Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonica
Abstract Background Gills of euryhaline fishes possess great physiological and structural plasticity to adapt to large changes in external osmolality and to participate in ion uptake/excretion, which is essential for the re-establishment of fluid and electrolyte homeostasis. The osmoregulatory plast...
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| Format: | Article |
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BMC
2020-03-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-6630-0 |
| _version_ | 1818943539293192192 |
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| author | Hoi Man Ng Jeff Cheuk Hin Ho Wenyan Nong Jerome Ho Lam Hui Keng Po Lai Chris Kong Chu Wong |
| author_facet | Hoi Man Ng Jeff Cheuk Hin Ho Wenyan Nong Jerome Ho Lam Hui Keng Po Lai Chris Kong Chu Wong |
| author_sort | Hoi Man Ng |
| collection | DOAJ |
| description | Abstract Background Gills of euryhaline fishes possess great physiological and structural plasticity to adapt to large changes in external osmolality and to participate in ion uptake/excretion, which is essential for the re-establishment of fluid and electrolyte homeostasis. The osmoregulatory plasticity of gills provides an excellent model to study the role of microRNAs (miRs) in adaptive osmotic responses. The present study is to characterize an ex-vivo gill filament culture and using omics approach, to decipher the interaction between tonicity-responsive miRs and gene targets, in orchestrating the osmotic stress-induced responses. Results Ex-vivo gill filament culture was exposed to Leibovitz’s L-15 medium (300 mOsmol l− 1) or the medium with an adjusted osmolality of 600 mOsmol l− 1 for 4, 8 and 24 h. Hypertonic responsive genes, including osmotic stress transcriptional factor, Na+/Cl−-taurine transporter, Na+/H+ exchange regulatory cofactor, cystic fibrosis transmembrane regulator, inward rectifying K+ channel, Na+/K+-ATPase, and calcium-transporting ATPase were significantly upregulated, while the hypo-osmotic gene, V-type proton ATPase was downregulated. The data illustrated that the ex-vivo gill filament culture exhibited distinctive responses to hyperosmotic challenge. In the hyperosmotic treatment, four key factors (i.e. drosha RNase III endonuclease, exportin-5, dicer ribonuclease III and argonaute-2) involved in miR biogenesis were dysregulated (P < 0.05). Transcriptome and miR-sequencing of gill filament samples at 4 and 8 h were conducted and two downregulated miRs, miR-29b-3p and miR-200b-3p were identified. An inhibition of miR-29b-3p and miR-200b-3p in primary gill cell culture led to an upregulation of 100 and 93 gene transcripts, respectively. Commonly upregulated gene transcripts from the hyperosmotic experiments and miR-inhibition studies, were overlaid, in which two miR-29b-3p target-genes [Krueppel-like factor 4 (klf4), Homeobox protein Meis2] and one miR-200b-3p target-gene (slc17a5) were identified. Integrated miR-mRNA-omics analysis revealed the specific binding of miR-29b-3p on Klf4 and miR-200b-3p on slc17a5. The target-genes are known to regulate differentiation of gill ionocytes and cellular osmolality. Conclusions In this study, we have characterized the hypo-osmoregulatory responses and unraveled the modulation of miR-biogenesis factors/the dysregulation of miRs, using ex-vivo gill filament culture. MicroRNA-messenger RNA interactome analysis of miR-29b-3p and miR-200b-3p revealed the gene targets are essential for osmotic stress responses. |
| first_indexed | 2024-12-20T07:28:56Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-12-20T07:28:56Z |
| publishDate | 2020-03-01 |
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| series | BMC Genomics |
| spelling | doaj.art-86818e9f5bd24dbd88b209c6476611d72022-12-21T19:48:28ZengBMCBMC Genomics1471-21642020-03-0121111310.1186/s12864-020-6630-0Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonicaHoi Man Ng0Jeff Cheuk Hin Ho1Wenyan Nong2Jerome Ho Lam Hui3Keng Po Lai4Chris Kong Chu Wong5Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist UniversityCroucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist UniversitySchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongGuanxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical UniversityCroucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist UniversityAbstract Background Gills of euryhaline fishes possess great physiological and structural plasticity to adapt to large changes in external osmolality and to participate in ion uptake/excretion, which is essential for the re-establishment of fluid and electrolyte homeostasis. The osmoregulatory plasticity of gills provides an excellent model to study the role of microRNAs (miRs) in adaptive osmotic responses. The present study is to characterize an ex-vivo gill filament culture and using omics approach, to decipher the interaction between tonicity-responsive miRs and gene targets, in orchestrating the osmotic stress-induced responses. Results Ex-vivo gill filament culture was exposed to Leibovitz’s L-15 medium (300 mOsmol l− 1) or the medium with an adjusted osmolality of 600 mOsmol l− 1 for 4, 8 and 24 h. Hypertonic responsive genes, including osmotic stress transcriptional factor, Na+/Cl−-taurine transporter, Na+/H+ exchange regulatory cofactor, cystic fibrosis transmembrane regulator, inward rectifying K+ channel, Na+/K+-ATPase, and calcium-transporting ATPase were significantly upregulated, while the hypo-osmotic gene, V-type proton ATPase was downregulated. The data illustrated that the ex-vivo gill filament culture exhibited distinctive responses to hyperosmotic challenge. In the hyperosmotic treatment, four key factors (i.e. drosha RNase III endonuclease, exportin-5, dicer ribonuclease III and argonaute-2) involved in miR biogenesis were dysregulated (P < 0.05). Transcriptome and miR-sequencing of gill filament samples at 4 and 8 h were conducted and two downregulated miRs, miR-29b-3p and miR-200b-3p were identified. An inhibition of miR-29b-3p and miR-200b-3p in primary gill cell culture led to an upregulation of 100 and 93 gene transcripts, respectively. Commonly upregulated gene transcripts from the hyperosmotic experiments and miR-inhibition studies, were overlaid, in which two miR-29b-3p target-genes [Krueppel-like factor 4 (klf4), Homeobox protein Meis2] and one miR-200b-3p target-gene (slc17a5) were identified. Integrated miR-mRNA-omics analysis revealed the specific binding of miR-29b-3p on Klf4 and miR-200b-3p on slc17a5. The target-genes are known to regulate differentiation of gill ionocytes and cellular osmolality. Conclusions In this study, we have characterized the hypo-osmoregulatory responses and unraveled the modulation of miR-biogenesis factors/the dysregulation of miRs, using ex-vivo gill filament culture. MicroRNA-messenger RNA interactome analysis of miR-29b-3p and miR-200b-3p revealed the gene targets are essential for osmotic stress responses.http://link.springer.com/article/10.1186/s12864-020-6630-0Fish gill osmoregulationHyperosmotic stressJapanese eelTranscriptomemicroRNA inhibitors |
| spellingShingle | Hoi Man Ng Jeff Cheuk Hin Ho Wenyan Nong Jerome Ho Lam Hui Keng Po Lai Chris Kong Chu Wong Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonica BMC Genomics Fish gill osmoregulation Hyperosmotic stress Japanese eel Transcriptome microRNA inhibitors |
| title | Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonica |
| title_full | Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonica |
| title_fullStr | Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonica |
| title_full_unstemmed | Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonica |
| title_short | Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonica |
| title_sort | genome wide analysis of microrna messenger rna interactome in ex vivo gill filaments anguilla japonica |
| topic | Fish gill osmoregulation Hyperosmotic stress Japanese eel Transcriptome microRNA inhibitors |
| url | http://link.springer.com/article/10.1186/s12864-020-6630-0 |
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