scholarly journals Comparison of characteristics of long noncoding RNA in Hanwoo according to sex

2020 ◽  
Vol 33 (5) ◽  
pp. 696-703
Author(s):  
Jae-Young Choi ◽  
KyeongHye Won ◽  
Seungwoo Son ◽  
Donghyun Shin ◽  
Jae-Don Oh
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Skeletal Muscles ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Physiological Mechanisms ◽  
Protein Coding ◽  
Future Studies ◽  
Hanwoo Cattle

Objective: Cattle were some of the first animals domesticated by humans for the production of milk, meat, etc. Long noncoding RNA (lncRNA) is defined as longer than 200 bp in non-protein coding transcripts. lncRNA is known to function in regulating gene expression and is currently being studied in a variety of livestock including cattle. The purpose of this study is to analyze the characteristics of lncRNA according to sex in Hanwoo cattle.Methods: This study was conducted using the skeletal muscles of 9 Hanwoo cattle include bulls, steers and cows. RNA was extracted from skeletal muscle of Hanwoo. Sequencing was conducted using Illumina HiSeq2000 and mapped to the Bovine Taurus genome. The expression levels of lncRNAs were measured by DEGseq and quantitative trait loci (QTL) data base was used to identify QTLs associated with lncRNA. The python script was used to match the nearby genesResults: In this study, the expression patterns of transcripts of bulls, steers and cows were identified. And we identified significantly differentially expressed lncRNAs in bulls, steers and cows. In addition, characteristics of lncRNA which express differentially in muscles according to the sex of Hanwoo were identified. As a result, we found differentially expressed lncRNAs according to sex were related to shear force and body weight.Conclusion: This study was classified and characterized lncRNA which differentially expressed by sex in Hanwoo cattle. We believe that the characterization of lncRNA by sex of Hanwoo will be helpful for future studies of the physiological mechanisms of Hanwoo cattle.

scholarly journals Differential Expression of Long Noncoding RNA in Primary and Recurrent Nasopharyngeal Carcinoma

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Wei Gao ◽  
Jimmy Yu-Wai Chan ◽  
Thian-Sze Wong
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Microarray Dataset ◽  
Differentially Expressed ◽  
Data Set ◽  
Protein Coding ◽  
Real Time Quantitative Pcr ◽  
Advanced Tumor ◽  
Tumor Stages

Background. Recent studies suggested that non-protein-coding genes are implicated in the tumorigenic process of nasopharyngeal carcinoma (NPC). In the present study, we aimed to identify the differentially expressed long noncoding RNA (lncRNA) using data available in the public domain.Methods. Microarray data set GSE12452 was reannotated with ncFANs. Real-time quantitative PCR was used to quantify and validate the identified lncRNAs in NPC.Results. In primary NPC, upregulation of lnc-C22orf32-1, lnc-AL355149.1-1, and lnc-ZNF674-1 was observed. High levels of lnc-C22orf32-1 and lnc-AL355149.1-1 were significantly associated with the male patients. In addition, increased expression of lnc-C22orf32-1 and lnc-ZNF674-1 was associated with advanced tumor stages. Recurrent NPC displayed a distinctive lncRNA expression pattern. lnc-BCL2L11-3 was significantly increased in the recurrent NPC tissues. In addition, significant reduction of lnc-AL355149.1-1 and lnc-ZNF674-1 was observed in the recurrent NPC tissues.Conclusions. Our results demonstrated that it is feasible to identify the differentially expressed lncRNA in the microarray dataset by functional reannotation. The association of lncRNA with gender and tumor size implicated that lncRNA possibly plays a part in the pathogenesis of primary NPC. Further, the distinctive lncRNA identified in the recurrent NPC may reveal a distinctive development mechanism underlying tumor recurrence.

scholarly journals Global Long Noncoding RNA and mRNA Expression Changes between Prenatal and Neonatal Lung Tissue in Pigs

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 443 ◽  
Author(s):  
Long Jin ◽  
Silu Hu ◽  
Teng Tu ◽  
Zhiqing Huang ◽  
Qianzi Tang ◽  
...  
Keyword(s):  
Immune Response ◽  
Cell Proliferation ◽  
Lung Tissue ◽  
Long Noncoding Rna ◽  
Lung Development ◽  
Noncoding Rna ◽  
Differentially Expressed ◽  
P Value ◽  
Distal Lung ◽  
Neonatal Lungs

Lung tissue plays an important role in the respiratory system of mammals after birth. Early lung development includes six key stages, of which the saccular stage spans the pre- and neonatal periods and prepares the distal lung for alveolarization and gas-exchange. However, little is known about the changes in gene expression between fetal and neonatal lungs. In this study, we performed transcriptomic analysis of messenger RNA (mRNA) and long noncoding RNA (lncRNA) expressed in the lung tissue of fetal and neonatal piglets. A total of 19,310 lncRNAs and 14,579 mRNAs were identified and substantially expressed. Furthermore, 3248 mRNAs were significantly (FDR-adjusted p value ≤ 0.05, FDR: False Discovery Rate) differentially expressed and were mainly enriched in categories related to cell proliferation, immune response, hypoxia response, and mitochondrial activation. For example, CCNA2, an important gene involved in the cell cycle and DNA replication, was upregulated in neonatal lungs. We also identified 452 significantly (FDR-adjusted p value ≤ 0.05) differentially expressed lncRNAs, which might function in cell proliferation, mitochondrial activation, and immune response, similar to the differentially expressed mRNAs. These results suggest that differentially expressed mRNAs and lncRNAs might co-regulate lung development in early postnatal pigs. Notably, the TU64359 lncRNA might promote distal lung development by up-regulating the heparin-binding epidermal growth factor-like (HB-EGF) expression. Our research provides basic lung development datasets and will accelerate clinical researches of newborn lung diseases with pig models.

scholarly journals Identification of Long Noncoding RNA Associated ceRNA Networks in Rosacea

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Lian Wang ◽  
Ruifeng Lu ◽  
Yujia Wang ◽  
Xiaoyun Wang ◽  
Dan Hao ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Control Group ◽  
Group 13 ◽  
Regulatory Processes ◽  
Coexpression Networks

Rosacea is a chronic and relapsing inflammatory cutaneous disorder with highly variable prevalence worldwide that adversely affects the health of patients and their quality of life. However, the molecular characterization of each rosacea subtype is still unclear. Furthermore, little is known about the role of long noncoding RNAs (lncRNAs) in the pathogenesis or regulatory processes of this disorder. In the current study, we established lncRNA-mRNA coexpression networks for three rosacea subtypes (erythematotelangiectatic, papulopustular, and phymatous) and performed their functional enrichment analyses using Gene Onotology, KEGG, GSEA, and WGCNA. Compared to the control group, 13 differentially expressed lncRNAs and 525 differentially expressed mRNAs were identified in the three rosacea subtypes. The differentially expressed genes identified were enriched in four signaling pathways and the GO terms found were associated with leukocyte migration. In addition, we found nine differentially expressed lncRNAs in all three rosacea subtype-related networks, including NEAT1 and HOTAIR, which may play important roles in the pathology of rosacea. Our study provided novel insights into lncRNA-mRNA coexpression networks to discover the molecular mechanisms involved in rosacea development that can be used as future targets of rosacea diagnosis, prevention, and treatment.

scholarly journals The Genome of Cucurbita argyrosperma (Silver-Seed Gourd) Reveals Faster Rates of Protein-Coding Gene and Long Noncoding RNA Turnover and Neofunctionalization within Cucurbita

2019 ◽  
Vol 12 (4) ◽  
pp. 506-520 ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Enrique Ibarra-Laclette ◽  
Alejandra Vázquez-Lobo ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
Guillermo Sánchez de la Vega ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Rna Turnover ◽  
Protein Coding

scholarly journals Long Noncoding RNA Expression Signatures of Metastatic Nasopharyngeal Carcinoma and Their Prognostic Value

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Wei Zhang ◽  
Lin Wang ◽  
Fang Zheng ◽  
Ruhai Zou ◽  
Changqing Xie ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Disease Progression ◽  
Noncoding Rna ◽  
Prognostic Value ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Lncrna Expression ◽  
Genome Wide ◽  
Independent Panel ◽  
Metastatic Nasopharyngeal Carcinoma

Long noncoding RNAs (lncRNAs) have recently been found to play important roles in various cancer types. The elucidation of genome-wide lncRNA expression patterns in metastatic nasopharyngeal carcinoma (NPC) could reveal novel mechanisms underlying NPC carcinogenesis and progression. In this study, lncRNA expression profiling was performed on metastatic and primary NPC tumors, and the differentially expressed lncRNAs between these samples were identified. A total of 33,045 lncRNA probes were generated for our microarray based on authoritative data sources, including RefSeq, UCSC Knowngenes, Ensembl, and related literature. Using these probes, 8,088 lncRNAs were found to be significantly differentially expressed (≥2-fold). To identify the prognostic value of these differentially expressed lncRNAs, four lncRNAs (LOC84740, ENST00000498296, AL359062, and ENST00000438550) were selected; their expression levels were measured in an independent panel of 106 primary NPC samples via QPCR. Among these lncRNAs, ENST00000438550 expression was demonstrated to be significantly correlated with NPC disease progression. A survival analysis showed that a high expression level of ENST00000438550 was an independent indicator of disease progression in NPC patients (P=0.01). In summary, this study may provide novel diagnostic and prognostic biomarkers for NPC, as well as a novel understanding of the mechanism underlying NPC metastasis and potential targets for future treatment.

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