The liver is an important central organ, which controls carbohydrate metabolism through maintaining glucose homeostasis by a tightly regulated system of genes or enzymes. The microRNAs are small non-coding RNAs playing an important role in the regulation of genes associated with developmental biology, physiology, metabolism, etc. Thus, in this study, we have intended to detect liver-specific microRNAs in farmed carp, Labeo bata, upon being fed a diet with different levels of carbohydrates. Here, we have conducted the experiment for 45 days using fingerlings of farmed carp fed with 20% (control), 40%, and 60% gelatinized starch levels. The liver tissues were collected from each treatment and processed for RNA isolation, small RNA library preparation, and high-throughput sequencing using Illumina NexSeq500. Through sequencing, 15,779,417 reads in 20% CHO, 13,959,039 in 40% CHO, and 13,661,950 in 60% CHO reads were generated for control and treated fishes using three small RNA libraries. We have investigated 445 novel and 231 conserved microRNAs in 20%, 40%, and 60% carbohydrate (CHO), respectively, through computational analysis. The differential expression analysis of miRNAs was carried out between different treatments compared with control and this study depicted 117 known and 114 novel miRNA genes involved in carbohydrate metabolic pathways. Further, target prediction and gene ontology analysis revealed that miRNAs were involved in several pathways such as signaling pathway, G protein pathway, complement receptor–mediated pathway, dopamine receptor signaling pathway, epidermal growth factor pathway, and notch signaling pathway. The predicted miRNA sites in targeted genes were associated with cellular activities, developmental biology, DNA binding, Golgi apparatus, extracellular region, catalytic activity, MAPK cascade, etc. Overall, we have generated a vital resource of liver-specific miRNAs involved in metabolic gene regulation. These studies further will help develop miRNA inhibitors to study their role during carbohydrate metabolism in farmed carp.
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Tax calculation will be finalised during checkout.
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
Tax calculation will be finalised during checkout.
- qRT PCR:
Real-time quantitative reverse transcription PCR
- LN2 :
Transcripts per million
Differentially expressed miRNAs
AMP-activated protein kinase
Janus kinase/signal transducers and activators of transcription
Mitogen-activated protein kinases
Agarwal V, Bell GW, Nam J-W, Bartel DP (2015) Predicting effective microRNA target sites in mammalian mRNAs. eLife 4:e05005
Bizuayehu TT, Babiak I (2014) MicroRNA in teleost fish. Genome biology and evolution 6:1911–1937
Cui L, Hu H, Wei W, Wang W, Liu H (2016) Identification and characterization of microRNAs in the liver of blunt snout bream (Megalobrama amblycephala) infected by Aeromonas hydrophila. Int J Mol Sci 17:1972
Deng Y, Li X, Feng J, Zhang X (2018) Overexpression of miR-202 resensitizes imatinib resistant chronic myeloid leukemia cells through targetting Hexokinase 2. Biosci Rep 38. https://doi.org/10.1042/BSR20171383
Girard M, Jacquemin E, Munnich A, Lyonnet S, Henrion-Caude A (2008) miR-122, a paradigm for the role of microRNAs in the liver. J Hepatol 48:648–656
Gomes F, Watanabe L, Nozawa S, Oliveira L, Cardoso J, Vianez J, Nunes M, Schneider H, Sampaio I (2017) Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing. Genomics 109:67–74
Hanin G, Yayon N, Tzur Y, Haviv R, Bennett ER, Udi S, Krishnamoorthy YR, Kotsiliti E, Zangen R, Efron B, Tam J, Pappo O, Shteyer E, Pikarsky E, Heikenwalder M, Greenberg DS, Soreq H (2018) miRNA-132 induces hepatic steatosis and hyperlipidaemia by synergistic multitarget suppression. Gut 67:1124–1134
Herkenhoff ME, Oliveira AC, Nachtigall PG, Costa JM, Campos VF, Hilsdorf AWS, Pinhal D (2018) Fishing into the microRNA transcriptome. Front Genet 9. https://doi.org/10.3389/fgene.2018.00088
Kamalam BS, Medale F, Panserat S (2017) Utilisation of dietary carbohydrates in farmed fishes: new insights on influencing factors, biological limitations and future strategies. Aquaculture 467:3–27
Krüger J, Rehmsmeier M (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34:W451–W454
Lau K, Lai KP, Bao JY, Zhang N, Tse A, Tong A, Li JW, Lok S, Kong RY, Lui WY, Wong A, Wu RS (2014) Identification and expression profiling of microRNAs in the brain, liver and gonads of marine medaka (Oryzias melastigma) and in response to hypoxia. PLoS One 9:e110698
Liu AM, Xu Z, Shek FH, Wong KF, Lee NP, Poon RT, Chen J, Luk JM (2014) miR-122 targets pyruvate kinase M2 and affects metabolism of hepatocellular carcinoma. PloS one 9:e86872
Massart J, Sjogren RJO, Lundell LS, Mudry JM, Franck N, O'gorman DJ, Egan B, Zierath JR, Krook A (2017) Altered miR-29 expression in type 2 diabetes influences glucose and lipid metabolism in skeletal muscle. Diabetes 66:1807–1818
Miao LH, Lin Y, Pan WJ, Huang X, Ge XP, Ren MC, Zhou QL, Liu B (2017) Identification of differentially expressed microRNAs associate with glucose metabolism in different organs of blunt snout bream (Megalobrama amblycephala). Int J Mol Sci 18. https://doi.org/10.3390/ijms18061161
Nrc (2011) Nutrient requirements of fish and shrimp. National Academies Press, Washington, D. C.
Prisingkorn W, Prathomya P, Jakovlic I, Liu H, Zhao YH, Wang WM (2017) Transcriptomics, metabolomics and histology indicate that high-carbohydrate diet negatively affects the liver health of blunt snout bream (Megalobrama amblycephala). BMC Genomics 18:856
Ramirez CM, Goedeke L, Rotllan N, Yoon JH, Cirera-Salinas D, Mattison JA, Suarez Y, De Cabo R, Gorospe M, Fernandez-Hernando C (2013) MicroRNA 33 regulates glucose metabolism. Mol Cell Biol 33:2891–2902
Rasal KD, Nandanpawar PC, Swain P, Badhe MR, Sundaray JK, Jayasankar P (2016) MicroRNA in aquaculture fishes: a way forward with high-throughput sequencing and a computational approach. Rev Fish Biol Fish 26:199–212
Ren M, Habte-Tsion H-M, Xie J, Liu B, Zhou Q, Ge X, Pan L, Chen R (2015) Effects of dietary carbohydrate source on growth performance, diet digestibility and liver glucose enzyme activity in blunt snout bream, Megalobrama amblycephala. Aquaculture 438:75–81
Rui L (2014) Energy metabolism in the liver. Compr Physiol 4:177–197
Vienberg S, Geiger J, Madsen S, Dalgaard LT (2017) MicroRNAs in metabolism. Acta Physiol 219:346–361
Zhao L, Lu H, Meng Q, Wang J, Wang W, Yang L, Lin L (2016) Profilings of microRNAs in the liver of common carp (Cyprinus carpio) infected with Flavobacterium columnare. Int J Mol Sci 17:566
We are thankful to Director, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar and Director, ICAR-IASRI, New Delhi, for providing the facility to undertake this work.
Conflict of Interest
The authors declare that they have no conflict of interest.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Rasal, K.D., Iquebal, M.A., Jaiswal, S. et al. Liver-Specific microRNA Identification in Farmed Carp, Labeo bata (Hamilton, 1822), Fed with Starch Diet Using High-Throughput Sequencing. Mar Biotechnol 21, 589–595 (2019). https://doi.org/10.1007/s10126-019-09912-y
- Labeo bata
- Next-generation sequencing