Large scale statistical inference of signaling pathways from RNAi and microarray data

Background/Aims: Recent research has improved our understanding of the pulmonary vein and surrounding left atrial (LA-PV) junction and the left atrial appendage (LAA), which are considered the ‘trigger’ and ‘substrate’ in the development of atrial fibrillation (AF), respectively. Herein, with the aim of identifying the underlying potential genetic mechanisms, we compared differences in gene expression between LA-PV junction and LAA specimens via bioinformatic analysis. Methods: Microarray data of AF (GSE41177) were downloaded from the Gene Expression Omnibus database. In addition, linear models for microarray data limma powers differential expression analyses and weighted correlation network analysis (WGCNA) were applied. Results: From the differential expression analyses, 152 differentially expressed genes and hub genes, including LEP, FOS, EDN1, NMU, CALB2, TAC1, and PPBP, were identified. Our analysis revealed that the maps of extracellular matrix (ECM)-receptor interactions, PI3K-Akt and Wnt signaling pathways, and ventricular cardiac muscle tissue morphogenesis were significantly enriched. In addition, the WGCNA results showed high correlations between genes and related genetic clusters to external clinical characteristics. Maps of the ECM-receptor interactions, chemokine signaling pathways, and the cell cycle were significantly enriched in the genes of corresponding modules and closely associated with AF duration, left atrial diameter, and left ventricular ejection function, respectively. Similarly, mapping of the TNF signaling pathway indicated significant association with genetic traits of ischemic heart disease, hypertension, and diabetes comorbidity. Conclusions: The ECM-receptor interaction as a possible central node of comparison between LA-PV and LAA samples reflected the special functional roles of ‘triggers’ and ‘substrates’ and may be closely associated with AF duration. Furthermore, LEP, FOS, EDN1, NMU, CALB2, TAC1, and PPBP genes may be implicated in the occurrence and maintenance of AF through their interactions with each other.

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N6-methyladenosine modification modulate in the heat stress of sheep (Ovis aries)

10.21203/rs.2.9885/v1 ◽

2019 ◽

Author(s):

Zengkui Lu ◽

Huihua Wang ◽

Youji Ma ◽

Mingxing Chu ◽

Kai Quan ◽

...

Keyword(s):

Heat Stress ◽

Signaling Pathways ◽

Stress Responses ◽

Large Scale ◽

Ovis Aries ◽

Stop Codons ◽

Coding Regions ◽

Mrna Methylation ◽

Response To Stress ◽

And Control

Abstract Background: Intensive and large-scale development of the sheep industry and increases in global temperature are increasingly exposing sheep to heat stress. N6-methyladenosine (m6A) mRNA methylation varies in response to stress, and can link external stress with complex transcriptional and post-transcriptional processes. However, no m6A mRNA methylation map has been obtained for sheep, nor is it known what effect this has on regulating heat stress in sheep. Results: A total of 8,306 and 12,958 m6A peaks were detected in heat stress and control groups, respectively, with 2,697 and 5,494 genes associated with each. Peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. Methylation levels of heat stress and control sheep were higher near stop codons, although methylation was significantly lower in heat stress sheep. GO revealed that differential m6A-containing genes were mainly enriched in the nucleus and were involved in several stress responses and substance metabolism processes. KEGG pathway analysis found that differential m6A-containing genes were significantly enriched in Rap1, FoxO, MAPK, and other signaling pathways of the stress response, and TGF-beta, AMPK, Wnt, and other signaling pathways involved in fat metabolism. These m6A-modified genes were moderately expressed in both heat stress and control sheep, and the enrichment of m6A modification was significantly negatively correlated with gene expression. Conclusions: Our results showed that m6A mRNA methylation modifications regulate heat stress in sheep, and it also provided a new way for the study of animal response to heat stress.

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Functions of Jasmonic Acid in Plant Regulation and Response to Abiotic Stress

International Journal of Molecular Sciences ◽

10.3390/ijms21041446 ◽

2020 ◽

Vol 21 (4) ◽

pp. 1446 ◽

Cited By ~ 9

Author(s):

Jia Wang ◽

Li Song ◽

Xue Gong ◽

Jinfan Xu ◽

Minhui Li

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Jasmonic Acid ◽

Signaling Pathways ◽

Signaling Pathway ◽

Large Scale ◽

Higher Plants ◽

Complex Signal ◽

Ja Signaling ◽

Signal Network

Jasmonic acid (JA) is an endogenous growth-regulating substance, initially identified as a stress-related hormone in higher plants. Similarly, the exogenous application of JA also has a regulatory effect on plants. Abiotic stress often causes large-scale plant damage. In this review, we focus on the JA signaling pathways in response to abiotic stresses, including cold, drought, salinity, heavy metals, and light. On the other hand, JA does not play an independent regulatory role, but works in a complex signal network with other phytohormone signaling pathways. In this review, we will discuss transcription factors and genes involved in the regulation of the JA signaling pathway in response to abiotic stress. In this process, the JAZ-MYC module plays a central role in the JA signaling pathway through integration of regulatory transcription factors and related genes. Simultaneously, JA has synergistic and antagonistic effects with abscisic acid (ABA), ethylene (ET), salicylic acid (SA), and other plant hormones in the process of resisting environmental stress.

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