Global characterization of microRNAs in Trichomonas gallinae

Xu, Min-Jun; Qiu, Shen-Ben; Nisbet, Alasdair J.; Fu, Jin-Dong; Shao, Chang‐Lun; Zhu, Xing‐Quan

doi:10.1186/1756-3305-7-99

“…With the widespread and cost-effective use of Next Generation Sequencing (NGS) technologies, miRNAs have been deeply explored in non-model organisms, including bacteria ( Xu et al, 2014 ), plants ( Rhee, Chae & Kim, 2015 ) and viruses ( Kincaid & Sullivan, 2012 ; Diebel et al, 2015 ). The basic set of genes involved in the miRNA biogenesis, and related protein interactions, are well known in mammals ( Lau & MacRae, 2009 ), and also in other metazoans like Cnidaria ( Moran et al, 2013 ), Platyhelminthes ( Resch & Palakodeti, 2012 ) and insects ( Lucas & Raikhel, 2013 ; Hussain & Asgari, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

The miRNA biogenesis in marine bivalves

Rosani

¹

,

Pallavicini

²

,

Venier

³

2016

PeerJ

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Small non-coding RNAs include powerful regulators of gene expression, transposon mobility and virus activity. Among the various categories, mature microRNAs (miRNAs) guide the translational repression and decay of several targeted mRNAs. The biogenesis of miRNAs depends on few gene products, essentially conserved from basal to higher metazoans, whose protein domains allow specific interactions with dsRNA. Here, we report the identification of key genes responsible of the miRNA biogenesis in 32 bivalves, with particular attention to the aquaculture species Mytilus galloprovincialis and Crassostrea gigas. In detail, we have identified and phylogenetically compared eight evolutionary conserved proteins: DROSHA, DGCR8, EXP5, RAN, DICER TARBP2, AGO and PIWI. In mussels, we recognized several other proteins participating in the miRNA biogenesis or in the subsequent RNA silencing. According to digital expression analysis, these genes display low and not inducible expression levels in adult mussels and oysters whereas they are considerably expressed during development. As miRNAs play an important role also in the antiviral responses, knowledge on their production and regulative effects can shed light on essential molecular processes and provide new hints for disease prevention in bivalves.

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“…miRNAs are widely present in organisms, including animals, plants [1], and bacteria [2]. The mechanism of miRNA action in mammals has been well studied [3], while in invertebrates it remains limited and requires further investigation [4].…”

Section: Introductionmentioning

confidence: 99%

microRNA-mRNA Analysis Reveals Tissue-Specific Regulation of microRNA in Mangrove Clam (Geloina erosa)

Liu,

Dong,

Chen

et al. 2023

Biology

0

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Geloina erosa is an important benthic animal in the mangrove, serving as an indicator organism for coastal environmental pollution. This study aimed to investigate the tissue-specific expression of miRNAs and their regulatory roles in predicted targets in G. erosa. Through miRNA sequencing and co-expression network analysis, we extensively studied the miRNA expression in three tissues: gills, hepatopancreas, and muscle. The results revealed a total of 1412 miRNAs, comprising 1047 known miRNAs, and 365 newly predicted miRNAs. These miRNAs exhibited distinct tissue-specific expression patterns. In the miRNA target gene prediction, a total of 7404 potential predicted targets were identified, representing approximately 33% of all unique transcripts associated with miRNAs. Further co-expression network analysis revealed nine modules, each showing a positive correlation with specific tissues (gills, hepatopancreas, or muscle). The blue module showed a significant correlation with gills (r = 0.83, p-value = 0.006), the black module was significantly related to the hepatopancreas (r = 0.78, p-value = 0.01), and the purple module was significantly correlated with muscle (r = 0.83, p-value = 0.006). Within these modules, related miRNAs tended to cluster together, while their correlations with other modules were relatively weak. Functional enrichment analysis was performed on miRNAs and their predicted targets in each tissue. In the gills, miRNAs primarily regulate immune-related genes, substance transport, and cytoskeletal organization. In the hepatopancreas, miRNAs suppressed genes involved in shell formation and played a role in cellular motor activity and metabolism. In muscle, miRNAs participate in metabolism and photoreceptive processes, as well as immune regulation. In summary, this study provides valuable insights into the tissue-specific regulation of miRNAs in G. erosa, highlighting their potential roles in immune response, metabolism, and environmental adaptation. These findings offer important clues for understanding the molecular mechanisms and biological processes in G. erosa, laying the foundation for further validation and elucidation of these regulatory relationships.

show abstract

“…With the widespread and cost-effective use of Next Generation Sequencing (NGS) technologies, miRNAs have been deeply explored in non-model organisms, including bacteria (Xu et al 2014), plants (Rhee et al 2015) and viruses (Kincaid and Sullivan 2012;Diebel et al 2015). The basic set of genes involved in the miRNA biogenesis, and related protein interactions, are well known in mammals (Lau and MacRae 2009), and also in other metazoans like Cnidaria (Moran et al 2013), Platyhelminthes (Resch and Palakodeti 2012) and insects (Lucas and Raikhel 2013;Hussain and Asgari 2014).…”

Section: Introductionmentioning

confidence: 99%

Peer Review #2 of "The miRNA biogenesis in marine bivalves (v0.2)"

2016

0

View full text Add to dashboard Cite

Small non-coding RNAs include powerful regulators of gene expression, transposon mobility and virus activity. Among the various categories, mature microRNAs (miRNAs) guide the translational repression and decay of several targeted mRNAs. The biogenesis of miRNAs depends on few gene products, essentially conserved from basal to higher metazoans, whose protein domains allow specific interactions with dsRNA. Here, we report the identification of key genes responsible of the miRNA biogenesis in 32 bivalves, with particular attention to the aquaculture species Mytilus galloprovincialis and Crassostrea gigas. In detail, we have identified and phylogenetically compared eight evolutionary conserved proteins: DROSHA, DGCR8, EXP5, RAN, DICER TARBP2, AGO and PIWI. In mussels, we recognized several other proteins participating in the miRNA biogenesis or in the subsequent RNA silencing. According to digital expression analysis, these genes display low and not inducible expression levels in adult mussels and oysters whereas they are considerably expressed during development. As miRNAs play an important role also in the antiviral responses, knowledge on their production and regulative effects can shed light on essential molecular processes and provide new hints for disease prevention in bivalves.

show abstract

Global characterization of microRNAs in Trichomonas gallinae

Cited by 9 publications

References 35 publications

The miRNA biogenesis in marine bivalves

The miRNA biogenesis in marine bivalves

microRNA-mRNA Analysis Reveals Tissue-Specific Regulation of microRNA in Mangrove Clam (Geloina erosa)

Peer Review #2 of "The miRNA biogenesis in marine bivalves (v0.2)"

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