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Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine.

Carrillo JA, He Y, Luo J, Menendez KR, Tablante NL, Zhao K, Paulson JN, Li B, Song J - PLoS ONE (2015)

Bottom Line: We found that global DNA methylation decreased in vaccinated birds, presenting 704 hypomethylated and 451 hypermethylated DMRs, respectively.The top four identified canonical pathways were EIF2 signaling, regulation of EIF4 and p70S6K signaling, axonal guidance signaling and mTOR signaling, providing new insight regarding the mechanisms of ILT etiology.Lastly, the association between DNA methylation and differentially expressed genes was examined, and detected negative correlation in seventeen of the eighteen genes.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America.

ABSTRACT
In this study we investigated the methylome of chickens immunized with Infectious laryngotracheitis (ILT) vaccine derived from chicken embryos. Methyl-CpG binding domain protein-enriched genome sequencing (MBD-Seq) method was employed in the detection of the 1,155 differentially methylated regions (DMRs) across the entire genome. After validation, we ascertained the genomic DMRs distribution and annotated them regarding genes, transcription start sites (TSS) and CpG islands. We found that global DNA methylation decreased in vaccinated birds, presenting 704 hypomethylated and 451 hypermethylated DMRs, respectively. Additionally, we performed an enrichment analysis detecting gene networks, in which cancer and RNA post-transcriptional modification appeared in the first place, followed by humoral immune response, immunological disease and inflammatory disease. The top four identified canonical pathways were EIF2 signaling, regulation of EIF4 and p70S6K signaling, axonal guidance signaling and mTOR signaling, providing new insight regarding the mechanisms of ILT etiology. Lastly, the association between DNA methylation and differentially expressed genes was examined, and detected negative correlation in seventeen of the eighteen genes.

No MeSH data available.


Related in: MedlinePlus

Differentially methylated regions visualization and cluster of samples considering their methylation levels a) The MA plot shows in red the differentially methylated regions obtained with a false discovery rate of < 0.1 b) Heat-map of samples demonstrates a perfect classification of the condition of the individuals based on methylation levels in the differentially methylated regions.
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pone.0100476.g002: Differentially methylated regions visualization and cluster of samples considering their methylation levels a) The MA plot shows in red the differentially methylated regions obtained with a false discovery rate of < 0.1 b) Heat-map of samples demonstrates a perfect classification of the condition of the individuals based on methylation levels in the differentially methylated regions.

Mentions: By using DiffBind, we defined a contrast based on conditions and detected 85,493 unique peaks and 47,356 overlapped peaks. The resulting matrix of 47,356 x 12 represents binding locations and number of samples for rows and columns, respectively. We detected 1,155 DMRs across the entire chicken genome for birds that were inoculated with ILT chicken embryo origin vaccine. The differentially methylated regions (DMRs) (FDR<0.1) are presented as red dots in the Fig 2a. We found that 451 and 704 DMRs were hypomethylated and hypermethylated in the vaccinated group, respectively. The clustering of samples, using only the identified DMRs, was shown in the Fig 2b. The extensive list of DMRs is provided as an excel spreadsheet in the S2 Table. The results coincide with the condition of the samples, especially for the vaccinated samples that were assigned to the same cluster, suggesting that these DNA varying methylation levels could be used to predict the outcome of the individual.


Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine.

Carrillo JA, He Y, Luo J, Menendez KR, Tablante NL, Zhao K, Paulson JN, Li B, Song J - PLoS ONE (2015)

Differentially methylated regions visualization and cluster of samples considering their methylation levels a) The MA plot shows in red the differentially methylated regions obtained with a false discovery rate of < 0.1 b) Heat-map of samples demonstrates a perfect classification of the condition of the individuals based on methylation levels in the differentially methylated regions.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4481310&req=5

pone.0100476.g002: Differentially methylated regions visualization and cluster of samples considering their methylation levels a) The MA plot shows in red the differentially methylated regions obtained with a false discovery rate of < 0.1 b) Heat-map of samples demonstrates a perfect classification of the condition of the individuals based on methylation levels in the differentially methylated regions.
Mentions: By using DiffBind, we defined a contrast based on conditions and detected 85,493 unique peaks and 47,356 overlapped peaks. The resulting matrix of 47,356 x 12 represents binding locations and number of samples for rows and columns, respectively. We detected 1,155 DMRs across the entire chicken genome for birds that were inoculated with ILT chicken embryo origin vaccine. The differentially methylated regions (DMRs) (FDR<0.1) are presented as red dots in the Fig 2a. We found that 451 and 704 DMRs were hypomethylated and hypermethylated in the vaccinated group, respectively. The clustering of samples, using only the identified DMRs, was shown in the Fig 2b. The extensive list of DMRs is provided as an excel spreadsheet in the S2 Table. The results coincide with the condition of the samples, especially for the vaccinated samples that were assigned to the same cluster, suggesting that these DNA varying methylation levels could be used to predict the outcome of the individual.

Bottom Line: We found that global DNA methylation decreased in vaccinated birds, presenting 704 hypomethylated and 451 hypermethylated DMRs, respectively.The top four identified canonical pathways were EIF2 signaling, regulation of EIF4 and p70S6K signaling, axonal guidance signaling and mTOR signaling, providing new insight regarding the mechanisms of ILT etiology.Lastly, the association between DNA methylation and differentially expressed genes was examined, and detected negative correlation in seventeen of the eighteen genes.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America.

ABSTRACT
In this study we investigated the methylome of chickens immunized with Infectious laryngotracheitis (ILT) vaccine derived from chicken embryos. Methyl-CpG binding domain protein-enriched genome sequencing (MBD-Seq) method was employed in the detection of the 1,155 differentially methylated regions (DMRs) across the entire genome. After validation, we ascertained the genomic DMRs distribution and annotated them regarding genes, transcription start sites (TSS) and CpG islands. We found that global DNA methylation decreased in vaccinated birds, presenting 704 hypomethylated and 451 hypermethylated DMRs, respectively. Additionally, we performed an enrichment analysis detecting gene networks, in which cancer and RNA post-transcriptional modification appeared in the first place, followed by humoral immune response, immunological disease and inflammatory disease. The top four identified canonical pathways were EIF2 signaling, regulation of EIF4 and p70S6K signaling, axonal guidance signaling and mTOR signaling, providing new insight regarding the mechanisms of ILT etiology. Lastly, the association between DNA methylation and differentially expressed genes was examined, and detected negative correlation in seventeen of the eighteen genes.

No MeSH data available.


Related in: MedlinePlus