Article
Agriculture, Multidisciplinary
Li Yong-ping, Liu Tian-jia, Luo Hui-feng, Liu Sheng-cai
Summary: This study utilized comprehensive transcriptomic analyses to investigate gene expression during fruit development in cultivated strawberries. Differences in gene expression, particularly in flavonoid biosynthesis, were found between diploid and octoploid strawberries. Species-specific regulated networks were identified in the fruit of both octoploid and diploid plants, providing insights for future molecular breeding in cultivated strawberries.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2021)
Article
Plant Sciences
Yupeng Zhang, Marcos Viejo, Igor Yakovlev, Torstein Tengs, Paal Krokene, Timo Hytoenen, Paul E. Grini, Carl Gunnar Fossdal
Summary: This study aimed to understand the impact of temperature on the transcriptomes of different strawberry ecotypes. The results showed that plants reproduced asexually had a general transcriptomic response to temperature conditions, while sexually reproduced plants displayed less significant responses. Very few differentially expressed genes were shared between ecotypes, possibly due to their significant genetic and epigenetic differences. Temperature-induced changes had differential effects on the epigenetic machinery during the two types of reproduction.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Hiroaki Tachiwana, Noriko Saitoh
Summary: LncRNAs are a class of non-coding RNAs widely present in mammalian cells, involved in regulating cellular functions. Their dysregulation in cancer is closely related to disease development and they have diagnostic and therapeutic potential.
CURRENT MEDICINAL CHEMISTRY
(2021)
Review
Cell Biology
Xuwen Li, Zijian Zhang, Xinlong Luo, Jacob Schrier, Andrew D. Yang, Tao P. Wu
Summary: N-6-methyladenine (N-6-mA, m(6)dA, or 6mA) is a prevalent DNA modification in prokaryotes and has been recently identified in higher eukaryotes, such as mammals. It can serve as an epigenetic mark and play critical roles in various biological processes, but the function and regulatory mechanism of 6mA in eukaryotes, especially mammals, are still poorly understood and require further research.
Review
Cell Biology
Fei Xu, Wenhui Li, Xiao Yang, Lixin Na, Linjun Chen, Guobin Liu
Summary: Osteoporosis is a metabolic disease characterized by decreased bone mineral density and bone microstructure destruction. Epigenetics, including DNA methylation, histone modification, and non-coding RNAs, play an important role in post-transcriptional regulation and are closely related to bone metabolism processes such as osteogenic differentiation and bone remodeling. Abnormal epigenetic regulation can lead to bone metabolism-related diseases like osteoporosis, highlighting the importance of understanding epigenetic mechanisms for potential treatments.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Oncology
Folake Orafidiya, Lin Deng, Charlotte Lynne Bevan, Claire Emily Fletcher
Summary: Non-coding RNAs play important roles in tumor, especially in response to DNA damage. Studying these non-coding RNAs can help design better treatments and tests for prostate cancer.
Review
Cell Biology
Chaohua Si, Chen Chen, Yaxin Guo, Qiaozhen Kang, Zhenqiang Sun
Summary: This review discusses the significant role of m6A RNA modifications in the tumor microenvironment, highlighting their potential as biomarkers and therapeutic targets for cancer therapy. Understanding the relationship between TME and m6A RNA modifications may lead to new approaches for future cancer treatment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Plant Sciences
Jiang-Shan Hao, Jian-Feng Xing, Xu Hu, Zhi-Yong Wang, Min-Qiang Tang, Li Liao
Summary: This study examined the distribution patterns and potential functions of 6mA DNA modification in the halophyte Seashore paspalum genome. The results showed that 6mA modification sites were widely distributed across the genome and exhibited different levels and patterns in different types of transcription genes. The moderate 6mA density genes were found to be functionally correlated with stress resistance, while a specific 6mA distribution pattern was observed in gene groups with higher RNA expression. These findings provide new insights into the association between 6mA methylation and gene expression in P. vaginatum.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Cell Biology
Luke Twenhafel, DiAnna Moreno, Trista Punt, Madeline Kinney, Rebecca Ryznar
Summary: Osteosarcoma is a common malignant bone tumor in children and adolescents. Despite improvements in clinical outcomes, early detection is crucial for better survival rates and reducing the need for debilitating treatments like amputations. Research in the field of epigenetics, focusing on changes in genetic expression above the genome, shows potential for understanding and improving the treatment of osteosarcoma.
Review
Neurosciences
Qing Chen, Dan Li, Weifeng Jin, Yun Shi, Zhenhua Li, Peijun Ma, Jiaqi Sun, Shuzi Chen, Ping Li, Ping Lin
Summary: This review highlights the importance of epigenetic modulations in the pathogenesis of schizophrenia, with DNA methylation, ncRNA transcriptional regulation, and histone modification playing key roles. These epigenetic alterations may be utilized for diagnosis and personalized treatment strategies in clinical practice.
FRONTIERS IN NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Sho Tsukiyama, Md Mehedi Hasan, Hiroyuki Kurata
Summary: N6-methyladenine (6mA) plays crucial roles in various epigenetic processes and diseases. To understand these mechanisms, researchers have developed a CNN-based 6mA site predictor, CNN6mA, which outperforms existing models and provides intelligible interpretation of the prediction mechanism through new architectures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Chemistry, Medicinal
Pia Loren, Nicolas Saavedra, Kathleen Saavedra, Tomas Zambrano, Patricia Moriel, Luis A. Salazar
Summary: Cisplatin, an antineoplastic drug, is most notably known for its nephrotoxicity among various side effects. Recent research shows that epigenetic regulation plays a key role in cisplatin-induced nephrotoxicity by altering different signaling pathways leading to cell death. Despite the ongoing development in this field, it offers new strategies for the diagnosis and treatment of diseases.
Review
Genetics & Heredity
Yuzhu Chen, Yumiao Sun, Xiangyu Xue, Huanzhi Ma
Summary: Epigenetic modification refers to the alteration of genetic expression, which can be inherited without changes in the DNA sequence. Osteoporosis is a metabolic disorder characterized by decreased bone density and increased risk of fractures. Recent research has shown that epigenetic mechanisms play a significant role in the development and progression of osteoporosis. This dissertation explores the progress in understanding epigenetic mechanisms, their regulation of bone metabolism, and their implications for the treatment of bone-related diseases.
FRONTIERS IN GENETICS
(2023)
Review
Cell Biology
Fernando Lizcano, Lizeth Bustamante
Summary: Epigenetic changes induced by environmental factors play a significant role in cardiovascular diseases, particularly in cardiac hypertrophy. Reactivation of fetal genes caused by various pathologies is a common molecular component in cardiac hypertrophy. However, the impact of these molecular changes on therapeutic strategies is still relatively limited. Recently, new information has been discovered about the proteins that modify gene expression in cardiac hypertrophy. These proteins covalently modify DNA and induce changes in chromatin structure. The relationship between histones and DNA has a significant influence on gene expression influenced by the environment, leading to epigenetic variations. The regulation of pathological cardiac hypertrophy through epigenetic modifications involves changes in genomic stability, chromatin architecture, and gene expression. Histone 3 trimethylation at lysine 4, 9, or 27 (H3-K4; -K9; -K27me3) and histone demethylation at lysine 9 and 79 (H3-K9; -K79) are important mediators of reprogramming in pathologic hypertrophy. Among the chromatin architecture modifiers, histone demethylases are a group of proteins that play a crucial role in cardiac cell differentiation and may also contribute to the development of cardiac hypertrophy. In this review, we provide an overview of the current understanding of the influence of epigenetic modifications on gene expression involved in cardiac hypertrophy and potential therapeutic approaches.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Milda Mickute, Kotryna Kvederaviciute, Aleksandr Osipenko, Raminta Mineikaite, Saulius Klimasauskas, Giedrius Vilkaitis
Summary: The study presents a novel chemo-enzymatic approach using RNA 2'-O-methyltransferases to append an adapter to target RNA for sequencing library preparation. This method efficiently identifies RNA species, avoiding misdetection of highly-structured RNA. The findings provide valuable resources for RNA-centered regulatory network studies and could potentially advance the analysis of eukaryotic and prokaryotic ssRNAs.
Article
Biotechnology & Applied Microbiology
Xu-Yuan Liu, Yu Li, Kai-Kai Ji, Jie Zhu, Peng Ling, Tao Zhou, Lan-Ying Fan, Shang-Qian Xie
Article
Genetics & Heredity
Yu Li, Xiao-Ming Zhang, Mei-Wei Luan, Jian-Feng Xing, Jianguo Chen, Shang-Qian Xie
FRONTIERS IN GENETICS
(2020)
Article
Genetics & Heredity
Mei-Wei Luan, Xiao-Ming Zhang, Zi-Bin Zhu, Ying Chen, Shang-Qian Xie
FRONTIERS IN GENETICS
(2020)
Article
Genetics & Heredity
De-Hui Yuan, Jian-Feng Xing, Mei-Wei Luan, Kai-Kai Ji, Jun Guo, Shang-Qian Xie, Yuan-Ming Zhang
FRONTIERS IN GENETICS
(2020)
Correction
Genetics & Heredity
Yu Li, Xiao-Ming Zhang, Mei-Wei Luan, Jian-Feng Xing, Jianguo Chen, Shang-Qian Xie
FRONTIERS IN GENETICS
(2020)
Article
Multidisciplinary Sciences
Ying Chen, Fan Nie, Shang-Qian Xie, Ying-Feng Zheng, Qi Dai, Thomas Bray, Yao-Xin Wang, Jian-Feng Xing, Zhi-Jian Huang, De-Peng Wang, Li-Juan He, Feng Luo, Jian-Xin Wang, Yi-Zhi Liu, Chuan-Le Xiao
Summary: The error correction and de novo assembly tool NECAT developed by the authors efficiently produces high-quality assemblies of nanopore reads. The tool utilizes adaptive read selection and a two-step progressive method to overcome the high error rates in nanopore reads.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Peidong Xu, Shangqian Xie, Wenbo Liu, Pengfei Jin, Dandan Wei, Dahar Ghulam Yaseen, Yu Wang, Weiguo Miao
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Plant Sciences
Xun Weng, Xiaoxia Zhou, Shangqian Xie, Jinbao Gu, Zhen-Yu Wang
Summary: Alternative splicing is an important post-transcriptional regulation strategy in eukaryotes, which plays a crucial role in increasing proteome diversity and regulating mRNA levels. In plants, alternative splicing can enhance adaptation to external stress conditions. The study identified 365 genes encoding AS-related proteins in cassava, with 13 genes undergoing alternative splicing under diverse environmental stress conditions.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Genetics & Heredity
Lijing Chen, Bingzheng Jiang, Yue Miao, Ziji Liu, Shangqian Xie, Peng Ling, Jie Zhu
Summary: In this study, the complete chloroplast genome of Oxalis corniculata was sequenced, revealing its circular genome structure with a variety of genes, and a close phylogenetic relationship with two other plant species.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Multidisciplinary Sciences
Yong-Hui Xin, Yuan-Xin Wu, Bin Qiao, Long Su, Shang-Qian Xie, Peng Ling
Summary: This study analyzed the phenotypic traits of Calamansi to investigate its genetic diversities. The results revealed the diversity indexes for both qualitative and quantitative traits and categorized the samples based on phenotypic traits. The study provides a basis for the genetic improvement of Calamansi.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Li Feng, Tianyu Dong, Peng Jiang, Zhenyu Yang, Ang Dong, Shang-Qian Xie, Christopher H. Griffin, Rongling Wu
Summary: The genetic basis of plants' ability to resist abiotic stresses is not well understood. Current genetic tools can identify individual genetic variants involved in defense mechanisms, but lack a comprehensive understanding of the overall genetic atlas behind stress resistance. This study takes a holistic eco-evo-devo approach to stress response, integrating functional mapping and evolutionary game theory to reconstruct genetic interaction networks. Using the example of salt resistance in desert-adapted Euphrates poplar, the researchers infer genome-wide interactome networks and trace the regulatory mechanisms and interactions involved in mediating stress resistance. The study provides insights into the genetic architecture of stress response and informs gene editing strategies for improving plants' ability to thrive in stressful environments.
HORTICULTURE RESEARCH
(2022)
Review
Multidisciplinary Sciences
Shangqian Xie, Amy Wing-Sze Leung, Zhenxian Zheng, Dake Zhang, Chuanle Xiao, Ruibang Luo, Ming Luo, Shoudong Zhang
Summary: The Human Genome Project has led to the development of new sequencing technologies, with Oxford Nanopore technology being one of the most popular methods for direct DNA and RNA sequencing. This technology allows for sequencing of native DNA and RNA molecules without the need for conversion of mRNA to cDNA, enabling the documentation of modifications to these molecules.
Article
Biochemistry & Molecular Biology
Mei-Wei Luan, Jia-Lun Lin, Ye-Fan Wang, Yu-Xiao Liu, Chuan-Le Xiao, Rongling Wu, Shang-Qian Xie
Summary: SCSit is an efficient preprocessing tool for single-cell sequencing data from SPLiTseq, improving the consistency of identified reads and doubling the mapped reads compared to the original method.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biotechnology & Applied Microbiology
Zhouqing Luo, Kang Yu, Shangqian Xie, Marco Monti, Daniel Schindler, Yuan Fang, Shijun Zhao, Zhenzhen Liang, Shuangying Jiang, Meiwei Luan, Chuanle Xiao, Yizhi Cai, Junbiao Dai
Summary: We have developed an iterative SGC method with the aid of eArray as a generic yet effective tool to compact the synthetic yeast genome. The study demonstrates that at least 39 out of 65 nonessential genes in synXIIL can be removed collectively without affecting cell viability, and approximately 40% of the synthetic sequence is found to be dispensable for cell growth in specified conditions.
