Circadian analysis of miRNAs and their targets
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE17629
PROVIDER: PRJNA118619 | ENA |
REPOSITORIES: ENA
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Project description:Background: MicroRNAs (miRNAs), a class of non-coding small RNAs, are crucial to the regulation of various developmental processes. Plant architecture is a collection of genetically controlled agronomic traits that determine crop production and mechanized harvesting. Although several genes had been found to regulate plant architecture, the mechanisms whereby miRNAs regulate plant architecture in the rapeseed Brassica napus remain unknown. Results: In this study, we characterized a rod-like rapeseed mutant with an ideal plant architecture that substantially enhanced its breeding potential. To explore miRNAs that contribute to the rapeseed plant architecture, backcross progenies that developed into small plants (rod-like) and tall plants (normal) were used for study. Four small RNA (sRNA) libraries and two degradome libraries from the shoot apex of normal and rod-like plants were sequenced. A total of 925 non-redundant B. napus miRNA precursors were identified, representing 315 precursors for 74 known miRNAs and 610 precursors for 327 novel miRNAs. Expression analysis revealed that 10 known miRNAs and 7 novel miRNAs were differentially expressed between the normal and rod-like plants. In addition, 408 targets were identified through degradome sequencing and 14 targets were further validated via RNA ligase-mediated 5′ rapid amplification of cDNA ends. Furthermore, the functions of miR319 and its target gene TCP4 were studied and provided a novel insight into how miR319 regulates plant architecture. Conclusions: Correlation analysis between differentially expressed miRNAs and their targets demonstrated that nutrition and metal deprivation, energy supply deficiency, senescence and TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCPs) contributed to the premature termination of shoot development in rod-like mutant. The work further elucidates the mechanism of miRNAs participate in the regulation of plant architecture.
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Project description:Circadian clock controls the physiological functions of a lot of tissues including liver by an autoregulatory transcription-translational feedback loop, of which CLOCK is a core positive component. And, many studies have indicated that microRNAs (miRNAs) regulate liver function. However, little is known about the molecular interpretation of how CLOCK-regulated miRNAs are link to liver function. To better understand this, we performed the expression profiles of miRNAs in the liver of Clock△19 mutant mice to obtain the putative CLOCK-regulated miRNAs. A total of 61 miRNAs were differentially expressed (FCA≥2) in the liver of Clock mutant mice at zeitgeber time 2 (ZT2) and 57 miRNAs at zeitgeber time 14 (ZT14) as compared with control mice. Then, we analyzed the pathways of differentially expressed miRNAs to evaluate the roles of these miRNAs. According to the pathway analysis, the circadian rhythms and circadian entrainment pathway were found, and the target genes of differentially expressed miRNAs were mainly involved in pathways in cancer, PI3K-Akt signaling pathway and MAPK signaling pathway. The protein-protein interaction (PPI) analysis indicated that the hub genes were mostly associated with the pathway in cancer and circadian rhythms. Moreover, we verified the expression level of five miRNAs across the circadian cycle. Although the expression levels of miR-195 and miR-340 were up-regulated, the rhythms of these two miRNAs were always remained. The results identify a number of miRNAs that may be regulated by CLOCK, and these miRNAs play a role in the various physiological processes of the liver, which will provide a reference to better understanding the potential regulatory mechanisms in the liver.
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