scholarly journals Discovery, Identification, and Functional Characterization of Long Noncoding RNAs in Arachis hypogaea L.

2020 ◽  
Author(s):  
Haiying Tian ◽  
Feng Guo ◽  
Zhimeng Zhang ◽  
Hong Ding ◽  
Jingjing Meng ◽  
...  
Keyword(s):  
Salt Stress ◽  
Arachis Hypogaea ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Occurrence Rate ◽  
Biological Processes ◽  
Arachis Hypogaea L ◽  
A Genome ◽  
Wide Range

Abstract Background Long noncoding RNAs (lncRNAs), which are typically >200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. Results A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1,442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. The majority of the lncRNAs featured an exon/intron structure, and approximately 44.17% were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. Conclusions This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.

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.

Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of peanut (Arachis hypogaea L.)

2016 ◽  
Vol 38 (6) ◽  
pp. 493-507 ◽  
Author(s):  
Na Chen ◽  
Maowen Su ◽  
Xiaoyuan Chi ◽  
Zhimeng Zhang ◽  
Lijuan Pan ◽  
...  
Keyword(s):  
Salt Stress ◽  
Arachis Hypogaea ◽  
Transcriptome Analysis ◽  
Biological Processes ◽  
Arachis Hypogaea L ◽  
Key Pathways

scholarly journals Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Haiying Tian ◽  
Feng Guo ◽  
Zhimeng Zhang ◽  
Hong Ding ◽  
Jingjing Meng ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Functional Characterization ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Arachis Hypogaea L

scholarly journals Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Xingli Ma ◽  
Xingguo Zhang ◽  
Sy Mamadou Traore ◽  
Zeyu Xin ◽  
Longlong Ning ◽  
...  
Keyword(s):  
Seed Development ◽  
Arachis Hypogaea ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Genome Wide ◽  
Arachis Hypogaea L

scholarly journals Portraying breast cancers with long noncoding RNAs

2016 ◽  
Vol 2 (9) ◽  
pp. e1600220 ◽  
Author(s):  
Olivier Van Grembergen ◽  
Martin Bizet ◽  
Eric J. de Bony ◽  
Emilie Calonne ◽  
Pascale Putmans ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Growth Factor ◽  
Transforming Growth Factor ◽  
Noncoding Rnas ◽  
Breast Tumors ◽  
Long Noncoding Rnas ◽  
Breast Cancers ◽  
Mesenchymal Transition ◽  
A Genome ◽  
Wide Range

Evidence is emerging that long noncoding RNAs (lncRNAs) may play a role in cancer development, but this role is not yet clear. We performed a genome-wide transcriptional survey to explore the lncRNA landscape across 995 breast tissue samples. We identified 215 lncRNAs whose genes are aberrantly expressed in breast tumors, as compared to normal samples. Unsupervised hierarchical clustering of breast tumors on the basis of their lncRNAs revealed four breast cancer subgroups that correlate tightly with PAM50-defined mRNA-based subtypes. Using multivariate analysis, we identified no less than 210 lncRNAs prognostic of clinical outcome. By analyzing the coexpression of lncRNA genes and protein-coding genes, we inferred potential functions of the 215 dysregulated lncRNAs. We then associated subtype-specific lncRNAs with key molecular processes involved in cancer. A correlation was observed, on the one hand, between luminal A–specific lncRNAs and the activation of phosphatidylinositol 3-kinase, fibroblast growth factor, and transforming growth factor–β pathways and, on the other hand, between basal-like–specific lncRNAs and the activation of epidermal growth factor receptor (EGFR)–dependent pathways and of the epithelial-to-mesenchymal transition. Finally, we showed that a specific lncRNA, which we called CYTOR, plays a role in breast cancer. We confirmed its predicted functions, showing that it regulates genes involved in the EGFR/mammalian target of rapamycin pathway and is required for cell proliferation, cell migration, and cytoskeleton organization. Overall, our work provides the most comprehensive analyses for lncRNA in breast cancers. Our findings suggest a wide range of biological functions associated with lncRNAs in breast cancer and provide a foundation for functional investigations that could lead to new therapeutic approaches.

scholarly journals Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Xiaoming Song ◽  
Jingjing Hu ◽  
Tong Wu ◽  
Qihang Yang ◽  
Xuehuan Feng ◽  
...  
Keyword(s):  
Heat Stress ◽  
Comparative Analysis ◽  
Chinese Cabbage ◽  
Target Genes ◽  
Expression Patterns ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Heat Stress Response ◽  
Functional Studies ◽  
A Genome

AbstractLong noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poorly conserved among different species, and only 960 lncRNAs were homologous to 524 miRNA precursors. We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment. In total, 18,253 lncRNAs were identified, of which 1229 differentially expressed (DE) lncRNAs were characterized as being heat-responsive. The ceRNA network revealed that 38 lncRNAs, 16 miRNAs, and 167 mRNAs were involved in the heat response in Chinese cabbage. Combined analysis of the cis- and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the “protein processing in endoplasmic reticulum” and “plant hormone signal transduction” pathways. Furthermore, the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly. Based on the networks of DE lncRNA-mRNAs, 29 and 22 lncRNAs were found to interact with HSP and PYL genes, respectively. Finally, the expression of several critical lncRNAs and their targets was verified by qRT-PCR. Overall, we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage. Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage, and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.

Abstract 91: Genome-wide Identification and Characterization of Cardiac Hypertrophy-related Long Noncoding RNAs in Mice

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Zhanpeng Huang ◽  
Gengze Wu ◽  
Jian-Hua Yang ◽  
Jian Ding ◽  
Jinghai Chen ◽  
...  
Keyword(s):  
Cardiac Hypertrophy ◽  
Target Genes ◽  
Troponin T ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Functional Screening ◽  
Loss Of Function ◽  
Specific Expression ◽  
Functional Conservation ◽  
Virus Serotype

Long noncoding RNAs (LncRNAs) are RNA transcripts longer than 200 nucleotides that lack protein-coding potential. Although thousands of lncRNAs have been identified, only a few have been linked to cardiac gene expression and function. In this study, we identified, from genome-scale RNA-seq data, 12 candidate lncRNAs associated with cardiac hypertrophy (CH-lncRNAs). The expression of these lncRNAs was altered in mouse models of cardiac hypertrophy induced by transverse aortic constriction (TAC)- or CnA transgene. To determine the function of these lncRNAs, we developed an adeno-associated virus serotype 9 (AAV9)-based functional screening in postnatal mice. An AAV9:cTNT vector, in which the cardiac troponin T (cTNT) promoter was used to direct cardiac-specific expression of target genes, was utilized to overexpress or knockdown candidate lncRNAs in mouse hearts. Postnatal day 1 wild type or CnA transgenic pups were injected with AAV9 viruses and cardiac function was measured one and two months later. Thus far, we have tested 15 candidate lncRNAs for both gain- and loss-of-function studies. Among them, two lncRNAs were demonstrated regulating hypertrophy growth when knocked down. Finally, we identified the human homologues of CH-lncRNA through analyzing the conservation of the promoter regions of lncRNA genes. We showed that the expression of these human CH-lncRNA was dysregulated in human diseased hearts, suggesting the functional conservation of these lncRNAs in cardiac disease. Our study therefore demonstrated that lncRNAs are important regulator of cardiac hypertrophy and disease.

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