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Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

Wan Q, Su J - Sci Rep (2015)

Bottom Line: Characterization of the transcriptomic response to infection is an effective approach to understanding the immune mechanisms.Furthermore, the splicing transcripts of IL-12p40 and IL-1R1 are firstly found to play diverse roles in the antiviral response of fishes.This study provides a complete transcriptome dataset of C. idella, which is valuable for the studies of immune complexity and, moreover, throws light on the regulatory role of AS in antiviral immunity.

View Article: PubMed Central - PubMed

Affiliation: 1] College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China [2] Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.

ABSTRACT
Characterization of the transcriptomic response to infection is an effective approach to understanding the immune mechanisms. Herein we challenged grass carp (Ctenopharyngodon idella) with grass carp reovirus (GCRV) and sequenced four cDNA libraries obtained from head-kidney and spleen by using Illumina Miseq. As a result, we gained a total of 21.52 Gb clean data with 107.96 million reads, and de novo assembled 55,199 unigenes with an average length of 1,470 bp. Comparative transcriptome analysis reveals that 217 unigenes are differentially expressed (fold-change of at least 4) between resistant and susceptible fish in both head-kidney and spleen, and of which 36 unigenes were validated by RT-qPCR experiment. The expression profile of immune-related genes demonstrates that the immune response of spleen is more intense than that of head-kidney. Remarkably, 11,811 unigenes contain multiple transcripts, of which 322 unigenes possess notably differentially expressed transcripts between the four transcriptomic datasets. Furthermore, the splicing transcripts of IL-12p40 and IL-1R1 are firstly found to play diverse roles in the antiviral response of fishes. This study provides a complete transcriptome dataset of C. idella, which is valuable for the studies of immune complexity and, moreover, throws light on the regulatory role of AS in antiviral immunity.

No MeSH data available.


Related in: MedlinePlus

Comparison results between RT-qPCR and RNA-seq data.The expression levels were normalized to 18S rRNA (red) and EF1α (blue), respectively. X axis and Y axis are the fold changes of gene expression, comparing KR4 with KS3 in section a; SR2 with SS1 in section b.
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f2: Comparison results between RT-qPCR and RNA-seq data.The expression levels were normalized to 18S rRNA (red) and EF1α (blue), respectively. X axis and Y axis are the fold changes of gene expression, comparing KR4 with KS3 in section a; SR2 with SS1 in section b.

Mentions: To validate the gene expression result of the RNA-seq data, 36 significant DEGs (P < 0.05, FDR < 0.05, fold-change of at least 8), recombination activating gene 1 (RAG1), and RAG2 were selected for RT-qPCR analysis. With 18S rRNA and EF1α as reference genes, the expression levels of these 38 genes were normalized. As was anticipated, the RT-qPCR data showed a positive linear relationship with RNA-seq data (Fig. 2 and Supplementary Table S3). And there was no statistically significant difference between the two data sets (t-test P > 0.05). This result suggested that the RNA-seq was a positive reference for expression profiling study on the whole, and that the assembly quality of the sequences was desirable.


Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

Wan Q, Su J - Sci Rep (2015)

Comparison results between RT-qPCR and RNA-seq data.The expression levels were normalized to 18S rRNA (red) and EF1α (blue), respectively. X axis and Y axis are the fold changes of gene expression, comparing KR4 with KS3 in section a; SR2 with SS1 in section b.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528194&req=5

f2: Comparison results between RT-qPCR and RNA-seq data.The expression levels were normalized to 18S rRNA (red) and EF1α (blue), respectively. X axis and Y axis are the fold changes of gene expression, comparing KR4 with KS3 in section a; SR2 with SS1 in section b.
Mentions: To validate the gene expression result of the RNA-seq data, 36 significant DEGs (P < 0.05, FDR < 0.05, fold-change of at least 8), recombination activating gene 1 (RAG1), and RAG2 were selected for RT-qPCR analysis. With 18S rRNA and EF1α as reference genes, the expression levels of these 38 genes were normalized. As was anticipated, the RT-qPCR data showed a positive linear relationship with RNA-seq data (Fig. 2 and Supplementary Table S3). And there was no statistically significant difference between the two data sets (t-test P > 0.05). This result suggested that the RNA-seq was a positive reference for expression profiling study on the whole, and that the assembly quality of the sequences was desirable.

Bottom Line: Characterization of the transcriptomic response to infection is an effective approach to understanding the immune mechanisms.Furthermore, the splicing transcripts of IL-12p40 and IL-1R1 are firstly found to play diverse roles in the antiviral response of fishes.This study provides a complete transcriptome dataset of C. idella, which is valuable for the studies of immune complexity and, moreover, throws light on the regulatory role of AS in antiviral immunity.

View Article: PubMed Central - PubMed

Affiliation: 1] College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China [2] Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.

ABSTRACT
Characterization of the transcriptomic response to infection is an effective approach to understanding the immune mechanisms. Herein we challenged grass carp (Ctenopharyngodon idella) with grass carp reovirus (GCRV) and sequenced four cDNA libraries obtained from head-kidney and spleen by using Illumina Miseq. As a result, we gained a total of 21.52 Gb clean data with 107.96 million reads, and de novo assembled 55,199 unigenes with an average length of 1,470 bp. Comparative transcriptome analysis reveals that 217 unigenes are differentially expressed (fold-change of at least 4) between resistant and susceptible fish in both head-kidney and spleen, and of which 36 unigenes were validated by RT-qPCR experiment. The expression profile of immune-related genes demonstrates that the immune response of spleen is more intense than that of head-kidney. Remarkably, 11,811 unigenes contain multiple transcripts, of which 322 unigenes possess notably differentially expressed transcripts between the four transcriptomic datasets. Furthermore, the splicing transcripts of IL-12p40 and IL-1R1 are firstly found to play diverse roles in the antiviral response of fishes. This study provides a complete transcriptome dataset of C. idella, which is valuable for the studies of immune complexity and, moreover, throws light on the regulatory role of AS in antiviral immunity.

No MeSH data available.


Related in: MedlinePlus