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
Multidisciplinary Sciences
H. Busra Cagirici, Hikmet Budak, Taner Z. Sen
Summary: This study identified and compared G4 motifs in barley with other monocot species, revealing their genomic distribution and molecular functions. The distribution of G4 motifs around genic regions was found to be relatively similar in the species studied, except for Arabidopsis.
SCIENTIFIC REPORTS
(2021)
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)
Article
Biochemistry & Molecular Biology
Souroprobho Chowdhury, Jiayi Wang, Sabrina Pia Nuccio, Hanbin Mao, Marco Di Antonio
Summary: This study investigates the disruption of G4s using LNA probes, finding that short LNA probes can accelerate the rate of G4 disruption and have the potential to study G4 biology.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Bartosz Adamczyk, Michal Zurkowski, Marta Szachniuk, Tomasz Zok
Summary: WebTetrado is a web server for analyzing quadruplex structures, providing a user-friendly interface and many advanced features such as automatic identification, annotation, classification, and visualization of the motifs. It supports various types of quadruplexes and can process 3D models from experimental or in silico sources.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Ye Teng, Ming Zhu, Zhidong Qiu
Summary: Repeat expansions are the main genetic cause of various neurodegeneration diseases. G-rich repeat sequences, such as CGG and GGGGCC, form functional G-quadruplexes and play important roles in bioprocesses. This review provides an overview of the contribution of G-quadruplex in repeat expansion disorders and summarizes the related mechanisms, including genetic instabilities, toxic RNA foci, and protein/peptide dysfunction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Emil Laust Kristoffersen, Andrea Coletta, Line Morkholt Lund, Birgit Schiott, Victoria Birkedal
Summary: G-quadruplexes are noncanonical DNA structures that play important roles in DNA metabolic processes. We investigated the folding of consecutive G-quadruplexes in both potassium- and sodium-containing solutions and found coexistence of partially and fully folded DNA. Full consecutive G-quadruplex formation is inhibited by other DNA structures randomly nucleating on the DNA. Our study provides insights into the formation of consecutive G-quadruplexes in both equilibrium and nonequilibrium conditions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Ilias Georgakopoulos-Soares, Guillermo E. Parada, Hei Yuen Wong, Ragini Medhi, Giulia Furlan, Roberto Munita, Eric A. Miska, Chun Kit Kwok, Martin Hemberg
Summary: This study reveals the enrichment of G4 motifs near splice junctions, suggesting their regulatory role in RNA stability and splicing. G4 motifs play important roles in exon skipping and inclusion, and are associated with multiple RNA binding proteins. Furthermore, G4 motifs show strong enrichment at splice sites in mammals and birds, indicating the evolutionary conservation of this splice regulatory mechanism.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Anirban Ghosh, Eric Largy, Valerie Gabelica
Summary: This study focuses on using native mass spectrometry for drug screening on G-quadruplex DNA structures. By studying 28 sequences, a standardized screening method was established and recommendations for future research were provided. Furthermore, an R-based open-source application was developed to build and consult a database for further exploration.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Ernest Wang, Ravi Thombre, Yajas Shah, Rachel Latanich, Jiou Wang
Summary: G-quadruplexes (G4s), higher-order DNA and RNA secondary structures with various conformations, play important roles in cellular processes and may have an impact on the pathogenic cascades of neurological diseases. Further research is needed to fully understand their functions and potential implications in disease development.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Medicinal
Emanuela Ruggiero, Sara N. Richter
Summary: With the emergence and fast mutation rates of new viruses, there is a need for new antiviral targets and compounds. Most existing antiviral drugs target only a few specific viruses by affecting viral nucleic acid processing. However, selectively targeting nucleic acids of interest is challenging. Recently, G-quadruplexes (G4s), which are alternative structures to the classic double helix, have attracted attention due to their important biological roles. Molecules that selectively target G4s have been developed and investigated as potential antiviral drugs for various human pathologies, including viral infections.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2023)
Article
Biochemical Research Methods
Marco Caterino, Katrin Paeschke
Summary: The nucleic acid structure known as G-quadruplex (G4) plays a significant role in nucleic acid-based mechanisms that impact cellular processes. DNA G4 is well-studied, while RNA G4 is gaining attention for its role in cellular homeostasis. Proper regulation of G4 structures within cells is crucial, and helicases are important in resolving them. However, only a few rG4 unwinding helicases have been identified and characterized so far.
Article
Biochemistry & Molecular Biology
Poulomi Das, Khac Huy Ngo, Fernaldo Richtia Winnerdy, Arijit Maity, Blaz Bakalar, Yves Mechulam, Emmanuelle Schmitt, Anh Tuan Phan
Summary: This study investigates the adaptability of left-handed G4 structures towards the presence of bulges, presenting the structural characteristics of left-handed G4s accommodating varying numbers of bulges. Bulges in left-handed G4s exhibit distinct features compared to those in right-handed G4s, and elucidation of the intricate structural details may enhance understanding of the potential roles and limitations of these unique structures.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Kaixin Lyu, Eugene Yui-Ching Chow, Xi Mou, Ting-Fung Chan, Chun Kit Kwok
Summary: G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures with significant regulatory roles in biological processes. Recently developed high-throughput methods have enabled the detection of RNA G4s (rG4s) on a transcriptome-wide scale, revealing novel functions of rG4s across different organisms. Challenges still exist in detecting these structural motifs globally and reliably.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Timo Hagen, Artur Laski, Anneke Bruemmer, Adam Pruska, Verena Schloesser, Antoine Clery, Frederic H-T Allain, Renato Zenobi, Sven Bergmann, Jonathan Hall
Summary: Gene expression is heavily influenced by RNA structure, with A-to-I editing activating latent rG4s and forming GI-quadruplexes, previously unrecognized structural motifs that may play a significant role in gene expression regulation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Jiuxin Qu, Zhao Cai, Xiangke Duan, Han Zhang, Hang Cheng, Shuhong Han, Kaiwei Yu, Zhaofang Jiang, Yingdan Zhang, Yang Liu, Fang Bai, Yingxia Liu, Lei Liu, Liang Yang
Summary: Our study suggests that SARS-CoV-2 infection can lead to genetic adaptation of bacterial pathogens, promoting chronic infections. The adapted bacteria exhibit characteristics such as excessive biofilm formation and reduced virulence, enabling them to evade immune clearance. This highlights the importance of understanding the lung microenvironment post-virus infections and superinfection mechanism in COVID-19 patients.
CELL AND BIOSCIENCE
(2022)
Article
Chemistry, Medicinal
Jing Wang, Xi Liu, Kaiwei Yu, Moxiao Liu, Jiuxin Qu, Yingxia Liu, Zhao Cai, Ke Wang, Chao Zhuo, Liang Yang, Yingdan Zhang
Summary: The co-infection of Pseudomonas aeruginosa (Pa) and Acinetobacter baumannii (Ab) in ICU patients is common but challenging to eliminate. Research suggests that antibiotic exposure reshapes the community compositions of dual-species biofilms, with different EPS structures playing roles in maintaining stability, highlighting the potential of targeting EPS structural fibers like Psi and extracellular DNA (eDNA) as a strategy for controlling polymicrobial biofilm-related infections.
ACS INFECTIOUS DISEASES
(2022)
Review
Biotechnology & Applied Microbiology
Xiaobo Liu, Bin Cao, Liang Yang, Ji-Dong Gu
Summary: Biofilm formation and biofilm-induced biodeterioration have significant impacts on the community. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a key signaling molecule in bacteria, regulating various bacterial processes. Understanding the regulatory mechanisms of c-di-GMP would benefit the control of bacterial processes and the development of anti-biofilm technologies.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Biochemical Research Methods
Mubarak Umar, Chun-Yin Chan, Chun Kit Kwok
Summary: The RNA G-quadruplex (rG4)-SELEX method generates L-RNA aptamers to target rG4 structures, effectively suppressing G-quadruplex-mediated interactions. This Protocol Extension improves aptamer discovery speed, showcasing the utility of L-RNA aptamers. The detailed procedure expands the current rG4 toolkit, facilitating exploration of innovative rG4-related applications.
Article
Multidisciplinary Sciences
Xingjian Chen, Zifan Zhu, Weitong Zhang, Yuchen Wang, Fuzhou Wang, Jianyi Yang, Ka-Chun Wong
Summary: Predicting human diseases from microbiome data is important in medical applications. Existing methods often overlook the abundance profiles of known and unknown microbial organisms, as well as the taxonomic relationships among them, resulting in information loss. To address these issues, we developed a comprehensive machine learning framework called MetaDR that combines deep learning and various information sources to predict human diseases.
Article
Biotechnology & Applied Microbiology
Yu-Ming Cai, Kai-Wei Yu, Ji-Hong Liu, Zhao Cai, Zun-Hao Zhou, Yang Liu, Tian-Fu Wang, Liang Yang
Summary: The c-di-GMP signaling pathways in P. aeruginosa are highly organized and play important roles in the transition between motile and sessile lifestyles. This study identified a phosphodiesterase, PipA, that regulates bacteriophage production, and uncovered a potential signaling circuit for biofilm treatment.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Zhe Liu, Xudong Liu, Fang Liu, Hui Zhao, Yu Zhang, Yafan Wang, Ying Ma, Fuzhou Wang, Weitong Zhang, Olutomilayo Olayemi Petinrin, Zhongyu Yao, Jingbo Liang, Qian He, Dayun Feng, Lei Wang, Ka-Chun Wong
Summary: Bladder urothelial carcinoma (BLCA) is a complex disease with high morbidity and mortality. Changes in alternative splicing and splicing factors play an important role in tumorigenesis. This study identified survival-related alternative splicing events in BLCA and constructed a regulatory network of splicing factors and alternative splicing events. The findings provide insights into potential therapeutic targets for BLCA.
Article
Computer Science, Information Systems
Weidun Xie, Zetian Zheng, Weitong Zhang, Lei Huang, Qiuzhen Lin, Ka-Chun Wong
Summary: This paper proposes a model that combines feature extraction methods, deep learning algorithms, and a voting system to study the relationship between miRNAs and genes. By using high-throughput technology to process large amounts of biological data, the model is able to reveal potential associations between miRNAs and genes in cancer therapy.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Yue Sun, Xiaolong Shao, Yingchao Zhang, Liangliang Han, Jiadai Huang, Yingpeng Xie, Jingui Liu, Xin Deng
Summary: Adequate nutrition is crucial for rapid translational elongation and protein synthesis in both eukaryotic cells and prokaryotic bacteria. The translational elongation rates of T3SS proteins in pathogenic bacteria are negatively regulated by nutrient concentration and culture duration. Rapid translational elongation and synthesis of T3SS proteins require sufficient tRNAs and elongation factors under nutrient-limiting conditions.
CELL AND BIOSCIENCE
(2022)
Article
Cell Biology
Yingpeng Xie, Jingwei Li, Yiqing Ding, Xiaolong Shao, Yue Sun, Fangzhou Xie, Shiyi Liu, Shaojun Tang, Xin Deng
Summary: The study integrates transcriptome and chromatin immunoprecipitation sequencing data to reveal the regulatory roles of TCSs in different environments, as well as their conservation and variability. Seven TCSs regulating the type III secretion system, motility, or exopolysaccharide production are identified.
Article
Microbiology
Tianyuan Jia, Dongjing Liu, Xianbiao Bi, Menglu Li, Zhao Cai, Jiapeng Fu, Zhi Liu, Pengyao Wu, Xue Ke, Aiqun Jia, Guoliang Zhang, Guobao Li, Liang Yang
Summary: This study reveals that the AhR ligand Pht and its vitamin K analogs can inhibit the quorum sensing mechanism of P. aeruginosa and activate immune-modulating functions, suggesting their potential as alternative treatments for infections.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Mingxing Tang, Shumin Liao, Jing Qu, Yixin Liu, Shuhong Han, Zhao Cai, Yunping Fan, Liang Yang, Shuo Li, Liang Li
Summary: This study used human airway organoids (HAOs) as a host model to investigate Pseudomonas aeruginosa biofilm development. Dual transcriptome sequencing revealed that quorum sensing (QS) was the most dominant virulence pathway, profoundly affecting both bacterial biofilm and host immune responses. The study demonstrated that HAOs are an optimal model for studying the interaction between the airway epithelium and bacterial pathogens.
MICROBIOLOGY SPECTRUM
(2022)
Review
Chemistry, Analytical
Sin Yu Lam, Hill Lam Lau, Chun Kit Kwok
Summary: Small-molecule contaminants pose a great threat to human health and the environment, emphasizing the importance of developing affordable, user-friendly, and portable biosensors for rapid detection. This review summarizes the recent strategies used for Capture-SELEX and discusses the commonly used methods for detecting and characterizing small-molecule-aptamer interactions. The development of aptamer-based biosensors for various applications is also explored, along with the challenges and future possibilities in this field.
Review
Biochemistry & Molecular Biology
Lingkuan Meng, Wai-Sum Chan, Lei Huang, Linjing Liu, Xingjian Chen, Weitong Zhang, Fuzhou Wang, Ke Cheng, Hongyan Sun, Ka -Chun Wong
Summary: This paper reviews the recent works in deep learning for identifying various types of PTMs and discusses PTM databases and future research directions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Microbiology
Guohui Xiao, Zhao Cai, Qinglong Guo, Taosheng Ye, Yimin Tang, Peikun Guan, Juanjuan Zhang, Min Ou, Xiangdong Fu, Lili Ren, Minfei Yu, Zhaoqin Wang, Lei Liu, Liang Yang, Guoliang Zhang
Summary: This study aimed to determine the lung microbiota profile associated with pulmonary tuberculosis (TB) and characterize the changes during anti-TB treatment. The lung microbiota of untreated pulmonary TB patients was found to be distinct from that of healthy individuals and lung cancer patients. Anti-TB treatment significantly affected the diversity of the lung microbiota and induced the presence of antibiotic resistance genes.
MICROBIOLOGY SPECTRUM
(2022)