Article
Chemistry, Multidisciplinary
Heng Tang, Junran Peng, Shuang Peng, Qi Wang, Xin Jiang, Xiaocheng Xue, Yanxin Tao, Limin Xiang, Quanjiang Ji, Song-Mei Liu, Xiaocheng Weng, Xiang Zhou
Summary: This study presents an efficient RNA imaging method based on the CRISPR-dPspCas13b system, which allows for imaging and tracking of endogenous RNA in live cells. The method utilizes fluorescent RNA aptamers with reduced background fluorescence, providing a simple and sensitive approach for RNA imaging, and color switching can be easily achieved by changing fluorogenic dye analogues.
Review
Biochemistry & Molecular Biology
Uciel Chorostecki, Nicolas G. Bologna, Federico Ariel
Summary: This review comprehensively analyzes the relationship between plant noncoding RNA transcripts and environmental cues, highlighting the importance of different types of noncoding RNAs in plant development and stress responses. It emphasizes the need for further research to uncover the molecular mechanisms and exploit the potential of noncoding transcripts for crop resilience.
Article
Multidisciplinary Sciences
Sadie L. Hennig, Bret R. McNabb, Josephine F. Trott, Alison L. Van Eenennaam, James D. Murray
Summary: A long intergenic non-coding RNA (lincRNA#1) is highly expressed in the horn bud region of polled bovine fetuses, but its absence alone does not result in a hornless phenotype.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
G. Ian Gallicano, John L. Casey, Jiayu Fu, Samiksha Mahapatra
Summary: Covid-19 has become a deadly global pandemic, and there is currently no specific drug for its treatment. However, recent advancements in using miRNA/siRNA molecular approach have made it feasible. Studies have shown that siRNAs and miRNAs can dose-dependently inhibit the production of SARS CoV-2 spike protein.
Review
Genetics & Heredity
Cecilia Studniarek, Sylvain Egloff, Shona Murphy
Summary: Effective synthesis of mammalian mRNAs relies on various factors, including transcription initiation, elongation, and termination, as well as the global regulatory role of noncoding RNAs. These non-protein regulators play critical roles in gene expression by directly associating with pol II or modulating the activity of transcription or RNA processing factors.
TRENDS IN GENETICS
(2021)
Article
Plant Sciences
Daniela Arias, Angelica Ortega, Christian Gonzalez-Calquin, Luis Felipe Quiroz, Jordi Moreno-Romero, Jaime F. Martinez-Garcia, Claudia Stange
Summary: A transcriptional cofactor, DcPAR1, plays a crucial role in regulating secondary root development and carotenoid synthesis in the underground taproot of carrot. Light suppresses the expression of DcPAR1 and carotenogenic genes, leading to decreased carotenoid accumulation. Overexpressing AtPAR1 in carrot increases carotenoid production and DcPSY1 expression in the underground taproot. DcPAR1 is a key factor in regulating carotenoid synthesis and taproot development.
Article
Biotechnology & Applied Microbiology
Nana Ma, Jie Pan, Yi Wen, Qi Wu, Bo Yu, Xi Chen, Jun Wan, Wei Zhang
Summary: The study revealed abundant circRNAs in the brain of APP/PS1 model mice, with circTulp4 potentially involved in regulating neural function through modulating the transcription of its parental gene Tulp4 and is suggested to participate in the development of Alzheimer's disease.
Article
Multidisciplinary Sciences
Razia Khalid, Hammad Naveed, Zoya Khalid
Summary: Long non-coding RNAs (lncRNAs) have emerged as important players in regulating biological processes and their mutations are associated with complex diseases. In this study, we developed a machine learning model that combines sequence and structure-based features to predict disease-related lncRNAs. Our model outperformed existing methods and achieved the highest F1 score of 76% on the SVM classifier. We also addressed limitations in previous methods by incorporating redundancy checking and oversampling techniques. Combining multiple features, particularly lncRNA sequence mutations, significantly contributed to the prediction of disease-related lncRNAs.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Valerie M. Stacey, Sulev Koks
Summary: This study identified differentially expressed long noncoding RNA (lncRNA) genes in samples from psoriasis patients through computational analysis. The differentially expressed genes were found to be associated with the pathogenesis of psoriasis and inflammatory skin diseases, as well as involved in cell cycle pathway and IFN-γ signaling pathway regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, Research & Experimental
Zhenyao Huang, Hao Yu, Guizhen Du, Li Han, Xiaomin Huang, Dan Wu, Xiumei Han, Yankai Xia, Xinru Wang, Chuncheng Lu
Summary: The enriched lnc-CES1-1 in URPL patients affects the levels of inflammatory factors and impairs cell migration ability, which may be attenuated by downregulating PPARγ. Upon activation by STAT4, lnc-CES1-1 interacts with FUS to upregulate PPARγ expression, thereby affecting cell migration in decidua-associated cell lines. These findings shed light on the potential use of lnc-CES1-1 as a biomarker for URPL diagnosis and treatment.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Multidisciplinary Sciences
Luisa Santus, Maria Sopena-Rios, Raquel Garcia-Perez, Aaron E. Lin, Gordon C. Adams, Kayla G. Barnes, Katherine J. Siddle, Shirlee Wohl, Ferran Reverter, John L. Rinn, Richard S. Bennett, Lisa E. Hensley, Pardis C. Sabeti, Marta Mele
Summary: In this study, the authors characterized the differential features of long non-coding RNAs (lncRNAs) and protein-coding genes upon Ebola infection in macaques at the single-cell level. They found that lncRNAs are expressed in fewer cells than protein-coding genes, but they are not expressed at lower levels nor are they more cell-type specific. Furthermore, lncRNAs exhibit similar changes in expression patterns to those of protein-coding genes during Ebola infection, and are often co-expressed with known immune regulators.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Pengling Wang, Tianli Zhang, Nan Jiang, Kun Wang, Liping Feng, Ting Liu, Xingsheng Yang
Summary: This study identifies PDIA6 as a significant player in endometrial cancer, promoting malignant behavior of cancer cells through regulation of the TGF-beta pathway and modulation by the TRPM2-AS/miR-424-5p axis. Therefore, PDIA6 may be a potential target for endometrial cancer therapy.
CELL DEATH & DISEASE
(2023)
Article
Multidisciplinary Sciences
Cheng Guo, You Duan, Weidong Ye, Wanting Zhang, Yingyin Cheng, Mijuan Shi, Xiao-Qin Xia
Summary: FishGET is an effort to collect and curate fish RNA-seq data in order to discover new RNAs and provide comprehensive transcriptome annotations. Through various steps including transcript assembly, meta-assembly, WGCNA, functional annotations, neighbor location annotation, lncRNA type annotation, and homology annotation, we obtained a total of 1362 RNA-seq paired-end data from 97 different studies of 8 fish species. To facilitate research on fish genes at the transcriptional level, we developed a user-friendly web interface that allows users to access all information and utilize dynamic interactive visualization services.
Article
Mathematical & Computational Biology
G. K. Ryabykh, S. Kuznetsov, Y. D. Korostelev, A. Sigorskikh, A. A. Zharikova, A. A. Mironov
Summary: There is increasing evidence to support the important role of non-coding RNAs in various biological processes. The creation of complementary databases can aid in studying non-coding RNAs at a system level. RNA-Chrom is a curated analytical database that contains billions of coordinates of RNA-chromatin contacts. The web interface allows users to analyze the interaction between RNA and chromatin in two different approaches.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Cell Biology
Lauren Winkler, Maria Jimenez, Joshua T. Zimmer, Adam Williams, Matthew D. Simon, Nadya Dimitrova
Summary: The study shows that the full transcription, splicing, and accumulation of lincRNA-p21 are not crucial for gene regulation, but the production of lincRNA-p21 through specific exon regions can promote cis-activation of the gene.
Article
Horticulture
Shan-Shan Tan, Min Jia, Xin-Yue Zhang, Ao-Qi Duan, Tong Li, Yan-Hua Liu, Ai-Sheng Xiong
Summary: The germination process of carrot seeds is regulated by phytohormones, and this study provides new insights into the relationship between phytohormones and carrot seed germination through morphological observation, transcriptome sequencing, and gene expression analysis.
JOURNAL OF HORTICULTURAL SCIENCE & BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Min Jia, Sheng-Qi Zhu, Ya-Hui Wang, Jie-Xia Liu, Shan-Shan Tan, Hui Liu, Sheng Shu, Jian-Ping Tao, Ai-Sheng Xiong
Summary: This study investigated the effects of different storage conditions on celery morphological characteristics, anatomical features, and antioxidant accumulation. The results showed that storing celery in darkness at low temperature was the optimal condition for maintaining its morphological characteristics and preserving antioxidant accumulation. Additionally, the genes GDP-d-mannose pyrophosphorylase and l-galactose dehydrogenase were found to play a crucial role in the accumulation of ascorbic acid in celery.
Article
Chemistry, Multidisciplinary
Guang-Long Wang, Ling-Yi Liu, Qi-Zhang Wang, Xu-Qin Ren, Ai-Sheng Xiong, Jie Tian
Summary: In this study, the changes in the transcriptome of garlic seedlings under drought stress were analyzed. The results revealed a coordinated interplay between abscisic acid and calcium in the response of garlic to drought stress.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Ni Yang, Miao-Hua Han, Rui-Min Teng, Ya-Zhuo Yang, Ya-Hui Wang, Ai-Sheng Xiong, Jing Zhuang
Summary: The study demonstrates the regulatory effects of exogenous melatonin on the photosynthetic characteristics and gene expression of tea plants, enhancing their photosynthetic capacity in a dose-dependent manner.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agronomy
Yan-Hua Liu, Miao Sun, Hao Wang, Jie-Xia Liu, Guo-Fei Tan, Jun Yan, Yuan-Hua Wang, Zhi-Ming Yan, Hui Liu, Jian-Ping Tao, Wei-Min Zhu, Sheng Shu, Ai-Sheng Xiong
Summary: BRs promote the growth of celery and increase cellulose accumulation, while PCZ and DCB inhibit these effects.
Article
Horticulture
Shan-Shan Tan, Ao-Qi Duan, Guang-Long Wang, Hui Liu, Zhi-Sheng Xu, Ai-Sheng Xiong
Summary: This study conducted a genome-wide identification and characteristic analysis of MADS-box transcription factors in carrots, and identified many important transcription factors involved in the nutritional and reproductive growth of plants. The results of subcellular localization, gene distribution, and protein interaction provide a theoretical basis for exploring the molecular mechanisms of carrot flower organ development.
SCIENTIA HORTICULTURAE
(2023)
Article
Plant Sciences
Ao-Qi Duan, Yuan-Jie Deng, Shan-Shan Tan, Zhi-Sheng Xu, Ai-Sheng Xiong
Summary: The study identified the DcMYB11c gene as a key factor in anthocyanin pigmentation in purple petioles of carrots. Overexpression of DcMYB11c in orange and yellow taproot carrots led to deep purple pigmentation, while knockout of DcMYB11c in purple taproot carrots resulted in pale purple pigmentation. DcMYB11c was found to activate the expression of genes responsible for anthocyanin biosynthesis and glycosylation/acetylation. This research provides new insights into the regulation of anthocyanin biosynthesis in carrots and may have implications for similar studies in other plants.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Genetics & Heredity
Zhipeng Zhu, Jianxiang Yu, Xinhui Tang, Aisheng Xiong, Miao Sun
Summary: In this study, 18 potential reference genes from okra were selected and their expression levels under different tissues and abiotic stress conditions were determined using Real-Time quantitative PCR. The most stable genes under cold, salt and drought stress were identified, providing a molecular basis for functional gene analysis and regulatory mechanism research of okra.
Article
Agronomy
Qian Jiang, Yu Wang, Aisheng Xiong, Hui Zhao, Ruizong Jia, Mengyao Li, Huaming An, Changmian Ji, Anping Guo
Summary: By analyzing the papaya genome and large-scale RNA-seq data, we found that the formation of the NLR gene family in papaya is mainly driven by duplication and these genes play a vital role in biotic stress responses.
Review
Agronomy
Jian Zhang, Weikai Fang, Chidong Xu, Aisheng Xiong, Michael Zhang, Randy Goebel, Guangyu Bo
Summary: Advances in optical sensing technology have revolutionized the determination of crop seed vigor. Traditional methods are time-consuming, labor-intensive, and prone to inaccuracies, leading to unreliable yield predictions. Optical sensing technology offers rapid, accurate, and non-destructive calibration methods for seed usage and agronomic evaluation. This review provides a summary of current research in using optical sensing technology for assessing seed vigor.
Article
Biochemistry & Molecular Biology
Xiaoyan Li, Mengyao Li, Weilong Li, Jin Zhou, Qiuju Han, Wei Lu, Qin Luo, Shunhua Zhu, Aisheng Xiong, Guofei Tan, Yangxia Zheng
Summary: This study identified the mitochondrial genomes of Apium graveolens and Apium leptophyllum using different sequencing platforms. It revealed specific gene coding preferences, RNA editing types, and homologous sequences in these two species. These findings provide important data for genetic and evolutionary research in the Apium genus, as well as for comparative genomic analysis in other species within the Apiaceae family.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agronomy
Jiageng Du, Huitao Zhang, Weilong Li, Xiaoyan Li, Zhuo Wang, Ying Zhang, Aisheng Xiong, Mengyao Li
Summary: This study focused on the isolation and transformation of celery protoplasts using celery seedling leaves as the primary materials. The most effective procedure for protoplast isolation was enzymatic digestion followed by filtration and centrifugation. The study also established a transient transformation system and used it to analyze the protein localization characteristics of the celery transcription factor AgMYB80. The findings confirmed the reliability and effectiveness of the transient transformation system.
Article
Horticulture
Rong-Rong Zhang, Jian-Ping Tao, Liu-Xia Song, Jia-Qi Zhang, Hui Liu, Wei-Min Zhu, Tong-Min Zhao, Ai-Sheng Xiong
Summary: Tomato is a widely cultivated vegetable with nutritious fruits. Soluble solids content (SSC) plays a decisive role in improving tomato quality. The molecular marker TGS0892 on chromosome 6 of tomato genome is closely related to soluble solids. In this study, bioinformatics methods were used to identify and analyze genes near TGS0892. The expression levels of these genes in different tomato cultivars showed variations, and two genes, Soly065970 and Soly066010, were found to be involved in regulating the soluble solids metabolic process.
Article
Agronomy
Guang-Long Wang, Jia-Qi Wu, Yang-Yang Chen, Yu-Jie Xu, Cheng-Ling Zhou, Zhen-Zhu Hu, Xu-Qin Ren, Ai-Sheng Xiong
Summary: This article focuses on the synthesis, accumulation, and regulation of lignin in horticultural crops in recent years, and provides insights into its impact on the quality of horticultural products. The importance of controlling lignin content is highlighted, and new directions for further research on lignin metabolism are proposed.
Article
Plant Sciences
Ao-Qi Duan, Yuan-Jie Deng, Shan-Shan Tan, Shan-Shan Liu, Hui Liu, Zhi-Sheng Xu, Sheng Shu, Ai-Sheng Xiong
Summary: This study investigates the molecular mechanism of purple carrot taproot color formation and successfully knocks out the key gene DcGST1, resulting in carrots with orange taproots. Furthermore, it is found that the anthocyanin activator DcMYB7 can activate the expression of DcGST1, and co-expression of DcGST1 and DcMYB7 significantly increases anthocyanin accumulation in carrot calli.