Crosstalk among lncRNAs, microRNAs and mRNAs in the muscle 'degradome' of rainbow trout

Scientific Reports
Bam PaneruMohamed Salem

Abstract

In fish, protein-coding and noncoding genes involved in muscle atrophy are not fully characterized. In this study, we characterized coding and noncoding genes involved in gonadogenesis-associated muscle atrophy, and investigated the potential functional interplay between these genes. Using RNA-Seq, we compared expression pattern of mRNAs, long noncoding RNAs (lncRNAs) and microRNAs of atrophying skeletal muscle from gravid females and control skeletal muscle from age-matched sterile individuals. A total of 852 mRNAs, 1,160 lncRNAs and 28 microRNAs were differentially expressed (DE) between the two groups. Muscle atrophy appears to be mediated by many genes encoding ubiquitin-proteasome system, autophagy related proteases, lysosomal proteases and transcription factors. Transcripts encoding atrogin-1 and mir-29 showed exceptional high expression in atrophying muscle, suggesting an important role in bulk muscle proteolysis. DE genes were co-localized in the genome with strong expression correlation, and they exhibited extensive 'lncRNA-mRNA', 'lncRNA-microRNA', 'mRNA-microRNA' and 'lncRNA-protein' physical interactions. DE genes exhibiting potential functional interactions comprised the highly correlated 'lncRNA-mRNA-microRNA' gen...Continue Reading

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Citations

Jul 21, 2020·Autophagy·Sophie TesseraudIban Seiliez
Jan 6, 2021·Animals : an Open Access Journal From MDPI·Prasanthi KogantiBeth M Cleveland
Aug 23, 2019·Molecular Therapy. Nucleic Acids·Li Zhang, Handong Wang

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Datasets Mentioned

BETA
SRP131630

Methods Mentioned

BETA
ubiquitination
PCR
RNA-Seq

Software Mentioned

CLC genomics workbench
ALGGEN PROMO TF
CatRapid Omics tool
PITA
sRNAtoolbox
Cufflinks
Coding Potential Calculator ( CPC )
IntaRNA
TopHat
TargetSpy

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