37 Integration analysis between differentially expressed mRNA and miRNA induced by BRCA1 gene

2010 ◽  
Vol 8 (5) ◽  
pp. 10
Author(s):  
M. Zajac ◽  
M. Tanic ◽  
G. Gomez-Lopez ◽  
J. Benitez ◽  
B. Martinez-Delgado
Keyword(s):  
Brca1 Gene ◽  
Differentially Expressed ◽  
Differentially Expressed Mrna ◽  
Integration Analysis

scholarly journals lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7491 ◽  
Author(s):  
Haibin Zhang ◽  
Cheng Chen ◽  
Yinghong Cui ◽  
Yuqing Li ◽  
Zhaojun Wang ◽  
...  
Keyword(s):  
Biological Function ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Human Chondrocytes ◽  
Loss Of Function ◽  
Knee Oa ◽  
System Disease ◽  
Chondrocyte Death ◽  
Differentially Expressed Mrna ◽  
Gain Loss

Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or < − 2.0-fold change; p < 0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. QPCR was used to validate chip results. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, the gain/loss of function experiments of lnc-SAMD14-4 was implemented in IL-1β-treated human chondrocytes. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA.

scholarly journals MicroRNA dynamics during hibernation of the Australian central bearded dragon (Pogona vitticeps)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alexander Capraro ◽  
Denis O‘Meally ◽  
Shafagh A. Waters ◽  
Hardip R. Patel ◽  
Arthur Georges ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Physiological State ◽  
Regulation Of Gene Expression ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Tissue Specific ◽  
Mrna Targets ◽  
Bearded Dragon ◽  
Pogona Vitticeps ◽  
Differentially Expressed Mrna

Abstract Hibernation is a physiological state employed by many animals that are exposed to limited food and adverse winter conditions. Controlling tissue-specific and organism wide changes in metabolism and cellular function requires precise regulation of gene expression, including by microRNAs (miRNAs). Here we profile miRNA expression in the central bearded dragon (Pogona vitticeps) using small RNA sequencing of brain, heart, and skeletal muscle from individuals in late hibernation and four days post-arousal. A total of 1295 miRNAs were identified in the central bearded dragon genome; 664 of which were novel to central bearded dragon. We identified differentially expressed miRNAs (DEmiRs) in all tissues and correlated mRNA expression with known and predicted target mRNAs. Functional analysis of DEmiR targets revealed an enrichment of differentially expressed mRNA targets involved in metabolic processes. However, we failed to reveal biologically relevant tissue-specific processes subjected to miRNA-mediated regulation in heart and skeletal muscle. In brain, neuroprotective pathways were identified as potential targets regulated by miRNAs. Our data suggests that miRNAs are necessary for modulating the shift in cellular metabolism during hibernation and regulating neuroprotection in the brain. This study is the first of its kind in a hibernating reptile and provides key insight into this ephemeral phenotype.

scholarly journals Disruption of miRNA-mRNA Networks Defines Novel Molecular Signatures for Penile Carcinogenesis

Cancers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 4745
Author(s):  
Tatiane Katsue Furuya ◽  
Claudio Bovolenta Murta ◽  
Alexis Germán Murillo Carrasco ◽  
Miyuki Uno ◽  
Laura Sichero ◽  
...  
Keyword(s):  
Penile Cancer ◽  
Total Sample ◽  
Differentially Expressed ◽  
Molecular Signatures ◽  
Mirna Microarray ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas ◽  
Integration Analysis ◽  
Potential Biomarkers ◽  
Independent Cohort

Penile cancer (PeC) carcinogenesis is not fully understood, and no biomarkers are reported in clinical practice. We aimed to investigate molecular signatures based on miRNA and mRNA and perform an integrative analysis to identify molecular drivers and pathways for PeC development. Affymetrix miRNA microarray was used to identify differentially expressed miRNAs (DEmiRs) comparing 11 tumoral tissues (TT) paired with non-neoplastic tissues (NNT) with further validation in an independent cohort (n = 13). We also investigated the mRNA expression of 83 genes in the total sample. Experimentally validated targets of DEmiRs, miRNA-mRNA networks, and enriched pathways were evaluated in silico. Eight out of 69 DEmiRs identified by microarray analysis were validated by qRT-PCR (miR-145-5p, miR-432-5p, miR-487b-3p, miR-30a-5p, miR-200a-5p, miR-224-5p, miR-31-3p and miR-31-5p). Furthermore, 37 differentially expressed genes (DEGs) were identified when comparing TT and NNT. We identified four downregulated DEmiRs (miR-30a-5p, miR-432-5p, miR-487b-3p, and miR-145-5p) and six upregulated DEGs (IL1A, MCM2, MMP1, MMP12, SFN and VEGFA) as potential biomarkers in PeC by their capacity of discriminating TT and NNT with accuracy. The integration analysis showed eight dysregulated miRNA-mRNA pairs in penile carcinogenesis. Taken together, our findings contribute to a better understanding of the regulatory roles of miRNAs and altered transcripts levels in penile carcinogenesis.

Differentially expressed circRNA and mRNA profiles of neural stem cells with radiation irradiation

2020 ◽  
Author(s):  
Zhaopeng Cai ◽  
Shan Wang ◽  
Zhongyu Xie ◽  
Peng Wang ◽  
Huiyong Shen ◽  
...  
Keyword(s):  
Regulatory Mechanism ◽  
Circular Rna ◽  
Signal Pathway ◽  
Differentially Expressed ◽  
Signal Pathways ◽  
Spine Metastasis ◽  
Radiation Induced ◽  
Differentially Expressed Mrna ◽  
Oncology Practice ◽  
Mapk Signal Pathway

Abstract Background Spine metastasis is common but highly problematic in clinical oncology practice. Radiotherapy plays an important role in the treatment of spine metastasis, but it at the same time damages the nervous tissue, especially the neural stem cell (NSC), and leads to radiation induced myelopathy. Circular RNA (circRNA) is a kind of non-coding RNA which responses to external stimulus and regulates cellular functions. However, the mechanism of radiotherapy affecting NSC and the role of circRNA in this process are still unclear. Methods The circRNA and mRNA of NSC treated with radiation or not were detect using next-generation sequencing. RT-PCR assays were preformed to confirm the sequencing results and the feature of differentially expressed circRNA. Bioinformation analyses were conducted to identified the critical circRNA and mRNA, as well as the enriched functions and pathways. Moreover, a circRNA-miRNA-mRNA network was constructed to investigate the possible regulatory mechanism. Results A total of 421 differentially expressed circRNA and 1602 differentially expressed mRNA of NSC were identified after radiotherapy. The GO and KEGG analysis of the differentially expressed mRNA as well as the host genes of the differentially expressed circRNA were performed and several key signal pathways such as MAPK signal pathway were identified. Moreover, a circRNA-miRNA-mRNA network focusing on MAPK signal pathway was shown and predicted that chr5:127160496|127165240 could be the critical circRNA in the regulatory mechanism of radiation treated NSCs. Conclusion Our finding showed the differentially expressed circRNA and mRNA profiles of NSC after radiotherapy, suggesting that circRNA may contribute to the pathogenesis of radiation induced myelopathy.

scholarly journals Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice

2019 ◽  
Vol 20 (1) ◽  
pp. 222 ◽  
Author(s):  
Wenqi Li ◽  
Yulin Jia ◽  
Fengquan Liu ◽  
Fangquan Wang ◽  
Fangjun Fan ◽  
...  
Keyword(s):  
Rice Variety ◽  
Genetic Resistance ◽  
Defense Responses ◽  
Resistance Mechanisms ◽  
Differentially Expressed ◽  
Bacterial Disease ◽  
Degradome Sequencing ◽  
Differentially Expressed Mirnas ◽  
Rot Disease ◽  
Integration Analysis

Rice foot rot disease caused by the pathogen Dickeya zeae (formerly known as Erwinia chrysanthemi pv. zeae), is a newly emerging damaging bacterial disease in China and the southeast of Asia, resulting in the loss of yield and grain quality. However, the genetic resistance mechanisms mediated by miRNAs to D. zeae are unclear in rice. In the present study, 652 miRNAs including osa-miR396f predicted to be involved in multiple defense responses to D. zeae were identified with RNA sequencing. A total of 79 differentially expressed miRNAs were detected under the criterion of normalized reads ≥10, including 51 known and 28 novel miRNAs. Degradome sequencing identified 799 targets predicted to be cleaved by 168 identified miRNAs. Among them, 29 differentially expressed miRNA and target pairs including miRNA396f-OsGRFs were identified by co-expression analysis. Overexpression of the osa-miR396f precursor in a susceptible rice variety showed enhanced resistance to D. zeae, coupled with significant accumulation of transcripts of osa-miR396f and reduction of its target the Growth-Regulating Factors (OsGRFs). Taken together, these findings suggest that miRNA and targets including miR396f-OsGRFs have a role in resisting the infections by bacteria D. zeae.

Sign in / Sign up

Export Citation Format

Share Document