Identification and Characterization of MicroRNAs in Snakehead Fish Cell Line upon Snakehead Fish Vesiculovirus Infection
Abstract
:1. Introduction
2. Results
2.1. Overview of the Illumine Hiseq2500 Sequencing Data of Small RNAs
2.2. Identification of Conserved miRNAs in SSN-1 Cells
2.3. Prediction and Validation of Novel miRNAs
Sequence (5′→3′) | Mature Reads | Fold Change (Log2 I24/C24) * | p-Value | |
---|---|---|---|---|
1 | UCCAUCAGUCACGUGACCUAC | 26 | −2.15182 | 2.03 × 10−16 |
2 | UCGGGUCGCUAAUGACGUCACC | 30 | −3.57979 | 4.64 × 10−21 |
3 | ACCAGGUGCUGUAAGCUU | 67 | <1 | – |
4 | CUUUUAAUCUGAGGGUCCA | 12 | <1 | – |
5 | AUGACUCGAACCCGAGGACUCG | 13 | 1.57979 | 0.019847 |
6 | AUCCGGCUCGAAGGACCAA | 157 | −4.36217 | 0 |
7 | AAACACUGCCAGCUGCCACA | 5 | −3.67933 | 0.00165 |
8 | GGGGCCUGAGUCCUUCUG | 17 | 13.75742 | 0 |
9 | ACCCCACUCCUGGUACCA | 51 | −4.59089 | 8.16 × 10−197 |
2.4. Differentially-Expressed miRNAs and Validation of the miRNAs by qRT-PCR
2.5. miRNA Targets Prediction
Name | Sequence (5′→3′) | Target | Fold Change (Log2 I24/C24) * |
---|---|---|---|
miR-23a-3-5p | GGAUUCCUGGCAGAGUGAUUU | N, L | −7.92953 |
miR-199-5p | CCCAGUGUUCAGACUACCUGUUC | N, L | −3.96545 |
miR-338 | UCCAGCAUCAGUGAUUUUGUUG | N, L | −4.16476 |
miR-145-3p | GGAUUCCUGGAAAUACUGUUCU | N, L | −6.05784 |
miR-100-3p | CAAGCUUGUAUCUAUAGGUAUC | N, G | −3.61793 |
miR-216b | UAAUCUCUGCAGGCAACUGUGA | N, G, L | −6.73689 |
miR-130c-5p | GCCCUUUUUCUGUUGUACUACU | N, G, L | −4.79246 |
miR-214 | ACAGCAGGCACAGACAGGCAG | N, P | −4.27387 |
miR-731 | AAUGACACGUUUUCUCCCGGAUCG | N | −3.18425 |
miR-29b | UAGCACCAUUUGAAAUCAGUGU | P | −3.20471 |
miR-29a | UAGCACCAUUUGAAAUCGGUUA | P | −3.25812 |
miR-135c | UAUGGCUUUCUAUUCCUAUGUG | M | −1.6469 |
miR-145-5p | GUCCAGUUUUCCCAGGAAUCCC | G | −7.017 |
miR-92b-3p | UAUUGCACUCGUCCCGGCCUCC | G | −4.75081 |
miR-153b-3p | UUGCAUAGUCACAAAAAUGAGC | G, L | −2.41897 |
miR-7147 | UGUACCAUGCUGGUAGCCAGU | G | −4.7948 |
miR-92a-3p | UAUUGCACUUGUCCCGGCCUGU | G | −3.97976 |
miR-184 | UGGACGGAGAACUGAUAAGGGC | G | −2.16476 |
miR-301c-3p | CAGUGCAAUAGUAUUGUCAUAG | G | −2.45693 |
miR-363-3p | AAUUGCACGGUAUCCAUCUGUA | G | −3.26429 |
miR-454b | UAGUGCAAUAUUGCUUAUAGGG | G | −2.98676 |
miR-301a | CAGUGCAAUAGUAUUGUCAAAG | G | −2.1425 |
miR-130a | CAGUGCAAUGUUAAAAGGGCAU | G | −3.11229 |
miR-23a-5p | GAAUUCCUGGCAGAGUGAUUU | G, L | −6.09946 |
miR-153a-3p | UUGCAUAGUCACAAAAGUGAUC | G, L | −2.95278 |
miR-25-3p | CAUUGCACUUGUCUCGGUCUGA | G | −2.31239 |
miR-730 | UCCUCAUUGUGCAUGCUGUGUGU | G | −4.60532 |
miR-204-5p | UUCCCUUUGUCAUCCUAUGCCU | G, L | −3.14817 |
miR-301b-3p | CAGUGCAAUAGUAUUGUCAUUG | G | −4.92954 |
miR-724 | UUAAAGGGAAUUUGCGACUGUU | L | −2.63081 |
miR-181c-5p | CACAUUCAUUGCUGUCGGUGGG | L | −1.84696 |
miR-125a | UCCCUGAGACCCUUAACCUGUG | L | −3.16476 |
miR-183-5p | UAUGGCACUGGUAGAAUUCACUG | L | −1.57979 |
miR-199-3p | UACAGUAGUCUGCACAUUGGUU | L | −2.97786 |
miR-26a-2-3p | CCUAUUCAUGAUUACUUGCACU | L | −3.8599 |
miR-140-3p | UACCACAGGGUAGAACCACGGAC | L | −3.03951 |
miR-146a | UGAGAACUGAAUUCCAUAGAUGG | L | −1.98658 |
miR-150 | UCUCCCAAUCCUUGUACCAGUG | L | −2.63751 |
miR-221-3p | AGCUACAUUGUCUGCUGGGUUUC | L | −2.48955 |
miR-34a | UGGCAGUGUCUUAGCUGGUUGU | L | −2.5756 |
miR-101b | UACAGUACUAUGAUAACUGAAG | L | −2.73747 |
miR-9-5p | UCUUUGGUUAUCUAGCUGUAUGA | L | −1.54182 |
miR-181b-5p | AACAUUCAUUGCUGUCGGUGGG | L | −1.75554 |
miR-107a-3p | AGCAGCAUUGUACAGGGCUAUCA | L | −2.81985 |
miR-101a | UACAGUACUGUGAUAACUGAAG | L | −3.05599 |
miR-181c-3p | CUCGCCGGACAAUGAAUGAGAA | L | −5.01275 |
miR-103 | AGCAGCAUUGUACAGGGCUAUGA | L | −2.61915 |
miR-146b | UGAGAACUGAAUUCCAAGGGUG | L | −3.91539 |
miR-138-5p | AGCUGGUGUUGUGAAUCAGGCC | L | −4.94236 |
miR-429a | UAAUACUGUCUGGUAAUGCCGU | L | −2.44487 |
miR-153b-5p | GUCAUUUUUGUGGUUUGCAGCU | L | −3.67933 |
miR-125c-5p | UCCCUGAGACCCUAACUCGUGA | L | −5.07926 |
miR-181a-5p | AACAUUCAACGCUGUCGGUGAGU | L | −1.97076 |
miR-199-3-3p | ACAGUAGUCCGCACAUUGGUU | L | −3.81683 |
miR-125b-5p | UCCCUGAGACCCUAACUUGUGA | L | −3.43276 |
miR-26a-5p | UUCAAGUAAUCCAGGAUAGGCU | L | −3.35436 |
miR-722 | UUUUUUGCAGAAACGUUUCAGAUU | L | −6.25146 |
miR-222a-3p | AGCUACAUCUGGCUACUGGGUCUC | L | −3.55456 |
2.6. Effects of Three Selected miRNAs on SHVV Multiplication
3. Discussion
4. Experimental Section
4.1. Virus, Cells and RNA Preparation
4.2. Small RNA Library Construction
4.3. Sequencing Data Analysis
4.4. Identification of Novel miRNAs
4.5. Analysis of Differentially-Expressed miRNAs
4.6. Prediction of miRNA Targets on the SHVV Genome
4.7. RT-PCR and qRT-PCR Analysis of miRNAs
4.8. Effects of Three Randomly-Selected Differentially-Expressed miRNAs on Virus Multiplication
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Liu, X.; Tu, J.; Yuan, J.; Liu, X.; Zhao, L.; Dawar, F.U.; Khattak, M.N.K.; Hegazy, A.M.; Chen, N.; Vakharia, V.N.; et al. Identification and Characterization of MicroRNAs in Snakehead Fish Cell Line upon Snakehead Fish Vesiculovirus Infection. Int. J. Mol. Sci. 2016, 17, 154. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17020154
Liu X, Tu J, Yuan J, Liu X, Zhao L, Dawar FU, Khattak MNK, Hegazy AM, Chen N, Vakharia VN, et al. Identification and Characterization of MicroRNAs in Snakehead Fish Cell Line upon Snakehead Fish Vesiculovirus Infection. International Journal of Molecular Sciences. 2016; 17(2):154. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17020154
Chicago/Turabian StyleLiu, Xiaodan, Jiagang Tu, Junfa Yuan, Xueqin Liu, Lijuan Zhao, Farman Ullah Dawar, Muhammad Nasir Khan Khattak, Abeer M. Hegazy, Nan Chen, Vikram N. Vakharia, and et al. 2016. "Identification and Characterization of MicroRNAs in Snakehead Fish Cell Line upon Snakehead Fish Vesiculovirus Infection" International Journal of Molecular Sciences 17, no. 2: 154. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17020154