Identification and profiling of Cyprinus carpio microRNAs during ovary differentiation by deep sequencing

Wang, Fang; Jia, Yongfang; Wang, Po; Yang, Qian-wen; Du, Qiyun; Chang, Zhongjie

doi:10.1186/s12864-017-3701-y

Cited by 48 publications

(58 citation statements)

References 73 publications

(78 reference statements)

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“…miR‐316 is found in a wide range of organisms including human, drosophila, mosquitoes and moths (Griffiths‐Jones et al., ; Kozomara & Griffiths‐Jones, ) and yet, it has not previously been shown to be responsive to host/microbe interactions. In contrast, miR‐3024 and miR‐3041 are known only from aphids (Legeai et al., ; Li et al., ; Mathers et al., ) and, until recently, miR‐3050 was also known only from aphids but has now been recognized in the genome of the freshwater fish, Cyprinus carpio (Wang et al., ). Our identification of a role for miR‐316, miR‐3024, miR‐3041 and miR‐3050 in mediating aphid/ Buchnera interactions extends previous work annotating miRNA function in the context of host/microbe interactions.…”

Section: Discussionmentioning

confidence: 99%

microRNA regulation in an ancient obligate endosymbiosis

et al. 2018

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Although many insects are associated with obligate bacterial endosymbionts, the mechanisms by which these host/endosymbiont associations are regulated remain mysterious. While microRNAs (miRNAs) have been recently identified as regulators of host/microbe interactions, including host/pathogen and host/facultative endosymbiont interactions, the role miRNAs may play in mediating host/obligate endosymbiont interactions is virtually unknown. Here, we identified conserved miRNAs that potentially mediate symbiotic interactions between aphids and their obligate endosymbiont, Buchnera aphidicola. Using small RNA sequence data from Myzus persicae and Acyrthosiphon pisum, we annotated 93 M. persicae and 89 A. pisum miRNAs, among which 69 were shared. We found 14 miRNAs that were either highly expressed in aphid bacteriome, the Buchnera-housing tissue, or differentially expressed in bacteriome vs. gut, a non-Buchnera-housing tissue. Strikingly, 10 of these 14 miRNAs have been implicated previously in other host/microbe interaction studies. Investigating the interaction networks of these miRNAs using a custom computational pipeline, we identified 103 miRNA::mRNA interactions shared between M. persicae and A. pisum. Functional annotation of the shared mRNA targets revealed only two over-represented cluster of orthologous group categories: amino acid transport and metabolism, and signal transduction mechanisms. Our work supports a role for miRNAs in mediating host/symbiont interactions between aphids and their obligate endosymbiont Buchnera. In addition, our results highlight the probable importance of signal transduction mechanisms to host/endosymbiont coevolution.

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Section: Discussionmentioning

confidence: 99%

microRNA regulation in an ancient obligate endosymbiosis

et al. 2018

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“…miR-199-5p was also abundantly expressed in the ovaries of the common carp, which indicated a crucial role in gonad development (Wang et al 2017). miR-214 and miR-199-5p are in the same cluster in humans and are regulated by Twist-1 (Youn-Bok et al 2009).…”

Section: Discussionmentioning

confidence: 99%

“…miR-101a is one of the most abundant miRNAs in the carp ovary (Wang et al 2017) and plays a key role in the response to nonylphenol exposure in mouse Sertoli cells (MadisonVillar and Michalak 2011), suggesting a function of this miRNA in gonad development. miR-199-5p was also abundantly expressed in the ovaries of the common carp, which indicated a crucial role in gonad development (Wang et al 2017).…”

Section: Discussionmentioning

confidence: 99%

MicroRNA Alternations in the Testes Related to the Sterility of Triploid Fish

Tao

Zhou

et al. 2018

Mar Biotechnol

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The knowledge of understanding the molecular traits of the sterile triploid fish is sparse. Herein, we analyzed the microRNA (miRNA) alternations in the testes of the sterile triploid fish produced by crossing the tetraploid fish with the diploid fish, compared with those of tetraploids and diploids used as the controls. A total of 136, 134, and 142 conserved miRNAs and 105, 112, and 119 novel miRNAs were identified in the diploid, triploid, and tetraploid fish, respectively. The genes targeted by the differentially expressed miRNAs were identified and were enriched in the GO term cell surface receptor signaling pathway, cellular process, G-protein coupled receptor signaling pathway, and metabolic process. KEGG pathway enrichment was also assessed to evaluate the target genes with differentially expressed miRNAs and these genes were enriched in four pathways (synthesis and degradation of ketone bodies, pentose and glucuronate interconversions, cyanoamino acid metabolic process, and ascorbate and aldarate metabolism). Nine differentially expressed miRNAs were verified by quantitative real-time PCR analysis (qPCR). The upregulated miRNAs in triploids, including miR-101a, miR-199-5p, miR-214, miR-222, and miR-193a, showed the same results with high-throughput sequencing. Among the selected downregulated miRNAs, miR-7b and miR-153b had significantly lower expression levels in triploids. Dnah3 and Tekt1 genes targeted by miR-199-5p showed lower expression in triploids by qPCR. These verified differentially expressed miRNAs may participate in testicular development and sperm activity by targeting functional genes, which were identified with differential expression in the triploid. This evidence provides insights into the epigenetic regulatory mechanisms of sterility in triploid cyprinids.

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“…Cytoscape was employed for visualization of the regulation networks between DEmiRNA and their target mRNAs. A single mRNA can be targeted by various miRNAs, whereas a single miRNA is also capable of targeting different mRNAs 49 . In these regulation networks, it can be clearly seen that DEmiRNAs and their target genes in AcT1 VS AcCK1 formed complex networks.…”

Section: Resultsmentioning

confidence: 99%

Comparative identification of microRNAs inApis cerana ceranaworkers’ midguts responding toNosema ceranaeinvasion

Guo

Chen

et al. 2019

Preprint

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30 MicroRNAs (miRNAs) are endogenous small noncoding RNAs that post 31 transcriptionally regulate gene expression and are involved in many biological 32 processes including host-pathogen interactions. However, the potential role of 33 miRNAs in the responses of eastern honeybees to Nosema ceranae invasion is 34 completely unknown. Here, the expression profiles and differentially expressed 35 miRNAs (DEmiRNAs) in the midguts of Apis cerana cerana workers 7 and 10 days 36 post infection (dpi) with N. ceranae were investigated via small RNA sequencing and 37 bioinformatics. In total, 529 miRNAs highly conserved between various species and 38 25 novel miRNAs with varied expressions were identified for the first time. In 39 addition, stem-loop RT-PCR confirmed the expression of 16 predicted miRNAs, 40 validating their existence. Eight up-regulated miRNAs and six down-regulated 41 miRNAs were detected in midguts at 7 dpi, while nine and three miRNAs were 42 significantly up-regulated and down-regulated, respectively, in midguts at 10 dpi. In 43 addition, Venn analysis showed that five DEmiRNAs were shared, while nine and 44 seven DEmiRNAs were specifically expressed in midguts at 7 and 10 dpi, 45 respectively. Gene ontology analysis suggested that a portion of the DEmiRNAs and 46 corresponding target genes were involved in various biological processes, cellular 47 components, and molecular functions including immune system processes and 48 response to stimulus and signaling. Moreover, KEGG pathway analysis shed light on 49 the potential functions of some DEmiRNAs in the regulation of target genes engaged 50 in material and energy metabolism, cellular immunity such as endocytosis and 51 phagosome, and the humoral immune system, including the Jak-STAT and MAPK 52 signaling pathways. Further investigation demonstrated a complex regulation network 53 between DEmiRNAs and their target mRNAs, with miR-598-y, miR-252-y, miR-92-x 54 and miR-3654-y at the center of the network, implying their key parts in host 55 responses. This comprehensive miRNA transcriptome analysis demonstrated that N. 56 ceranae invasion influenced the expression of miRNAs in the midguts of A. c. 57 ceranae workers; the results can not only facilitate future exploration of the regulatory 58 roles and mechanisms of miRNAs in hosts' responses, especially their immune 59 3 responses to N. ceranae, but also provide potential candidates for further investigation 60 of the molecular mechanisms underlying eastern honeybee-microsporidian 61 interactions. 62

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Identification and profiling of Cyprinus carpio microRNAs during ovary differentiation by deep sequencing

Cited by 48 publications

References 73 publications

microRNA regulation in an ancient obligate endosymbiosis

microRNA regulation in an ancient obligate endosymbiosis

MicroRNA Alternations in the Testes Related to the Sterility of Triploid Fish

Comparative identification of microRNAs inApis cerana ceranaworkers’ midguts responding toNosema ceranaeinvasion

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