
Lu Han, Bin Song, Peilin Zhang, Zhi Zhong, Yongxiang Zhang, Xiaochen Bo, Hongyang Wang, Yong Zhang, Xiuliang Cui, Wenxia Zhou
Summary: Cellular transitions play a crucial role in translational medicine research. This study introduces a computational framework, PC3T, which enriches small molecules that induce desired cellular transitions. The framework was able to predict the reprogramming of fibroblasts into hepatic progenitor-like cells and provide a valuable resource for cell state transition research.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Shengen Hu, Dawei Huo, Zhaowei Yu, Yujie Chen, Jing Liu, Lin Liu, Xudong Wu, Yong Zhang
Article
Biotechnology & Applied Microbiology
Chengchen Zhao, Naiqian Zhang, Yalin Zhang, Nuermaimaiti Tuersunjiang, Shaorong Gao, Wenqiang Liu, Yong Zhang
Article
Cell Biology
Haibo Gao, Rui Gao, Linfeng Zhang, Wenchao Xiu, Ruge Zang, Hong Wang, Yong Zhang, Jiayu Chen, Yawei Gao, Shaorong Gao
JOURNAL OF MOLECULAR CELL BIOLOGY
(2019)