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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

Heat-maps obtained at different stages of the analysis a) Occupancy analysis result based on rows cross-correlations from the peaks detected by MACS. The dendogram describes the similarity of peaks among samples and serves as a quality control for the peak calling step b) Clustering employing the reads counts of each sample in the entire set of potential binding sites, which are represented by rows in the matrix.
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pone.0100476.g001: Heat-maps obtained at different stages of the analysis a) Occupancy analysis result based on rows cross-correlations from the peaks detected by MACS. The dendogram describes the similarity of peaks among samples and serves as a quality control for the peak calling step b) Clustering employing the reads counts of each sample in the entire set of potential binding sites, which are represented by rows in the matrix.

Mentions: To evaluate the data quality, we did occupancy analysis based on the cross-correlations of each row using only the peak calling data (Fig 1a), indicating the similarity of peak scores and serving as a technical quality control as well. The samples clustered based on concentration instead on replication, excepting for the high concentration samples where they paired by replication and condition (HC1-HC2 and HV1-HV2), as is reflected in the larger correlation coefficient among these samples. Then, a binding matrix was generated using the read counts instead of the previously used peak confidence scores (Fig 1b). The results show affinity scores correlation (reads counts) in all possible binding locations. For most of the samples correlations are higher than in Fig 1a. Obviously, this approach worked well for grouping high concentration samples by condition and replicates but failed to classify all samples based on condition.


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)

Heat-maps obtained at different stages of the analysis a) Occupancy analysis result based on rows cross-correlations from the peaks detected by MACS. The dendogram describes the similarity of peaks among samples and serves as a quality control for the peak calling step b) Clustering employing the reads counts of each sample in the entire set of potential binding sites, which are represented by rows in the matrix.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0100476.g001: Heat-maps obtained at different stages of the analysis a) Occupancy analysis result based on rows cross-correlations from the peaks detected by MACS. The dendogram describes the similarity of peaks among samples and serves as a quality control for the peak calling step b) Clustering employing the reads counts of each sample in the entire set of potential binding sites, which are represented by rows in the matrix.
Mentions: To evaluate the data quality, we did occupancy analysis based on the cross-correlations of each row using only the peak calling data (Fig 1a), indicating the similarity of peak scores and serving as a technical quality control as well. The samples clustered based on concentration instead on replication, excepting for the high concentration samples where they paired by replication and condition (HC1-HC2 and HV1-HV2), as is reflected in the larger correlation coefficient among these samples. Then, a binding matrix was generated using the read counts instead of the previously used peak confidence scores (Fig 1b). The results show affinity scores correlation (reads counts) in all possible binding locations. For most of the samples correlations are higher than in Fig 1a. Obviously, this approach worked well for grouping high concentration samples by condition and replicates but failed to classify all samples based on condition.

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