scholarly journals Identification and functional annotation of differentially expressed long noncoding RNAs in retinoblastoma

2021 ◽  
Vol 22 (6) ◽  
Author(s):  
Xiaofen Feng ◽  
Jian Gong ◽  
Qian Li ◽  
Chao Xing ◽  
Jiandong Pan ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed

scholarly journals Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 232
Author(s):  
Weiran Zheng ◽  
Haichao Hu ◽  
Qisen Lu ◽  
Peng Jin ◽  
Linna Cai ◽  
...  
Keyword(s):  
Virus Infection ◽  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Chinese Wheat

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

scholarly journals Genomic data mining for functional annotation of human long noncoding RNAs

2019 ◽  
Vol 20 (6) ◽  
pp. 476-487 ◽  
Author(s):  
Brian L. Gudenas ◽  
Jun Wang ◽  
Shu-zhen Kuang ◽  
An-qi Wei ◽  
Steven B. Cogill ◽  
...  
Keyword(s):  
Data Mining ◽  
Functional Annotation ◽  
Noncoding Rnas ◽  
Genomic Data ◽  
Long Noncoding Rnas ◽  
Genomic Data Mining

scholarly journals Functional annotation of human long noncoding RNAs via molecular phenotyping

2020 ◽  
Vol 30 (7) ◽  
pp. 1060-1072 ◽  
Author(s):  
Jordan A. Ramilowski ◽  
Chi Wai Yip ◽  
Saumya Agrawal ◽  
Jen-Chien Chang ◽  
Yari Ciani ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Molecular Phenotyping

scholarly journals Transcriptional profiling of long noncoding RNAs associated with leaf-color mutation in Ginkgo biloba L

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yaqiong Wu ◽  
Jing Guo ◽  
Tongli Wang ◽  
Fuliang Cao ◽  
Guibin Wang
Keyword(s):  
Ginkgo Biloba ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Leaf Color ◽  
Wide Range ◽  
Color Mutation

Abstract Background Long noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. However, the roles of lncRNAs in leaf pigment formation in ginkgo (Ginkgo biloba L.) remain poorly understood. Results In this study, lncRNA libraries for mutant yellow-leaf and normal green-leaf ginkgo trees were constructed via high-throughput sequencing. A total of 2044 lncRNAs were obtained with an average length of 702 nt and typically harbored 2 exons. We identified 238 differentially expressed lncRNAs (DELs), 32 DELs and 49 differentially expressed mRNAs (DEGs) that constituted coexpression networks. We also found that 48 cis-acting DELs regulated 72 target genes, and 31 trans-acting DELs regulated 31 different target genes, which provides a new perspective for the regulation of the leaf-color mutation. Due to the crucial regulatory roles of lncRNAs in a wide range of biological processes, we conducted in-depth studies on the DELs and their targets and found that the chloroplast thylakoid membrane subcategory and the photosynthesis pathways (ko00195) were most enriched, suggesting their potential roles in leaf coloration mechanisms. In addition, our correlation analysis indicates that eight DELs and 68 transcription factors (TFs) might be involved in interaction networks. Conclusions This study has enriched the knowledge concerning lncRNAs and provides new insights into the function of lncRNAs in leaf-color mutations, which will benefit future selective breeding of ginkgo.

scholarly journals Expression Profile of Long Noncoding RNAs in Human Earlobe Keloids: A Microarray Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Liang Guo ◽  
Kai Xu ◽  
Hongbo Yan ◽  
Haifeng Feng ◽  
Linlin Chai ◽  
...  
Keyword(s):  
Microarray Analysis ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Diagnostic Biomarkers ◽  
Pathway Enrichment ◽  
Normal Tissues ◽  
Wide Range ◽  
Skin Scar

Background. Long noncoding RNAs (lncRNAs) play key roles in a wide range of biological processes and their deregulation results in human disease, including keloids. Earlobe keloid is a type of pathological skin scar, and the molecular pathogenesis of this disease remains largely unknown. Methods. In this study, microarray analysis was used to determine the expression profiles of lncRNAs and mRNAs between 3 pairs of earlobe keloid and normal specimens. Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to identify the main functions of the differentially expressed genes and earlobe keloid-related pathways. Results. A total of 2068 lncRNAs and 1511 mRNAs were differentially expressed between earlobe keloid and normal tissues. Among them, 1290 lncRNAs and 1092 mRNAs were upregulated, and 778 lncRNAs and 419 mRNAs were downregulated. Pathway analysis revealed that 24 pathways were correlated to the upregulated transcripts, while 11 pathways were associated with the downregulated transcripts. Conclusion. We characterized the expression profiles of lncRNA and mRNA in earlobe keloids and suggest that lncRNAs may serve as diagnostic biomarkers for the therapy of earlobe keloid.

Common and differentially expressed long noncoding RNAs for the characterization of high and low grade bladder cancer

Gene ◽  
2016 ◽  
Vol 592 (1) ◽  
pp. 78-85 ◽  
Author(s):  
Miao Wang ◽  
Xingyuan Xiao ◽  
Fuqing Zeng ◽  
Fei Xie ◽  
Yebin Fan ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Low Grade

scholarly journals Expression Signatures of Long Noncoding RNAs in Adolescent Idiopathic Scoliosis

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Xiao-Yang Liu ◽  
Liang Wang ◽  
Bin Yu ◽  
Qian-yu Zhuang ◽  
Yi-Peng Wang
Keyword(s):  
Adolescent Idiopathic Scoliosis ◽  
Idiopathic Scoliosis ◽  
Acid Metabolism ◽  
Bone Mineralization ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Nucleic Acid Metabolism ◽  
Healthy Children ◽  
Healthy Control

Purpose. Adolescent idiopathic scoliosis (AIS), the most common pediatric spinal deformity, is considered a complex genetic disease. Causing genes and pathogenesis of AIS are still unclear. This study was designed to identify differentially expressed long noncoding RNAs (lncRNAs) involving the pathogenesis of AIS.Methods. We first performed comprehensive screening of lncRNA and mRNA in AIS patients and healthy children using Agilent human lncRNA + mRNA Array V3.0 microarray. LncRNAs expression in different AIS patients was further evaluated using quantitative PCR.Results. A total of 139 lncRNAs and 546 mRNAs were differentially expressed between AIS patients and healthy control. GO and Pathway analysis showed that these mRNAs might be involved in bone mineralization, neuromuscular junction, skeletal system morphogenesis, nucleotide and nucleic acid metabolism, and regulation of signal pathway. Four lncRNAs (ENST00000440778.1, ENST00000602322.1, ENST00000414894.1, and TCONS_00028768) were differentially expressed between different patients when grouped according to age, height, classification, severity of scoliosis, and Risser grade.Conclusions. This study demonstrates the abnormal expression of lncRNAs and mRNAs in AIS, and the expression of some lncRNAs was related to clinical features. This study is helpful for further understanding of lncRNAs in pathogenesis, treatment, and prognosis of AIS.

scholarly journals Expression Signatures of Long Noncoding RNAs in Left Ventricular Noncompaction

2021 ◽  
Vol 8 ◽  
Author(s):  
Qingshan Tian ◽  
Hanxiao Niu ◽  
Dingyang Liu ◽  
Na Ta ◽  
Qing Yang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Noncoding Rnas ◽  
Enrichment Analysis ◽  
Left Ventricular ◽  
Long Noncoding Rnas ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Control Group ◽  
Left Ventricular Noncompaction ◽  
Ventricular Noncompaction

Long noncoding RNAs have gained widespread attention in recent years for their crucial role in biological regulation. They have been implicated in a range of developmental processes and diseases including cancer, cardiovascular, and neuronal diseases. However, the role of long noncoding RNAs (lncRNAs) in left ventricular noncompaction (LVNC) has not been explored. In this study, we investigated the expression levels of lncRNAs in the blood of LVNC patients and healthy subjects to identify differentially expressed lncRNA that develop LVNC specific biomarkers and targets for developing therapies using biological pathways. We used Agilent Human lncRNA array that contains both updated lncRNAs and mRNAs probes. We identified 1,568 upregulated and 1,141 downregulated (log fold-change > 2.0) lncRNAs that are differentially expressed between LVNC and the control group. Among them, RP11-1100L3.7 and XLOC_002730 are the most upregulated and downregulated lncRNAs. Using quantitative real-time reverse transcription polymerase chain reaction (RT-QPCR), we confirmed the differential expression of three top upregulated and downregulated lncRNAs along with two other randomly picked lncRNAs. Gene Ontology (GO) and KEGG pathways analysis with these differentially expressed lncRNAs provide insight into the cellular pathway leading to LVNC pathogenesis. We also identified 1,066 upregulated and 1,017 downregulated mRNAs. Gene set enrichment analysis (GSEA) showed that G2M, Estrogen, and inflammatory pathways are enriched in differentially expressed genes (DEG). We also identified miRNA targets for these differentially expressed genes. In this study, we first report the use of LncRNA microarray to understand the pathogenesis of LVNC and to identify several lncRNA and genes and their targets as potential biomarkers.

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