Article
Genetics & Heredity
Tingyi Cao, Marcella E. O'Reilly, Caitlin Selvaggi, Esther Cynn, Heidi Lumish, Chenyi Xue, Anjali Jha, Muredach P. Reilly, Andrea S. Foulkes
Summary: The genetically regulated expression of non-conserved lincRNAs shows similar rates of association with complex cardiometabolic traits as conserved lincRNAs, challenging the conventional notion of conservation and highlighting the need for comprehensive strategies to study non-conserved lincRNAs in human disease.
JOURNAL OF HUMAN GENETICS
(2022)
Article
Chemistry, Analytical
Xiaohan Li, Kequan Yu, Fuyu Li, Wenxiang Lu, Ying Wang, Weizhong Zhang, Yunfei Bai
Summary: This study presents a new comprehensive sequencing approach that allows for the capture of both poly(A) and non-poly(A) transcripts, enabling a deeper exploration of the transcriptome.
ANALYTICAL CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Dongliang Yu, Yuqing Wu, Leilei Zhu, Yuying Wang, Donglai Sheng, Xiaofeng Zhao, Guoqing Liang, Lin Gan
Summary: Based on established gene models and ab initio prediction, this study characterized 4,523 lncRNA genes in developing mouse retinas, providing the most comprehensive collection of retinal lncRNAs to date. These lncRNAs were found to be highly spatiotemporal specific in expression and played essential roles in regulating retinal genesis and function. The expression of certain lncRNAs was found to be implicated in the regulation of retinal neuron differentiation and development through specific pathways.
Article
Biochemistry & Molecular Biology
Adam Frankish, Silvia Carbonell-Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet, Daniel Cerdan-Velez, Fiona Cunningham, Claire Davidson, Sarah Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos Garcia Giron, Jose Manuel Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike Kay, Julien Lagarde, Fergal J. Martin, Laura Martinez Gomez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew Yates, Zahoor Zafrulla, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigo, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek
Summary: GENCODE provides high quality gene and transcript annotation for the human and mouse genomes, supported by experimental data, serving as a reference for genome biology and clinical genomics. The consortium generates data, develops tools and carries out analyses to support the identification and annotation of transcript structures and their function.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Cell Biology
Rong Rong, Mengxiao Wang, Mengling You, Haibo Li, Xiaobo Xia, Dan Ji
Summary: ncRNAs play important roles in glaucoma, but current research is still fragmented. A deeper understanding of ncRNAs is crucial for facilitating early diagnosis and treatment.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Agronomy
Lili Fu, Deguan Tan, Xuepiao Sun, Zehong Ding, Jiaming Zhang
Summary: This study investigated the regulatory mechanism of long noncoding RNAs (lncRNAs) in salicylic acid (SA)-induced flowering in duckweed. Through full-length sequencing and RNA sequencing, 31 differentially expressed lncRNAs were identified and found to be involved in stress metabolism, photosynthesis, jasmonate metabolism, and transport. Co-expression analysis revealed 15 lncRNAs that were co-expressed with flowering-related genes, and lncRNA03 and lncRNA25 were identified as key players in flowering through lncRNA-miRNA-mRNA interactions. qRT-PCR validation confirmed the expression of 12 lncRNAs involved in transcriptional regulation, miRNA targets, or co-expression with flowering-related genes. These findings provide valuable resources for future in-depth functional analysis of lncRNAs in SA-induced flowering in duckweed.
Article
Biochemistry & Molecular Biology
Stefan R. Stefanov, Irmtraud M. Meyer
Summary: Researchers have developed a computational method called CYCLeR that accurately identifies the sequence and abundance of new and alternatively spliced circRNAs, while also estimating the abundance of known linear splicing isoforms. CYCLeR outperforms existing methods in terms of F score and transcript quantification in simulated data, and shows advantages compared to existing methods when analyzing long-read data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Mahsa RezaSoltani, Flora Forouzesh, Zahra Salehi, Mohammad-Reza Zabihi, Leili Rejali, Ehsan Nazemalhosseini-Mojarad
Summary: LncPVT1 and CircPVT1, isoforms of the PVT1 gene, are significantly overexpressed in colon adenoma polyps compared to normal-adjacent tissues. In silico analysis suggests their involvement in colon cancer development through the CircPVT1/miR-484, miR-24-3p, miR-423-5p/PLAGL2 axis.
SCIENTIFIC REPORTS
(2023)
Article
Entomology
Li Shi, Wen-Lin Li, Hai-Xin Zeng, Yao Shi, Xiao-Lan Liao
Summary: This study sequenced the RNA of Spodoptera litura and identified several lncRNAs that play a key role in conferring insecticide resistance, particularly indoxacarb resistance. The differentially expressed lncRNAs were found to regulate the expression of various detoxification and cuticle protein genes, and may mediate resistance through multiple regulatory pathways. Overexpressed lncRNAs LNC_004867 and LNC_006576 were shown to be involved in indoxacarb resistance.
Article
Biology
Iria Gonzalez-Vasconcellos, Maria A. Cobos-Fernandez, Michael J. Atkinson, Jose Fernandez-Piqueras, Javier Santos
Summary: Telomeric-associated long non-coding RNAs TERRA and TERC can be quantified in culture cell lines and human PBMCs using peptide nucleic acid probes with flow cytometry (RNA-Flow). This method, called RNA-Flow, allows easy and reliable quantification of lncRNAs, with broad applications in basic research and clinical diagnostics. Additionally, the staining protocol presented in this study has been proven useful for detecting and quantifying these lncRNAs on unfixed cells using confocal microscopy.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Deng Chen, Lina Zhu, Xin Lin, Dong Zhou, Ling Liu
Summary: This study aimed to investigate differentially expressed lncRNAs and mRNAs in the SUDEP model, revealing a total of 502 dysregulated lncRNAs and 263 mRNAs, some of which are potentially related to SUDEP such as Adora3, Lmnb2, and Hspa1a. Further analysis showed that these dysregulated RNAs may play a role in neurological diseases like SUDEP.
Article
Biochemistry & Molecular Biology
Wen-Fang Wang, Hui-Juan Zhong, Shu Cheng, Di Fu, Yan Zhao, Hua-Man Cai, Jie Xiong, Wei-Li Zhao
Summary: This study identified a long intergenic noncoding RNA, LINC00486, which is downregulated in lymphoma cells infected with Epstein-Barr virus (EBV), especially in natural killer T cell lymphoma (NKTCL). LINC00486 was found to have tumor-suppressive effects by inhibiting tumor cell growth and inducing cell cycle arrest, and it enhanced EBV eradication through activation of NF-KB/TNF-a signaling. The upregulation of SLC1A1, which promotes tumor progression in NKTCL, was negatively correlated with the expression of the tumor suppressor protein NKRF, and NKRF transcriptionally downregulated SLC1A1 expression by binding to its promoter.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2023)
Article
Virology
Yimin Xue, Jun Ke, Jiuyun Zhang, Mingguang Chen, Lijuan Zeng, Qiaolian Fan, Chunfu Zheng, Feng Chen
Summary: This study investigates the expression profiles of lncRNAs and mRNAs associated with AVMC. It identifies differentially expressed genes involved in metabolic and immune-related processes and explores the molecular interactions between these molecules. These findings shed light on the roles of lncRNAs in disease pathogenesis and provide insights for discovering new therapeutic targets.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Lina Zhu, Deng Chen, Xin Lin, Ling Liu
Summary: In this study, the expression profiles of long noncoding RNAs (lncRNAs) and mRNAs were analyzed in DBA/1 and C57BL/6 mice with different susceptibility to audiogenic seizures (AGSz) and seizure-induced respiratory arrest (S-IRA). The results suggest that TGF-beta signaling and metabolic process might contribute to the differential sensitivity to AGSz and S-IRA.
Article
Multidisciplinary Sciences
Odei Barrenada, Eduardo Larriba, Daniel Fernandez-Perez, Miguel angel Brieno-Enriquez, Jesus del Mazo Martinez
Summary: Recent studies have shown that mitochondrial small noncoding RNAs (sncRNAs) play important roles in germ cell development and differentiation. By analyzing sequencing data, we identified the origins, expression levels, and potential functions of piRNAs, as well as their association with other sncRNAs and the mitochondrial regulatory region. Our findings suggest that mitochondria-associated piRNAs may mediate nucleo-mitochondrial communication.
SCIENTIFIC REPORTS
(2022)
Letter
Biotechnology & Applied Microbiology
Dongliang Yu, Liping Ke, Diandian Zhang, Yuqing Wu, Yujie Sun, Jun Mei, Jie Sun, Yuqiang Sun
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Yujie Sun, Diandian Zhang, Hongli Zheng, Yuqing Wu, Jun Mei, Liping Ke, Dongliang Yu, Yuqiang Sun
Summary: This study analyzed the accumulation of proanthocyanidins (PAs) and the expression of PA biosynthetic genes in the fiber of wild cotton species G. stocksii, providing insights into the molecular mechanisms of its fiber coloration. The results suggest that PAs play a crucial role in the fiber coloration of G. stocksii, and the transcription factor TT8 may have a regulatory role in controlling the PA branch genes. Additionally, the anthocyanidin reductase ANR is highly expressed and upregulated during fiber elongation, indicating its major role in PA synthesis in G. stocksii fiber.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jun Mei, Yuqing Wu, Qingqing Niu, Meng Miao, Diandian Zhang, Yanyan Zhao, Fangfang Cai, Dongliang Yu, Liping Ke, Hongjie Feng, Yuqiang Sun
Summary: Cotton resistance to Verticillium wilt is regulated by miRNAs and target genes, but limited research has been conducted in this area. Transcriptome and small RNA sequencing analysis of upland cotton revealed differential gene and miRNA expression under V. dahliae stress and their association with specific biological processes. Additionally, 31 differentially expressed miRNA-mRNA pairs were identified to be involved in the response to V. dahliae.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Liping Ke, Dongliang Yu, Hongli Zheng, Yihan Xu, Yuqing Wu, Junye Jiao, Xiaoli Wang, Jun Mei, Fangfang Cai, Yanyan Zhao, Jie Sun, Xianlong Zhang, Yuqiang Sun
Summary: Naturally coloured cotton fibres (NCC) are low-carbon emission and environment-friendly due to little or no dyeing process. However, the monotonous fibre colours of NCCs limit their wide application. In this study, a mutant (HS2) with enhanced anthocyanidins biosynthesis was found and crossed with NCCs, resulting in the production of novel lines with improved fibre colours. This work sheds light on mechanisms of NCC colouration and provides a potential molecular breeding strategy for diversified NCCs.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Developmental Biology
Wei Zhang, Jiaojiao Yu, Guoquan Fu, Jianying Li, Huarong Huang, Jing Liu, Dongliang Yu, Mengsheng Qiu, Feixue Li
Summary: This study provides the first genetic evidence that the ISL1/SHH/CXCL12 axis regulates myoblast migration during tongue development. Deletion of Isl1 in the mouse mandibular epithelium leads to defects in myoblast migration, which is regulated by the Shh/Wnt5a cascade. Cxcl12+ mesenchymal cells in Isl1ShhCre embryos fail to migrate to the distal region and instead accumulate in the proximal domain of the mandible. This is due to the concentration-dependent bidirectional cue of CXCL12, which attracts myoblast invasion at low concentrations but repels it at high concentrations.