Article
Biology
Jieyu Zhao, Eugene Yui-Ching Chow, Pui Yan Yeung, Qiangfeng Cliff Zhang, Ting-Fung Chan, Chun Kit Kwok
Summary: RNA G-quadruplex structure sequencing (rG4-seq) technique has been enhanced in version 2.0 to eliminate the need for gel purification, reduce PCR cycles, and increase PCR product yield, allowing for reliable identification of rG4s in low abundance transcripts. The improvements in rG4-seq 2.0 also address nucleotide biases and enhance the quality of cDNA libraries for further optimization in related methods.
Article
Biochemistry & Molecular Biology
Rongxin Zhang, Yajun Liu, Xingxing Zhang, Ke Xiao, Yue Hou, Hongde Liu, Xiao Sun
Summary: The study profiles and depicts RNA G-quadruplexes in the human transcriptome using DMS-seq and bioinformatics pipeline, revealing their significant association with immune pathways and COVID-19-related gene sets. The bioinformatics analysis also suggests potential regulatory functions of G-quadruplexes on miRNA targeting at the whole transcriptome level. Moreover, G-quadruplexes are found to be depleted in putative, but not real, PAS-strong poly(A) sites, weakening their likelihood of being actual cleaved sites.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Jun Fang, Lijuan Zheng, Yan Liu, Yuxin Peng, Qinghui Yang, Yuewen Huang, Jiali Zhang, Lixin Luo, Dunkai Shen, Yuyan Tan, Xuefen Lu, Guangfu Feng
Summary: In recent years, the development of G-quadruplexes and hydrogels has led to the advancement of intelligent biomaterials. By combining the biocompatibility and biological functions of G-quadruplexes with the hydrophilicity, high-water retention, flexibility, and biodegradability of hydrogels, G-quadruplex hydrogels have found wide applications in various fields. This paper provides a systematic classification of G-quadruplex hydrogels based on preparation strategies and applications, and discusses their utilization of biological functions and structure in biomedicine, biocatalysis, biosensing, and biomaterials. The challenges and future development directions of G-quadruplex hydrogels in terms of preparation, applications, stability, and safety are also analyzed.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Pharmacology & Pharmacy
Joana Figueiredo, Mojgan Djavaheri-Mergny, Lucille Ferret, Jean-Louis Mergny, Carla Cruz
Summary: In this review, we summarize the recent advancements in the development of G4 ligands capable of targeting specific genes associated with the development and progression of lung cancer.
DRUG DISCOVERY TODAY
(2023)
Article
Biochemistry & Molecular Biology
Mingming Lu, Yadong Zhang, Fengchun Yang, Jialin Mai, Qianwen Gao, Xiaowei Xu, Hongyu Kang, Li Hou, Yunfei Shang, Qiheng Qain, Jie Liu, Meiye Jiang, Hao Zhang, Congfan Bu, Jinyue Wang, Zhewen Zhang, Zaichao Zhang, Jingyao Zeng, Jiao Li, Jingfa Xiao
Summary: Transcriptome-wide association studies have led to a better understanding of genetic variants in regulating diseases and traits. However, there is a lack of databases curating public TWAS information. To fill this gap, TWAS Atlas is introduced as an integrated knowledgebase with 401,266 gene-trait associations from 200 publications, providing a user-friendly web interface for browsing, searching, and downloading relevant information.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Chen Cao, Jianhua Wang, Devin Kwok, Feifei Cui, Zilong Zhang, Da Zhao, Mulin Jun Li, Quan Zou
Summary: webTWAS is a new resource that combines comprehensive disease GWAS datasets with information on potential causal genes, allowing researchers to explore gene-disease associations. With data from 1298 high-quality GWAS summary statistics, a total of 235,064 gene-disease associations can be accessed, and custom TWAS analyses can be run on a user-friendly web server.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Zhongyuan Deng, Yudong Ren, Lina Guo, Xingcheng Xie, Lixiang Wang, Xianchun Li
Summary: In this study, G-quadruplex (G4) motifs were identified in the genome of Spodoptera frugiperda, and it was found that they were enriched in genic regions, particularly in the upstream regions of start codons. The G4 structures were more frequently present in the promoters of P450 and CarE gene families. Furthermore, the G4 ligand N-methyl mesoporphyrin IX (NMM) was shown to decrease P450 protein activity in larval midgut tissue, and it had synergistic effects with pesticides on toxicity. These findings suggest that G4 motifs could serve as a potential target for pest control.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Mathematical & Computational Biology
Hong-Sheng Zhong, Mei-Jing Dong, Feng Gao
Summary: G-quadruplex (G4), a non-canonical nucleic acid structure, plays a key role in important cellular processes and can be detected and predicted through high-throughput sequencing methods. The G4Bank database collects and analyzes experimentally identified DNA G-quadruplex sequences, providing comprehensive G4 data for further investigation. The database can be accessed at http://tubic.tju.edu.cn/g4bank/.
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
(2023)
Article
Microbiology
Elishiba Muturi, Fei Meng, Huan Liu, Mengwei Jiang, Hongping Wei, Hang Yang
Summary: The study found that functional PQSs in the ASFV genome, which can form stable G4s in the presence of K+ and be stabilized by G4 ligands such as NMM and PDS, could serve as potential targets for antiviral drugs. Experimental results showed that NMM and PDS can significantly suppress the expression of ASFV genes and inhibit the replication of ASFV in Porcine Alveolar Macrophages.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sheng Hu Qian, Meng-Wei Shi, Yu-Li Xiong, Yuan Zhang, Ze-Hao Zhang, Xue-Mei Song, Xin-Yin Deng, Zhen-Xia Chen
Summary: EndoQuad is a comprehensive database for eG4 research, providing genome-wide annotation and systematic characterization based on high-throughput experimental data. The database includes validated DNA eG4s and offers easy access and download, serving as an important resource for the study of eG4s.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Di Bai, Song-Wang Shan, Xin Zhang, Yan Li, Jie Xie, Wen-Qiang Wu
Summary: In this study, the folding, dynamics induced by environment, and protein-catalyzed unfolding of plant telomeric G4s were comprehensively studied. It was found that various plant telomeric sequences can fold into G4 structures, and the stability of G4s in dilute solution is decreased by both 5' and 3' ssDNA. Molecular crowding promotes the formation of parallel structures for three-layer G4s and increases the stability of all selected G4s. AtRecQ2 helicase can resolve the stable parallel structure of typical plant telomeric G4 in crowded solution, while ssDNA binding protein AtRPA cannot. Furthermore, AtRecQ2 unwinds the structure more efficiently in the presence of AtRPA. These results expand our understanding of the structures and dynamics of plant telomeric G4s.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biotechnology & Applied Microbiology
Vaishnovi Sekar, Emilio Marmol-Sanchez, Panagiotis Kalogeropoulos, Laura Stanicek, Eduardo A. Sagredo, Albin Widmark, Evangelos Doukoumopoulos, Franziska Bonath, Inna Biryukova, Marc R. Friedlander
Summary: In this study, a new method called agoTRIBE is developed to comprehensively detect miRNA targets at the single-cell level. By fusing Argonaute2 protein with the RNA editing domain of ADAR2, the method allows sensitive single-cell RNA sequencing to identify miRNA targets. The results show that agoTRIBE can identify functional miRNA targets and obtain transcriptome-wide measurements of RNA abundance.
NATURE BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Shweta Shekhar, Archana S. Prasad, Kalpana Banjare, Abhijeet Kaushik, Ajit K. Mannade, Mahima Dubey, Arun Patil, Vinay Premi, Ashish K. Vishwakarma, Abhinav Sao, Ravi R. Saxena, Amit Dubey, Girish Chandel
Summary: Little millet, a climate-resilient and nutritionally rich crop, has been largely overlooked due to the lack of Omic studies. The Little Millet Transcriptome Database (LMTdb) was developed to decipher the genetic signatures of this unknown crop and provide comprehensive information for breeders and scientists. The freely available database includes transcriptome sequences, functional annotation, microsatellite markers, DEGs, and pathway information, facilitating functional and applied Omic studies in millet crops.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Chemistry, Medicinal
Domen Oblak, Hadzi, Crtomir Podlipnik, Jurij Lah
Summary: The authors investigated the (un)folding and binding process of a human telomeric fragment with ligands through calorimetry and spectroscopy. The results showed that the presence of specific ligands can alter the topology of G-quadruplex nucleic acids. By analyzing thermodynamic parameters and conducting molecular modeling, the driving forces behind the topological transformations were clarified.
Article
Cell Biology
Yaping Jiang, Xin Zhang, Xiaoyan Zhang, Kun Zhao, Jing Zhang, Chuanxi Yang, Yihui Chen
Summary: Our research indicates that m6A modification plays a crucial role in the development of pterygium and may serve as a potential new target for the future treatment of this condition.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Huakun Zhang, Yiliang Ding
Summary: RNA folding plays a crucial role in post-transcriptional regulation in plants, with recent genome-wide RNA structure profiling methods enabling researchers to study tens of thousands of RNAs. The new insights into RNA structure functionality within the context of post-transcriptional regulation, including mRNA maturation, translation, and RNA degradation in plants, have been discussed, along with an overview of how plants exhibit different RNA structures in response to environmental changes.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2021)
Article
Plant Sciences
Shaoyan Zheng, Jingfang Dong, Jingqin Lu, Jing Li, Dagang Jiang, Haopeng Yu, Simiao Ye, Wenli Bu, Zhenlan Liu, Hai Zhou, Yiliang Ding, Chuxiong Zhuang
Summary: This study reveals the important regulatory role of the cytosolic PPR protein OsCPPR1 in pollen development in rice. OsCPPR1 inhibits the transcription factor OsGLK1 to regulate plastid development and programmed cell death. The findings highlight the novel functions of cytosolic PPRs and identify a new regulatory mechanism for pollen development in rice.
Review
Biochemistry & Molecular Biology
Haopeng Yu, Yiman Qi, Yiliang Ding
Summary: The article discusses the successful applications of deep learning in solving RNA structure problems, including RNA structure prediction, non-canonical G-quadruplex, RNA-protein interactions, and RNA switches. It also provides a general guide to using deep learning for solving RNA structure problems.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Minglei Yang, Pan Zhu, Jitender Cheema, Rebecca Bloomer, Pawel Mikulski, Qi Liu, Yueying Zhang, Caroline Dean, Yiliang Ding
Summary: Cellular RNAs are heterogeneous in terms of their alternative processing and secondary structures, and the functional importance of this complexity is still not well understood. COOLAIR, a group of alternatively processed antisense non-coding transcripts generated at the Arabidopsis FLC locus, influences FLC transcriptional output under different temperature conditions. The study reveals that different isoforms of COOLAIR adopt multiple distinct structural conformations and change in response to external conditions.
Review
Plant Sciences
Haifeng Liu, Zhaohui Chu, Xiaofei Yang
Summary: RNA G-quadruplex (RG4) is a complex RNA structure that plays key roles in plant growth, development, and adaptation. Recent studies have shown that RG4 is widespread in plants and has new functions in regulating plant growth and development. Additionally, RG4 may play an important role in adapting to environmental conditions and evolutionary processes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Xiaofei Yang, Haopeng Yu, Susan Duncan, Yueying Zhang, Jitender Cheema, Haifeng Liu, J. Benjamin Miller, Jie Zhang, Chun Kit Kwok, Huakun Zhang, Yiliang Ding
Summary: This study analyzes the nucleotide composition of plant transcriptomes and their corresponding habitats, revealing that plants in cold climates have guanine-enriched transcriptomes that are prone to forming RNA G-quadruplex structures. The formation of RNA G-quadruplexes in response to cold enhances mRNA stability and promotes plant cold response.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Susan Duncan, Hans E. Johansson, Yiliang Ding
Summary: This study presents a modified protocol for validating reference genes suitable for quantitative single molecule RNA fluorescence in situ hybridization studies in Arabidopsis root apical meristem cells. The authors also propose selection criteria for the first set of Arabidopsis smFISH reference genes. These findings provide a solid foundation for future quantitative single molecule RNA studies.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Biochemistry & Molecular Biology
Pablo A. Manavella, Micaela A. Godoy Herz, Alberto R. Kornblihtt, Reed Sorenson, Leslie E. Sieburth, Kentaro Nakaminami, Motoaki Seki, Yiliang Ding, Qianwen Sun, Hunseung Kang, Federico D. Ariel, Martin Crespi, Axel J. Giudicatti, Qiang Cai, Hailing Jin, Xiaoqi Feng, Yijun Qi, Craig S. Pikaard
Summary: This article presents and discusses new and long-standing open questions in plant RNA biology, covering topics such as alternative splicing, dynamics, translation, structures, epitranscriptomics, long non-coding RNAs, small RNA production and functions, and more. It provides insights into the current state-of-the-art in the field and aims to provoke future discoveries and reflections.
Article
Plant Sciences
Bibo Yang, Liangda Li, Jianquan Liu, Lushui Zhang
Summary: By analyzing plastome data, this study confirms the phylogenetic position of Parapteropyrum tibeticum within the genus Fagopyrum, and suggests that the sampled woody genera of the family Polygonaceae are polyphyletic. This study provides taxonomic evidence for placing the woody Parapteropyrum tibeticum under Fagopyrum as Fagopyrum tibeticum.
Article
Biotechnology & Applied Microbiology
Zhenshan Liu, Qi Liu, Xiaofei Yang, Yueying Zhang, Matthew Norris, Xiaoxi Chen, Jitender Cheema, Huakun Zhang, Yiliang Ding
Summary: This study identified specific RNA structures in nuclear mRNAs that are associated with splicing and polyadenylation events, revealing a new regulatory mechanism for mRNA processing.