Global identification and integrated analysis of heat-responsive long non-coding RNAs in contrasting rice cultivars

2021 ◽  
Author(s):  
Zhengfeng Zhang ◽  
Huahua Zhong ◽  
Bo Nan ◽  
Benze Xiao
Keyword(s):  
Integrated Analysis ◽  
Rice Cultivars ◽  
Global Identification ◽  
Non Coding Rnas

scholarly journals Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus)

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2006
Author(s):  
Hongyu Liu ◽  
Ibrar Muhammad Khan ◽  
Huiqun Yin ◽  
Xinqi Zhou ◽  
Muhammad Rizwan ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Age Groups ◽  
Adherens Junction ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Rna Interaction ◽  
Long Non Coding Rna

The mRNAs and long non-coding RNAs axes are playing a vital role in the regulating of post-transcriptional gene expression. Thereby, elucidating the expression pattern of mRNAs and long non-coding RNAs underlying testis development is crucial. In this study, mRNA and long non-coding RNAs expression profiles were investigated in 3-month-old calves and 3-year-old mature bulls’ testes by total RNA sequencing. Additionally, during the gene level analysis, 21,250 mRNAs and 20,533 long non-coding RNAs were identified. As a result, 7908 long non-coding RNAs (p-adjust < 0.05) and 5122 mRNAs (p-adjust < 0.05) were significantly differentially expressed between the distinct age groups. In addition, gene ontology and biological pathway analyses revealed that the predicted target genes are enriched in the lysine degradation, cell cycle, propanoate metabolism, adherens junction and cell adhesion molecules pathways. Correspondingly, the RT-qPCR validation results showed a strong consistency with the sequencing data. The source genes for the mRNAs (CCDC83, DMRTC2, HSPA2, IQCG, PACRG, SPO11, EHHADH, SPP1, NSD2 and ACTN4) and the long non-coding RNAs (COX7A2, COX6B2, TRIM37, PRM2, INHBA, ERBB4, SDHA, ATP6VOA2, FGF9 and TCF21) were found to be actively associated with bull sexual maturity and spermatogenesis. This study provided a comprehensive catalog of long non-coding RNAs in the bovine testes and also offered useful resources for understanding the differences in sexual development caused by the changes in the mRNA and long non-coding RNA interaction expressions between the immature and mature stages.

scholarly journals Integrated analysis of coding genes and non-coding RNAs during hair follicle cycle of cashmere goat (Capra hircus)

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Shanhe Wang ◽  
Wei Ge ◽  
Zhixin Luo ◽  
Yang Guo ◽  
Beilei Jiao ◽  
...  
Keyword(s):  
Hair Follicle ◽  
Capra Hircus ◽  
Integrated Analysis ◽  
Cashmere Goat ◽  
Non Coding Rnas ◽  
Hair Follicle Cycle

scholarly journals Integrated Analysis of Stemness-Related LncRNAs Helps Predict the Immunotherapy Responsiveness of Gastric Cancer Patients

2021 ◽  
Vol 9 ◽  
Author(s):  
Quan Jiang ◽  
Lingli Chen ◽  
Hao Chen ◽  
Zhaoqing Tang ◽  
Fenglin Liu ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Independent Risk Factor ◽  
Critical Role ◽  
Tumor Biology ◽  
Integrated Analysis ◽  
Lasso Regression ◽  
Immune Microenvironment ◽  
Critical Feature ◽  
Non Coding Rnas ◽  
Gastric Cancer Patients

The immune microenvironment plays a critical role in tumor biology. As a critical feature of cancers, stemness is acknowledged as a contributor to the development of drug resistance in gastric cancers (GCs). Long non-coding RNAs (lncRNAs) have been revealed to participate in this process. In this study, we aimed to develop a stemness-related lncRNA signature (SRLncSig) with guiding significance for immunotherapy. Three cohorts (TCGA, Zhongshan, and IMvigor210) were enrolled for analysis. A list of stemness-related lncRNAs (SRlncRNAs) was collected by co-expression strategy under the threshold of coefficient value &gt;0.35 and p-value &lt; 0.05. Cox and Lasso regression analysis was further applied to find out the SRlncRNAs with prognosis-predictive value to establish the SRLncSig in the TCGA cohort. IPS and TIDE algorithms were further applied to predict the efficacy of SRLncSig in TCGA and Zhongshan cohorts. IMvigor210 was composed of patients with clinical outcomes of immunotherapy. The results indicated that SRLncSig not only was confirmed as an independent risk factor for GCs but also identified as a robust indicator for immunotherapy. The patient with a lower SRLncSig score was more likely to benefit from immunotherapy, and the results were highly consistent in three cohorts. In conclusion, our study not only could clarify the correlations between stemness and immunotherapy in GC patients but also provided a model to guide the applications of immunotherapy in clinical practice.

scholarly journals Integrated Analysis of Metabolome and Volatile Profiles of Germinated Brown Rice from the Japonica and Indica Subspecies

Foods ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2448
Author(s):  
Chenguang Zhou ◽  
Yaojie Zhou ◽  
Yuqian Hu ◽  
Bin Li ◽  
Roujia Zhang ◽  
...  
Keyword(s):  
Raw Materials ◽  
Indica Rice ◽  
Brown Rice ◽  
Essential Amino Acids ◽  
Integrated Analysis ◽  
Japonica Rice ◽  
Rice Cultivars ◽  
Germinated Brown Rice ◽  
Metabolomics Data ◽  
Volatile Profiles

Abstract: In the present study, germinated brown rice (GBR) from three Japonica and three Indica rice cultivars were subjected to metabolomics analysis and volatile profiling. The statistical assessment and pathway analysis of the metabolomics data demonstrated that in spite of significant metabolic changes in response to the germination treatment, the Japonica rice cultivars consistently expressed higher levels of several health-promoting compounds, such as essential amino acids and γ-aminobutyric acid (GABA), than the Indica cultivars. No clear discriminations of the volatile profiles were observed in light of the subspecies, and the concentrations of the volatile organic compounds (VOCs), including alkenes, aldehydes, furans, ketones, and alcohols, all exhibited significant reductions ranging from 26.8% to 64.1% after the germination. The results suggest that the Japonica cultivars might be desirable as the raw materials for generating and selecting GBR food products for health-conscious consumers.

Integrated analysis profiles of long non–coding RNAs reveal potential biomarkers across brain regions in post–traumatic stress disorder

2020 ◽  
Author(s):  
Yaoyao Bian ◽  
Lili Yang ◽  
Zhongli Wang ◽  
Wen Li ◽  
Qing Wang ◽  
...  
Keyword(s):  
Post Traumatic Stress Disorder ◽  
Traumatic Stress ◽  
Stress Disorder ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Post Traumatic Stress ◽  
Post Traumatic ◽  
Non Coding Rnas ◽  
Potential Biomarkers

Abstract Background Post–traumatic stress disorder (PTSD) is characterized by impaired fear extinction, excessive anxiety and depression. However, underlying mechanisms, especially the function roles of long non–coding RNAs (lncRNAs) involved in PTSD is still unclear. We argued that the lncRNAs, co–expressed mRNAs, as well as the associated pathways, are altered and may thus serve as potential biomarkers and key pathways related to PTSD.Methods The gene expression profiles of GSE68077 was downloaded from the GEO database, and the differentially expressed lncRNAs and mRNAs were identified. Gene ontology (GO) and Kyto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis were performed. Subsequently, protein–protein interaction (PPI) network was analyzed, and module analysis of the differentially expressed mRNAs was performed with Cytoscape software. Finally, lncRNAs–mRNAs co–expression network was constructed and core pair lncRNAs involved in PTSD were mapped.Results A total of 45 differentially expressed lncRNAs and 726 differentially expressed mRNAs were obtained. Among of which, 17 lncRNAs and 86 mRNAs were inter–regulated, and most of the lncRNAs–mRNAs co–expression showed positive correlations. The lncRNAs–mRNAs co–expressed network suggested the potentially functional roles of lncRNAs, regulated mRNAs and related pathways in PTSD. By implication of the core pair network, lncRNA–NONMMUT010120.2 synergistically up–regulated Ppargc1a and down–regulated Cir1, Slc38a9, Atp6v0a2. Moreover, lncRNA–NONMMUT023440.2, NONMMUT034155.2, NONMMUT105407.1 and NONMMUT149972.1 were co–expressed with 10 co–expressed mRNAs, which indicated that lncRNAs involved in PTSD might work by regulating the co–expressed mRNAs.

scholarly journals Integrated analysis of long non-coding RNAs and mRNAs associated with peritendinous fibrosis

2019 ◽  
Vol 15 ◽  
pp. 49-58 ◽  
Author(s):  
Wei Zheng ◽  
Chen Chen ◽  
Shuai Chen ◽  
Cunyi Fan ◽  
Hongjiang Ruan
Keyword(s):  
Integrated Analysis ◽  
Non Coding Rnas

scholarly journals Human Long Noncoding RNA Interactome: Detection, Characterization and Function

2020 ◽  
Vol 21 (3) ◽  
pp. 1027 ◽  
Author(s):  
Kazimierczyk ◽  
Kasprowicz ◽  
Kasprzyk ◽  
Wrzesinski
Keyword(s):  
Noncoding Rna ◽  
Potential Role ◽  
Integrated Analysis ◽  
Biological Functions ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
And Function ◽  
New Generation ◽  
Cellular Components ◽  
Proteins And Peptides

The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter” belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information about the human lncRNA interactome. The term lncRNA interactome refers to cellular biomolecules, such as nucleic acids, proteins, and peptides that interact with lncRNA. The lncRNA interactome was characterized in the last decade, however, understanding what role the biomolecules associated with lncRNA play and the nature of these interactions will allow us to better understand lncRNA's biological functions in the cell. We also describe a set of methods currently used for the detection of lncRNA interactome components and the analysis of their interactions. We think that such a holistic and integrated analysis of the lncRNA interactome will help to better understand its potential role in the development of organisms and cancers.

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