Article
Plant Sciences
Yong Chen, Ting Ma, Tingting Zhang, Lei Ma
Summary: Intronless genes (IGs) are a characteristic feature of prokaryotes and can also be found in eukaryotes. A study on Poaceae genomes suggests that the origin of IGs may involve ancient intronic splicing, reverse transcription, and retrotranspositions. Furthermore, IGs display rapid evolution with recent duplications, variable copy numbers, low divergence between paralogs, and high non-synonymous to synonymous substitution ratios. The evolutionary dynamics of IGs differ among Poaceae subfamilies, with rapid development before divergence and gradual, consistent emergence in different clades during evolution.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Hui Liu, Hai-Meng Lyu, Kaikai Zhu, Yves Van de Peer, Zong-Ming (Max) Cheng
Summary: This study identified multiple gene families in plant genomes containing intronless or intron-poor genes, which play important roles in response to drought and salt stress, epigenetic processes, and plant development. The origin, evolution, and potential functions of these intronless and intron-poor sub-families provide insights into plant genome evolution and gene functional divergence.
Article
Genetics & Heredity
Katia Avina-Padilla, Jose Antonio Ramirez-Rafael, Gabriel Emilio Herrera-Oropeza, Vijaykumar Yogesh Muley, Dulce I. Valdivia, Erik Diaz-Valenzuela, Andres Garcia-Garcia, Alfredo Varela-Echavarria, Maribel Hernandez-Rosales
Summary: The presence of introns is crucial for gene expression control, while intronless genes (IGs) play important roles in neuro-specific functions, cancer, and developmental disorders. IGs have specialized transcriptional regulatory roles and occupy a unique position in eukaryotic genes.
FRONTIERS IN GENETICS
(2021)
Review
Obstetrics & Gynecology
Hiromitsu Tanaka, Akira Tsujimura
Summary: Recent research has found that many genes are specifically expressed in male germ cells, with functional intronless genes being significantly enriched in haploid germ cell-specific genes. This suggests that genes associated with fertility are more likely to be inherited in haploid germ cells.
REPRODUCTIVE MEDICINE AND BIOLOGY
(2021)
Article
Biochemical Research Methods
Giovanni Marques de Castro, Zandora Hastenreiter, Thiago Augusto Silva Monteiro, Thieres Tayroni Martins da Silva, Francisco Pereira Lobo
Summary: This article presents and validates a machine learning strategy to predict essential genes in insects using sequence-based intrinsic attributes and transcriptomic data. Even models trained using only intrinsic attributes can predict genes in other insect species, including lineage-specific essential genes. Furthermore, the inclusion of RNA-Seq data contributes to increased classifier performance.
Article
Multidisciplinary Sciences
Marta Seczynska, Stuart Bloor, Sergio Martinez Cuesta, Paul J. Lehner
Summary: HUSH complex transcriptionally represses L1s and retroviruses through H3K9me3. It recognizes and silences various long, intronless transgenes. HUSH binds and represses endogenous intronless genes, providing immediate protection against new elements.
Article
Engineering, Environmental
Shaojing Wang, Yuan Yun, Xuefeng Tian, Zhaoying Su, Zitong Liao, Guoqiang Li, Ting Ma
Summary: The investigation of hydrocarbon degradation potential of environmental microorganisms is crucial for understanding global carbon cycle and remediating oil pollution. To facilitate the process, a professional gene database called HMDB was developed, which includes 38 genes encoding 11 monooxygenases responsible for the hydroxylation of 8 hydrocarbons. Validations showed high sensitivity and low false positive rate for HMDB.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Multidisciplinary Sciences
Apoorv Gupta, Sandhya Pathak, Rajeev Varshney, Yasmin Ahmad, Pankaj Khurana
Summary: HighAltitudeOmicsDB is a unique resource that provides detailed information on genes/proteins, protein-protein interactions, and gene ontology semantic similarities related to high altitude conditions, aiming to facilitate research and analysis on the complex mechanisms of high altitude acclimatization.
SCIENTIFIC REPORTS
(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
Junhong Huang, Wujian Zheng, Ping Zhang, Qiao Lin, Zhirong Chen, Jiajia Xuan, Chang Liu, Di Wu, Qiaojuan Huang, Lingling Zheng, Shurong Liu, Keren Zhou, Lianghu Qu, Bin Li, Jianhua Yang
Summary: This study updated ChIPBase to version 3.0 and provided the most comprehensive transcriptional regulation atlas of non-coding RNAs and protein-coding genes. By analyzing a large number of ChIP-seq datasets, ChIPBase identified millions of regulatory relationships and identified thousands of motif matrices of transcription factors. It also constructed modules to predict regulation regions, explore disease-associated variations, and investigate interactions between epitranscriptome and epigenome.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Jorge Francisco Cutigi, Adriane Feijo Evangelista, Rui Manuel Reis, Adenilso Simao
Summary: Identifying significantly mutated genes in cancer is crucial for understanding tumor mechanisms. DiSCaGe, a computational method, considers mutation type and network influence to prioritize possible cancer genes. Experimental evaluation shows the potential of DiSCaGe in discovering known and novel significant cancer genes.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Tim E. Putman, Kevin Schaper, Nicolas Matentzoglu, Vincent P. Rubinetti, Faisal S. Alquaddoomi, Corey Cox, J. Harry Caufield, Glass Elsarboukh, Sarah Gehrke, Harshad Hegde, Justin T. Reese, Ian Braun, Richard M. Bruskiewich, Luca Cappelletti, Seth Carbon, Anita R. Caron, Lauren E. Chan, Christopher G. Chute, Katherina G. Cortes, Vinicius De Souza, Tommaso Fontana, Nomi L. Harris, Emily L. Hartley, Eric Hurwitz, Julius O. B. Jacobsen, Madan Krishnamurthy, Bryan J. Laraway, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Kathleen R. Mullen, Shawn T. O'Neil, Kent A. Shefchek, Ray Stefancsik, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Patricia L. Whetzel, David Osumi-Sutherland, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres
Summary: The Monarch Initiative aims to bridge the gap between genetic variations, environmental determinants, and phenotypic outcomes by developing an integrated platform with open ontologies, semantic data models, and knowledge graphs. It provides advanced analysis tools and curated datasets for clinical diagnosis and understanding disease mechanisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Qianyi Chen, Shilin Xia, Hua Sui, Xueying Shi, Bingqian Huang, Tingxin Wang
Summary: The study found that there are common differentially expressed genes (DEGs) in IPF and COVID-19, which are associated with cytokine function and extracellular matrix disassembly. These DEGs may serve as therapeutic targets for preventing the progression of IPF and SARS-CoV-2 infections.
Article
Mathematical & Computational Biology
Merve Guel Turan, Mehmet Emin Orhan, Sebiha Cevik, Oktay Kaplan
Summary: Cilia are essential for cell and organism functioning, but not present in plants. Abnormalities or impairments in cilia can cause rare disorders known as ciliopathy. To address the complexity and growing number of ciliopathies and ciliopathy genes, a comprehensive and up-to-date database called CiliaMiner has been developed.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Multidisciplinary Sciences
Yujie Mao, Xiaohui Liu, Na Zhang, Zhi Wang, Maozhen Han
Summary: Antibiotic resistance genes (ARGs) are emerging pollutants found in various environments, and identifying these genes has become a growing concern. In this study, a non-redundant antibiotic resistance genes database (NRD) was constructed by consolidating sequences from existing databases. The advantages of NRD in detecting potential ARGs were demonstrated through comparisons with other databases using metagenome datasets.
