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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

Bisulfite sequencing validation of MBD-Seq result (e.g., MBD22 region) a) Methylation concentration levels from MBD-seq b) Bisulfite sequencing results.Each line represents a plasmid sequence and each dot indicates a CpG site. An open circle indicates an unmethylated CpGs and a black dot methylated CpGs. The double-cross shape was the mutation. The methylation level was calculated as the number of methylated CpG sites divided by the total detected CpGs (mutation excluded).
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pone.0100476.g005: Bisulfite sequencing validation of MBD-Seq result (e.g., MBD22 region) a) Methylation concentration levels from MBD-seq b) Bisulfite sequencing results.Each line represents a plasmid sequence and each dot indicates a CpG site. An open circle indicates an unmethylated CpGs and a black dot methylated CpGs. The double-cross shape was the mutation. The methylation level was calculated as the number of methylated CpG sites divided by the total detected CpGs (mutation excluded).

Mentions: In order to assess the reliability and accuracy of MBD-seq in DMRs detection, 36 DMRs were arbitrarily selected for validation. At least 10 colonies were cultured and then sequenced from each group. Twenty-two of those 36 DMRs (61%) had been sequenced. The calculated methylation levels are shown in the Fig 4b. We found that methylation levels of 19 of these 22 DMRs (86.4%) agreed with the directionality of the change revealed by MBD-seq, although only 36.8% of DMRs had significant differences (p< 0.01), detected by bisulfite sequencing. This technic employs only a segment of the DMR to perform the validation, thus the orientation of the change is more descriptive than the magnitude of methylation differences. For example, the methylation level of ILTV group was extremely higher than the control group for the MBD22 region (FDR = 0.016), employing the MBD-Seq method. In this case, the MBD-Seq result was accurate validated by the bisulfite sequencing approach (Fig 5).


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)

Bisulfite sequencing validation of MBD-Seq result (e.g., MBD22 region) a) Methylation concentration levels from MBD-seq b) Bisulfite sequencing results.Each line represents a plasmid sequence and each dot indicates a CpG site. An open circle indicates an unmethylated CpGs and a black dot methylated CpGs. The double-cross shape was the mutation. The methylation level was calculated as the number of methylated CpG sites divided by the total detected CpGs (mutation excluded).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0100476.g005: Bisulfite sequencing validation of MBD-Seq result (e.g., MBD22 region) a) Methylation concentration levels from MBD-seq b) Bisulfite sequencing results.Each line represents a plasmid sequence and each dot indicates a CpG site. An open circle indicates an unmethylated CpGs and a black dot methylated CpGs. The double-cross shape was the mutation. The methylation level was calculated as the number of methylated CpG sites divided by the total detected CpGs (mutation excluded).
Mentions: In order to assess the reliability and accuracy of MBD-seq in DMRs detection, 36 DMRs were arbitrarily selected for validation. At least 10 colonies were cultured and then sequenced from each group. Twenty-two of those 36 DMRs (61%) had been sequenced. The calculated methylation levels are shown in the Fig 4b. We found that methylation levels of 19 of these 22 DMRs (86.4%) agreed with the directionality of the change revealed by MBD-seq, although only 36.8% of DMRs had significant differences (p< 0.01), detected by bisulfite sequencing. This technic employs only a segment of the DMR to perform the validation, thus the orientation of the change is more descriptive than the magnitude of methylation differences. For example, the methylation level of ILTV group was extremely higher than the control group for the MBD22 region (FDR = 0.016), employing the MBD-Seq method. In this case, the MBD-Seq result was accurate validated by the bisulfite sequencing approach (Fig 5).

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