Article
Multidisciplinary Sciences
Xiaobo Wang, Jinhua Wang, Li Lyu, Xin Gao, Yinuo Cai, Bo Tang
Summary: This study provides the first pan-cancer analysis of TOP2A, revealing its oncogenic role and upstream molecular mechanism in multiple tumor types. The results highlight the prognostic and immunological roles of TOP2A in different cancers.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Clara-L. Sandmann, Jana F. Schulz, Jorge Ruiz-Orera, Marieluise Kirchner, Matthias Ziehm, Eleonora Adami, Maike Marczenke, Annabel Christ, Nina Liebe, Johannes Greiner, Aaron Schoenenberger, Michael B. Muecke, Ning Liang, Robert L. Moritz, Zhi Sun, Eric W. Deutsch, Michael Gotthardt, Jonathan M. Mudge, John R. Prensner, Thomas E. Willnow, Philipp Mertins, Sebastiaan van Heesch, Norbert Hubner
Summary: This study analyzes the evolutionary origins of 7,264 recently cataloged human short open reading frames (sORFs) and finds that most of them are evolutionarily young and emerged de novo. The researchers also identify 221 previously missed sORFs that potentially encode peptides smaller than the smallest annotated human microprotein. By conducting mass-spectrometry-based interactome screens and cellular assays, the study associates some of these sORFs with mRNA splicing, translational regulation, and endocytosis-related functions.
Review
Biochemistry & Molecular Biology
Selvaraj Barathi, Nadana Sabapathi, Kandasamy Nagarajan Aruljothi, Jin-Hyung Lee, Jae-Jin Shim, Jintae Lee
Summary: Small RNA (sRNA) has emerged as a potential tool in biotechnology for sustainable agriculture and environmental management. Plants produce sRNA to silence genes of pests and immune inhibitory proteins, while microbial networks can detect toxic elements and enhance degradation of pollutants. Bacterial and plant sRNA systems can synergistically establish a sustainable eco-agriculture system, replacing xenobiotic pesticides and chemical remediation elements. This review highlights the applications of sRNA in sustained agriculture and bioremediation, along with recommendations for future improvements.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Oncology
Qunli Xiong, Yaguang Zhang
Summary: Small RNAs are short RNA molecules that play various important roles in cells. Different types of small RNAs, such as miRNA, piRNA, siRNA, and tsRNA, have diverse functions. Current research suggests that small RNAs can be modified, affecting their stability and nuclear export, and these modifications are relevant to cellular processes like biogenesis, cell proliferation, and differentiation. This review focuses on the molecular characteristics and cellular functions of small RNAs and their modifications, as well as techniques for reliable detection. The potential clinical applications of small RNA modifications in the diagnosis and treatment of conditions like cancer are also discussed.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Zhiqi Deng, Liqun Ma, Peiyu Zhang, Hongliang Zhu
Summary: Small RNAs play significant roles in plant development, stress response, and antiviral immunity. This paper reviews the mechanisms by which small RNAs regulate viral defense in plants and the strategies employed by viruses to overcome host immune responses. Additionally, the current development status of new virus defense applications based on small RNA silencing is discussed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biotechnology & Applied Microbiology
Behzad Hajieghrari, Naser Farrokhi
Summary: Not all transcribed RNAs encode proteins. Some non-coding RNAs (ncRNAs) are non-functional and result from accidental transcription, while many others play significant roles in the translation process. Gene expression relies on complex networks of diverse gene regulatory pathways, and several ncRNAs act as major components in regulating gene expression either at the transcriptional or posttranscriptional level in a sequence-specific manner. RNA-mediated gene regulation machinery is evolutionarily ancient and highly complex. This review summarizes the current knowledge in the field of RNA-mediated gene silencing.
Article
Biochemical Research Methods
Diego de S. Lima, Luiz J. A. Amichi, Maria A. Fernandez, Ademir A. Constantino, Flavio A. V. Seixas
Summary: In this study, an attention-based LSTM network was developed and a classification model was built to directly classify short non-coding RNAs (including Y RNA) from nucleotide sequences. The performance evaluation demonstrated that the proposed method accurately predicts Y RNA sequences and their homologs, as well as 11 additional classes, achieving comparable results with state-of-the-art methods. Furthermore, applying t-SNE on learned sequence representations was shown to be useful for sequence analysis.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Review
Biotechnology & Applied Microbiology
Samira Samarfard, Abozar Ghorbani, Thomas P. Karbanowicz, Zhi Xian Lim, Mahshid Saedi, Niloofar Fariborzi, Alistair R. McTaggart, Keramatollah Izadpanah
Summary: This review discusses the importance of non-coding RNAs in plant immunity, particularly the interactions among long-ncRNAs, small-ncRNAs, and circular RNAs. By studying plant ncRNAs, we can better utilize molecular-based technologies for crop protection.
JOURNAL OF BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Olivier Saulnier, Katia Guedri-Idjouadiene, Marie-Ming Aynaud, Alina Chakraborty, Jonathan Bruyr, Josephine Pineau, Tina O'Grady, Olivier Mirabeau, Sandrine Grossetete, Bartimee Galvan, Margaux Claes, Zahra Al Oula Hassoun, Benjamin Sadacca, Karine Laud, Sakina Zaidi, Didier Surdez, Sylvain Baulande, Xavier Rambout, Franck Tirode, Martin Dutertre, Olivier Delattre, Franck Dequiedt
Summary: ERG family proteins (ERG, FLI1 and FEV) are ETS transcription factors that regulate splicing through association with spliceosomal components and induction of alternative splicing. They are associated with RBFOX2 and regulate alternative spliced exons enriched with RBFOX2 motifs. EWS-FLI1, while also associated with RBFOX2, acts differently by often antagonizing its effects on exon inclusion.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Jinqiu Fu, Shijing Xu, Huan Lu, Fanchi Li, Shengchun Li, Ling Chang, David G. Heckel, Ralph Bock, Jiang Zhang
Summary: Plant-mediated RNA interference (RNAi) using dsRNA or siRNA has shown promise in pest control, but little is known about the molecular mechanisms. This study found that siRNAs derived from transgenic plants may be more effective triggers of RNAi in Lepidoptera than dsRNAs.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Ewelina M. Malecka, Daria Sobanska, Mikolaj Olejniczak
Summary: Bacterial small RNAs in association with the chaperone protein Hfq play a crucial role in regulating the expression of target mRNAs. This regulation involves sponge RNAs that sequester sRNAs affecting their regulatory output. Hfq facilitates the annealing of sponge RNAs to targeted sRNAs, suggesting a complex but efficient regulation mechanism.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Plant Sciences
Junpeng Zhan, Blake C. Meyers
Summary: Plant cells accumulate small RNA molecules that regulate plant development, genome stability, and environmental responses. These small RNAs fall into three major classes-microRNAs, heterochromatic small interfering RNAs, and secondary small interfering RNAs-plus several other less well-characterized categories, and their biogenesis mechanisms, targets, modes of action, and functions have been extensively studied in Arabidopsis and other plant species, contributing to a better understanding of plant small RNA biology.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Article
Biochemical Research Methods
Thomas Binet, Berangere Avalle, Miraine Davila Felipe, Irene Maffucci
Summary: AptaMat, a simple and sensitive algorithm, has been developed for comparing the secondary structures of single-stranded nucleic acids (ssNAs). It outperforms other commonly used metrics in discriminating similar structures and correctly classifying RFAM families during clustering.
Review
Microbiology
Sabine Brantl, Peter Mueller
Summary: sRNAs act as abundant posttranscriptional regulators in all three kingdoms of life, with various methods being used to study chromosome-encoded sRNAs in bacteria over the past 20 years; while improved bioinformatics tools can predict potential sRNA targets, experimental confirmation remains challenging; known sRNAs in B. subtilis have defined targets and regulatory mechanisms.
Article
Biochemistry & Molecular Biology
Xiaowei Mo, Haolang Chen, Xiaolan Yang, Beixin Mo, Lei Gao, Yu Yu
Summary: This study reveals the regulatory mechanisms of M. micrantha mediated by miRNAs, and identifies the vital roles of miRNAs in gene expression and growth of this rapidly growing plant.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Letter
Biochemistry & Molecular Biology
Yi Zheng, Chen Jiao, Honghe Sun, Hernan G. Rosli, Marina A. Pombo, Peifen Zhang, Michael Banf, Xinbin Dai, Gregory B. Martin, James J. Giovannoni, Patrick X. Zhao, Seung Y. Rhee, Zhangjun Fei
Article
Plant Sciences
Jiading Yang, Eric Worley, Qin Ma, Jun Li, Ivone Torres-Jerez, Gaoyang Li, Patrick X. Zhao, Ying Xu, Yuhong Tang, Michael Udvardi
Article
Biochemical Research Methods
Wenchao Zhang, Xinbin Dai, Qishan Wang, Shizhong Xu, Patrick X. Zhao
PLOS COMPUTATIONAL BIOLOGY
(2016)
Article
Plant Sciences
Jun Li, Patrick X. Zhao
FRONTIERS IN PLANT SCIENCE
(2016)
Article
Plant Sciences
Thomas C. de Bang, Peter K. Lundquist, Xinbin Dai, Clarissa Boschiero, Zhaohong Zhuang, Pooja Pant, Ivone Torres-Jerez, Sonali Roy, Joaquina Nogales, Vijaykumar Veerappan, Rebecca Dickstein, Michael K. Udvardi, Patrick X. Zhao, Wolf-Rudiger Scheible
Article
Biochemistry & Molecular Biology
Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao
NUCLEIC ACIDS RESEARCH
(2018)
Review
Plant Sciences
Ji Huang, Ruqin Wang, Xinbin Dai, Jiejie Feng, Hongsheng Zhang, Patrick X. Zhao
JOURNAL OF EXPERIMENTAL BOTANY
(2019)
Article
Plant Sciences
Magda Karlo, Clarissa Boschiero, Katrine Gram Landerslev, Gonzalo Sancho Blanco, Jiangqi Wen, Kirankumar S. Mysore, Xinbin Dai, Patrick X. Zhao, Thomas C. de Bang
JOURNAL OF EXPERIMENTAL BOTANY
(2020)
Article
Plant Sciences
Firoz Ahmed, Muthappa Senthil-Kumar, Xinbin Dai, Vemanna S. Ramu, Seonghee Lee, Kirankumar S. Mysore, Patrick Xuechun Zhao
Article
Plant Sciences
Jose Pedro Fonseca, Hee-Kyung Lee, Clarissa Boschiero, Marcus Griffiths, Seonghee Lee, Patrick Zhao, Larry M. York, Kirankumar S. Mysore
Article
Plant Sciences
Raja Sekhar Nandety, Upinder S. Gill, Nick Krom, Xinbin Dai, Yibo Dong, Patrick X. Zhao, Kirankumar S. Mysore
Summary: Switchgrass rust caused by Puccinia novopanici has a significant impact on the biomass yield of switchgrass in the United States. Comparative genome analysis reveals larger structural variations in P. novopanici compared to other rust pathogens infecting cereal crops. Analysis of the enriched protein families in Puccinia spp. shows the importance of certain proteins in their pathogenicity. Effector proteins from Puccinia spp. genomes have similarities with validated proteins in the Pathogen-Host Interactions database.
Article
Genetics & Heredity
Wenchao Zhang, Yun Kang, Xinbin Dai, Shizhong Xu, Patrick X. Zhao
Summary: This study tackles the challenges of high dimensionality of SNP genotypes and missing value imputation in genome-wide association studies. It utilizes a stochastic process to describe SNP signals, calculates autocorrelation coefficients to construct LD bins, and employs a k-nearest neighbors algorithm for genotype imputation. Novel methods for finding synthetic markers and evaluating information loss or conservation are proposed, resulting in satisfactory performance on real-life SNP data.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Xinbin Dai, Zhaohong Zhuang, Clarissa Boschiero, Yibo Dong, Patrick X. Zhao
Summary: Legumes have been contributing to human health and sustainable food production for centuries. The study of model legumes is important for deciphering key genes and pathways. The LegumeIP V3 database provides valuable data and tools for identifying important genes in non-model legume crops.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Wenchao Zhang, Xinbin Dai, Shizhong Xu, Patrick X. Zhao
NAR GENOMICS AND BIOINFORMATICS
(2020)
Article
Biology
Wenchao Zhang, Xinbin Dai, Shizhong Xu, Patrick X. Zhao
COMMUNICATIONS BIOLOGY
(2018)