Expressed micro-RNA (miRNA) affects messenger RNA (mRNA) abundance, hindering the accuracy of upstream regulator analysis. Our objective was to provide an algorithm to correct such bias. Large mRNA and miRNA analyses were performed on RNA extracted from bovine liver and mammary tissue. Using four levels of target scores from TargetScan (all miRNA:mRNA target gene pairs or only the top 25%, 50%, or 75%) Using four levels of target scores from TargetScan (all miRNA:mRNA target gene pairs or only the top 25%, 50%, or 75%) and four levels of the magnitude of miRNA effect (ME) on mRNA expression (30%, 50%, 75%, and 83% mRNA reduction), we generated 17 different datasets (including the original dataset). For each dataset, we performed upstream regulator analysis using two bioinformatics tools. We detected an increased effect on the upstream regulator analysis with larger miRNA:mRNA pair bins and higher ME. The miRNA correction allowed identification of several upstream regulators not present in the analysis of the original dataset. Thus, the proposed algorithm improved the prediction of upstream regulators.
Tag: transcriptome
Metabolomic and transcriptomic analyses reveal new insights into the role of abscisic acid in modulating mango fruit ripening
Mango (Mangifera indica L.) is a climacteric tropical fruit consumed around the world. Although ethylene and abscisic acid (ABA) have been considered to be stimulators that trigger mango fruit ripening, their regulation mechanisms in modulating mango fruit ripening remain uncertain. In this study, we performed integrative analyses of metabolome and transcriptome data combined with a series of physiology and experiment analysis on ‘Keitt’ mango, and we characterized changes in specific metabolite accumulation at different stages during mango fruit development and ripening, which were strongly correlated with transcriptional changes and embodied the physiological changes as well as taste formation. Specifically, we found that ABA, rather than ethylene, was highly associated with mango ripening, and exogenous ABA application promoted mango fruit ripening. Transcriptomic analysis identified diverse ripening-related genes involved in sugar and carotenoid biosynthesis and softening-related metabolic processes. Furthermore, networks of ABA and ripening-related genes (such as MiHY5, MiGBF4, MiABI5 and MibZIP9) were constructed, and the direct regulation of the key ABA responsive transcription factor MiHY5 to ripening-related genes were experimentally confirmed by ranges of evidence. Taken together, our results indicate that ABA plays a key role in directly modulating mango fruit ripening through MiHY5, suggesting the need for a re-conceiving about how we understand ABA function in modulating climacteric fruit ripening.