Article
Biochemistry & Molecular Biology
Inga Loedige, Artem Baranovskii, Samantha Mendonsa, Sayaka Dantsuji, Niko Popitsch, Laura Breimann, Nadja Zerna, Vsevolod Cherepanov, Miha Milek, Stefan Ameres, Marina Chekulaeva
Summary: Cells require specific shapes and subcellular compartments to perform biological functions, which is achieved through the asymmetric distribution of mRNAs. The current model of mRNA localization involves specific sequences called zipcodes, but additional mechanisms are likely involved. This study investigates the role of mRNA stability in localization and reveals that mRNA destabilization elements mediate the localization of mRNAs associated with housekeeping functions to neurites in various types of neurons.
Article
Biotechnology & Applied Microbiology
Jia-Xiang Zhang, Pei-Jie Huang, Da-Peng Wang, Wen-Yu Yang, Jian Lu, Yong Zhu, Xiao-Xiao Meng, Xin Wu, Qiu-Hai Lin, Hui Lv, Hui Xie, Rui-Lan Wang
Summary: The study reveals the critical role of m6A modification in pulmonary fibrosis, suggesting that manipulating m6A modification through targeting METTL3 may be a promising strategy for the treatment of pulmonary fibrosis.
Article
Environmental Sciences
Wenxue Li, Mingxue Tan, Huiqi Wang, Ziwei Wang, Yaqin Pang, Rongfang Yang, Shiyuan Zhong, Xinhong Pan, Shen Chen, Qing Wang, Daochuan Li, Yongmei Xiao, Wen Chen, Liping Chen
Summary: This study investigates the role of m6A methylation in the development of liver disease caused by long-term exposure to cadmium. The findings suggest that METTL3 plays a crucial role in cadmium-induced hepatotoxicity, and its overexpression attenuates liver injury in mice. Transcriptome analysis reveals the dysregulation of metabolic pathways, signaling pathways, and circadian rhythm as potential mechanisms underlying cadmium-induced liver toxicity.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biochemistry & Molecular Biology
Sungyun Cho, Gina Lee, Brian F. Pickering, Cholsoon Jang, Jin H. Park, Long He, Lavina Mathur, Seung-Soo Kim, Sunhee Jung, Hong-Wen Tang, Sebastien Monette, Joshua D. Rabinowitz, Norbert Perrimon, Samie R. Jaffrey, John Blenis
Summary: The study found that mTORC1 and its downstream kinase S6K enhance the translation of WTAP, affecting cellular metabolism and cancer progression. WTAP regulates MXD2 to impact the proliferation of mTORC1-activated cancer cells, revealing a mechanism by which mTORC1 stimulates oncogenic signaling through m(6)A RNA modification.
Review
Cell Biology
Hanxiao Sun, Kai Li, Cong Liu, Chengqi Yi
Summary: Nucleobase modifications are widespread in eukaryotic mRNA and play crucial roles in post-transcriptional gene regulation. The most extensively studied modification is N-6-methyladenosine (m(6)A), but other modifications are also being investigated. This Review focuses on the emerging mechanisms and functions of these non-m(6)A modifications.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Medicine, Research & Experimental
Lina Quan, Chuiming Jia, Yiwei Guo, Yao Chen, Xinya Wang, Qiuting Xu, Yu Zhang
Summary: This study investigates the methylation pattern of multiple myeloma and its effect on the expression of HNRNPA2B1 and downstream targets. The findings suggest that HNRNPA2B1 increases cell proliferation and deregulates cell apoptosis in multiple myeloma through TLR4 signaling.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Teng Zhang, Shao-Wu Zhang, Song-Yao Zhang, Shou-Jiang Gao, Yidong Chen, Yufei Huang
Summary: A novel algorithm, m(6)A-express, was developed to predict condition-specific m(6)A regulation of gene expression, demonstrating high prediction specificity and sensitivity. METTL3 and METTL14 were found to competitively regulate the transcriptional processes by mediating m(6)A-reg-exp of different genes in different cell types, highlighting the complex nature of m(6)A regulation of gene expression. Unique m(6)A-reg-exp patterns were discovered in human brain and intestine tissues, enriched in organ-specific processes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Yanfen Zheng, Xingyang Li, Shuang Deng, Hongzhe Zhao, Ying Ye, Shaoping Zhang, Xudong Huang, Ruihong Bai, Lisha Zhuang, Quanbo Zhou, Mei Li, Jiachun Su, Rui Li, Xiaoqiong Bao, Lingxing Zeng, Rufu Chen, Jian Zheng, Dongxin Lin, Chuan He, Jialiang Zhang, Zhixiang Zuo
Summary: This study investigates the role of N-6-methyladenosine (m(6)A) modification in gene transcripts in pancreatic ductal adenocarcinoma (PDAC). The results show that m(6)A modifications can distinguish PDAC subtypes with different prognosis outcomes. The study also identifies a new m(6)A regulator, CSTF2, which affects the formation of PDAC subtypes by regulating m(6)A installation and is mainly recognized by IGF2BP2. These findings provide potential therapeutic targets for precision medicine in PDAC.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Zhong-xin Jiang, Yi-ning Wang, Zi-yuan Li, Zhi-hui Dai, Yi He, Kun Chu, Jia-yi Gu, Yi-Xuan Ji, Ning-xia Sun, Fu Yang, Wen Li
Summary: The study demonstrates that m6A adenine regulates the function of GCs in female ovarian aging by modulating FTO demethylase, which in turn affects ovarian aging. FTO retards ovarian cell aging by regulating FOS expression.
CELL DEATH & DISEASE
(2021)
Article
Biochemical Research Methods
Teng Zhang, Shao-Wu Zhang, Song-Yao Zhang, Qian-qian Ma
Summary: N-6-methyladenosine (m(6)A) is the most abundant form of mRNA modification that plays an important role in regulating gene expression. This study proposed a novel method (m(6)Aexpress-Reader) to predict m(6)A-regulated gene expression in specific contexts, integrating m(6)A sites and reader binding information. The findings reveal the complex characteristic of m(6)A on gene expression regulation and the distinct regulated pattern of m(6)A-regulated genes with different reader binding, especially in cancer.
Article
Biotechnology & Applied Microbiology
Zihao Dai, Wanjie Zhu, Yingdong Hou, Xinyue Zhang, Xuxin Ren, Kai Lei, Junbin Liao, Haining Liu, Zhihang Chen, Sui Peng, Shaoqiang Li, Shuibin Lin, Ming Kuang
Summary: This study discovered that the m(6)A modification of 18S rRNA and its methyltransferase METTL5 were aberrantly upregulated in intrahepatic cholangiocarcinoma (ICC) and associated with poorer survival. Loss- and gain-of-function assays in vitro and in vivo revealed the critical role of METTL5-mediated 18S rRNA m(6)A modification in regulating ICC cell growth and metastasis. Mechanistically, METTL5 depletion impairs the synthesis of ribosomes and inhibits the translation of G-quadruplex-containing mRNAs in the transforming growth factor (TGF)-beta pathway.
Article
Cell Biology
Sung Ho Boo, Hongseok Ha, Yoon Ki Kim
Summary: This study reveals that N-1-methyladenosine (m(1)A) accelerates the degradation of N-6-methyladenosine (m(6)A) on RNA and identifies HRSP12 as an RNA-binding protein that recognizes m(1)A. The binding of HRSP12 promotes the interaction of YTHDF2 with m(6)A, facilitating RNA degradation.
Review
Biochemistry & Molecular Biology
Shino Murakami, Samie R. Jaffrey
Summary: Information in mRNA is not only confined to its nucleotide sequence but also includes chemical modifications, such as N-6-methylade-nosine (m(6)A). m(6)A modifies mRNA and can affect nuclear processes and promote degradation of mRNA in the cytoplasm. It marks a specific group of mRNAs associated with certain biological processes and is enriched in other groups as well.
Article
Biochemistry & Molecular Biology
Anna Uzonyi, David Dierks, Ronit Nir, Oh Sung Kwon, Ursula Toth, Isabelle Barbosa, Cindy Burel, Alexander Brandis, Walter Rossmanith, Herve Le Hir, Boris Slobodin, Schraga Schwartz
Summary: N6-methyladenosine (m6A) is a widespread destabilizing mark on mRNA with non-uniform distribution across the transcriptome. In this study, the authors propose that m6A deposition is exclusion-based rather than selective. They demonstrate that m6A consensus motifs are methylated by default unless they are near splice junctions. By validating a simple model based on the presence of m6A motifs and exon-intron architecture, they show that mRNA decay is mechanistically mediated via m6A.
Article
Multidisciplinary Sciences
WeiChao Hao, MeiJuan Dian, Ying Zhou, QiuLing Zhong, WenQian Pang, ZiJian Li, YaYan Zhao, JiaCheng Ma, XiaoLin Lin, RenRu Luo, YongLong Li, JunShuang Jia, HongFen Shen, ShiHao Huang, GuanQi Dai, JiaHong Wang, Yan Sun, Dong Xiao
Summary: The m(6)A modification plays a crucial role in maintaining cellular energy homeostasis and adapting to nutrient deficiency. The m(6)A reader YTHDF3 is essential for autophagy induction and promotes autophagosome formation and lysosomal degradation upon nutrient deficiency.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Jie Jiang, Bowen Song, Kunqi Chen, Zhiliang Lu, Rong Rong, Yu Zhong, Jia Meng
Summary: N6,2'-O-dimethyladenosine (m(6)A(m)) is a reversible modification found on various RNA molecules, and its biological function is still unknown. In order to identify m(6)A(m) sites on RNA and aid researchers in understanding its biological functions, m6AmPred, the first web server for in silico prediction of m(6)A(m) sites from RNA sequences, has been developed using the eXtreme Gradient Boosting with Dart algorithm (XgbDart) and EIIP-PseEIIP encoding scheme.
Article
Computer Science, Artificial Intelligence
Sifan Song, Tianming Bai, Yanxin Zhao, Wenbo Zhang, Chunxiao Yang, Jia Meng, Fei Ma, Jionglong Su
Summary: This research focuses on the automatic segmentation of overlapping pairs of chromosomes, proposing a novel convolutional neural network called Compact Seg-UNet and a method to generate more realistic images with opaque overlapping regions. The proposed model achieves significantly higher segmentation performance for overlapping chromosomes compared to existing methods.
NEURAL PROCESSING LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Jiongming Ma, Bowen Song, Zhen Wei, Daiyun Huang, Yuxin Zhang, Jionglong Su, Joao Pedro de Magalhaes, Daniel J. Rigden, Jia Meng, Kunqi Chen
Summary: The paragraph introduces a database called m(5)C-Atlas, which contains information on 166,540 m(5)C sites from 13 different species. It provides data on methylation levels under specific conditions and some novel features for exploring the m(5)C epitranscriptomes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Enakshi Sivasudhan, Neil Blake, Zhiliang Lu, Jia Meng, Rong Rong
Summary: This review article provides a comprehensive overview of the role of HBx in modulating the various hallmarks of HCC, and emphasizes the potential of targeting HBx for novel combinatorial therapies against liver cancer.
Article
Biochemistry & Molecular Biology
Bowen Song, Xuan Wang, Zhanmin Liang, Jiongming Ma, Daiyun Huang, Yue Wang, Joao Pedro de Magalhaes, Daniel J. Rigden, Jia Meng, Gang Liu, Kunqi Chen, Zhen Wei
Summary: Recent advances in epitranscriptomics have revealed the functional associations between RNA modifications (RMs) and multiple human diseases. This study presents an updated database, RMDisease v2.0, which identifies RM-associated genetic variants that may affect different types of RNA modifications in various organisms. These variants, including disease- and trait-associated genetic variants, may function through perturbations of epitranscriptomic markers. RMDisease v2.0 serves as a valuable resource for studying the genetic drivers of phenotypes in the epitranscriptome layer circuitry.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yuxin Zhang, Jie Jiang, Jiongming Ma, Zhen Wei, Yue Wang, Bowen Song, Jia Meng, Guifang Jia, Joao Pedro de Magalhaes, Daniel J. Rigden, Daiyun Hang, Kunqi Chen
Summary: Mapping RNA modifications with advanced technologies has revolutionized our understanding of them. Current modification profiling methods are limited and require selective treatments. Direct RNA sequencing enables the direct study of modifications and has the potential to overcome the limitations of previous methods. The DirectRMDB database provides a fresh perspective on RNA modifications and allows exploration of the epitranscriptome in an isoform-specific manner.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Medicine, Research & Experimental
Jingxian Zhou, Xuan Wang, Zhen Wei, Jia Meng, Daiyun Huang
Summary: This study presents a computational framework for predicting 4acC-carrying regions in Arabidopsis genomic DNA and demonstrates its promising performance through cross-validation and independent testing. The framework also enables motif mining and provides a user-friendly web server. The findings of this study will contribute to 4acC research.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Medicine, Research & Experimental
Yue Wang, Xuan Wang, Xiaodong Cui, Jia Meng, Rong Rong
Summary: DPred is the first computational tool for predicting D on mRNAs in yeast from the primary RNA sequences. The deep learning model outperformed classic machine learning approaches and achieved reasonable accuracy and reliability in cross-validation and testing.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Biochemical Research Methods
Yiyou Song, Yue Wang, Xuan Wang, Daiyun Huang, Anh Nguyen, Jia Meng
Summary: In this study, a multi-task computational method called AdaptRM was proposed for synergetic learning of multi-tissue, type, and species RNA modifications from both high- and low-resolution epitranscriptome datasets. The AdaptRM approach outperformed existing models and deep-learning architectures in three case studies, demonstrating its effectiveness and generalization ability. Furthermore, by interpreting the learned models, the potential association between different tissues in terms of epitranscriptome sequence patterns was revealed for the first time.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Zhanmin Liang, Haokai Ye, Jiongming Ma, Zhen Wei, Yue Wang, Yuxin Zhang, Daiyun Huang, Bowen Song, Jia Meng, Daniel J. Rigden, Kunqi Chen
Summary: m(6)A-Atlas v2.0 is a valuable research tool that includes a large number of m(6)A sites and their functional annotations from different technologies and experimental conditions, to facilitate the study of this important RNA modification.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xuan Wang, Yuxin Zhang, Kunqi Chen, Zhanmin Liang, Jiongming Ma, Rong Xia, Joao Pedro de Magalhaes, Daniel J. Rigden, Jia Meng, Bowen Song
Summary: With the advancement in mapping N7-methylguanosine (m(7)G) RNA methylation sites, a comprehensive resource (m7Ghub v.2.0) has been developed to study m(7)G modification under various physiological contexts. The resource includes the m7GDB database collecting hundreds of thousands of putative m(7)G sites identified in 23 species, the m7GDiseaseDB hosting m(7)G-associated variants including disease-relevant m(7)G-SNPs, and two enhanced analysis modules for interactive analyses.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yue Wang, Zhen Wei, Jionglong Su, Frans Coenen, Jia Meng
Summary: RgnTX is an R/Bioconductor tool for colocalization analysis of transcriptome elements. It considers transcriptome heterogeneity and isoform ambiguity, and directly utilizes transcriptome annotation. It offers various permutation test models to simulate realistic transcriptome-wide backgrounds. The tool supports testing of transcriptome elements without clear isoform association and provides pre-defined functions for visualization and multiple hypothesis testing.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Xichen Zhao, Yuxin Zhang, Daiyun Hang, Jia Meng, Zhen Wei
Summary: This article reviews 15 published RNA modification prediction tools based on direct RNA sequencing data, including their computational models, input-output formats, supported modification types, and reported performance. The article also discusses the challenges and future improvements of nanopore sequencing-based methods for RNA modification detection.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Proceedings Paper
Neuroimaging
Jinfeng Wang, Qiming Huang, Feilong Tang, Jia Meng, Jionglong Su, Sifan Song
Summary: In this study, we propose a novel medical image segmentation model called SSFormer, which utilizes a pyramid Transformer encoder to improve the generalization ability of the model. Experimental results demonstrate that SSFormer achieves state-of-the-art performance in both learning and generalization assessment.
MEDICAL IMAGE COMPUTING AND COMPUTER ASSISTED INTERVENTION, MICCAI 2022, PT III
(2022)
Article
Biochemical Research Methods
Shutao Chen, Lin Zhang, Lin Lu, Jia Meng, Hui Liu
Summary: Recent studies have shown that studying the epi-transcriptomic patterns of N6-methyladenosine (m(6)A) can help understand its complex functions and co-regulatory mechanisms. A weighted Plaid biclustering model (FBCwPlaid) was proposed to discover potential functional patterns in m(6)A methylation profiles. The model uses RNA expression levels as weights to address confidence of methylation levels and allows overlapping biclusters. FBCwPlaid was applied on MeRIP-Seq data and identified three patterns highly relevant to m(6)A methyltransferases, some of which were condition-specific.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
