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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

Binding sites reads counts and comparison of bisulfite sequencing and MBD-Seq approaches a) Normalized reads in binding sites per condition. The first two boxplots represent the overall methylation level in the control and vaccinated groups. The boxplots marked with the + and - signs correspond to the DMRs with enriched methylation levels in the vaccinated and control clusters, accordingly b) DNA methylation levels expressed in -log2 fold change from bisulfite sequencing (y-axis) and MBD-Seq (x-axis) methods.
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pone.0100476.g004: Binding sites reads counts and comparison of bisulfite sequencing and MBD-Seq approaches a) Normalized reads in binding sites per condition. The first two boxplots represent the overall methylation level in the control and vaccinated groups. The boxplots marked with the + and - signs correspond to the DMRs with enriched methylation levels in the vaccinated and control clusters, accordingly b) DNA methylation levels expressed in -log2 fold change from bisulfite sequencing (y-axis) and MBD-Seq (x-axis) methods.

Mentions: The binding affinity between conditions was shown in the Fig 4a. We found that global DNA methylation decreased in vaccinated individuals. The + sign marked the 451 sites with increased affinity in the vaccinated group and the—sign for the 704 regions that also augmented its binding, but in the control cluster. The gray and white boxes corresponded to control and vaccinated within + or—groups, correspondingly. To test whether the distribution of the values was significantly different among them, a two-sided Wilcoxon-Mann-Whitney test was applied. From the Table 3, all were significant different (p<0.05), excepting (Control.DB+ versus Vacc.DB).


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)

Binding sites reads counts and comparison of bisulfite sequencing and MBD-Seq approaches a) Normalized reads in binding sites per condition. The first two boxplots represent the overall methylation level in the control and vaccinated groups. The boxplots marked with the + and - signs correspond to the DMRs with enriched methylation levels in the vaccinated and control clusters, accordingly b) DNA methylation levels expressed in -log2 fold change from bisulfite sequencing (y-axis) and MBD-Seq (x-axis) methods.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0100476.g004: Binding sites reads counts and comparison of bisulfite sequencing and MBD-Seq approaches a) Normalized reads in binding sites per condition. The first two boxplots represent the overall methylation level in the control and vaccinated groups. The boxplots marked with the + and - signs correspond to the DMRs with enriched methylation levels in the vaccinated and control clusters, accordingly b) DNA methylation levels expressed in -log2 fold change from bisulfite sequencing (y-axis) and MBD-Seq (x-axis) methods.
Mentions: The binding affinity between conditions was shown in the Fig 4a. We found that global DNA methylation decreased in vaccinated individuals. The + sign marked the 451 sites with increased affinity in the vaccinated group and the—sign for the 704 regions that also augmented its binding, but in the control cluster. The gray and white boxes corresponded to control and vaccinated within + or—groups, correspondingly. To test whether the distribution of the values was significantly different among them, a two-sided Wilcoxon-Mann-Whitney test was applied. From the Table 3, all were significant different (p<0.05), excepting (Control.DB+ versus Vacc.DB).

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