Limits...
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

Length and chromosomal location frequencies of the DMRs a) DMRs' length density. The abscissa represents the extent of the DMRs in base pairs. The dashed and dotted lines correspond for the median and mean respectively b) Distribution of the Differentially Methylated Regions per chromosome without normalization (ignoring chromosome length).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4481310&req=5

pone.0100476.g003: Length and chromosomal location frequencies of the DMRs a) DMRs' length density. The abscissa represents the extent of the DMRs in base pairs. The dashed and dotted lines correspond for the median and mean respectively b) Distribution of the Differentially Methylated Regions per chromosome without normalization (ignoring chromosome length).

Mentions: As for the distribution of the DMRs’ length, as shown in Fig 3a, we found the average was 1,215 with extreme values of 80 and 13,200 base pairs, respectively. Approximately more than 55% of the DMRs were less than 1,000 bp and only one percent of the DMRs accounted for fragments longer than 4,000 bp. Fig 3b illustrates the number of DMRs per chromosome. Due to the large number of unassigned locations in the chicken genome, the random chromosome accounted for 222 regions, followed by chromosome one with 172 DMRs. Chromosomes 16, 22 and 25 had the lowest numbers of DMRs with values of 5, 5 and 6, correspondingly.


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)

Length and chromosomal location frequencies of the DMRs a) DMRs' length density. The abscissa represents the extent of the DMRs in base pairs. The dashed and dotted lines correspond for the median and mean respectively b) Distribution of the Differentially Methylated Regions per chromosome without normalization (ignoring chromosome length).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0100476.g003: Length and chromosomal location frequencies of the DMRs a) DMRs' length density. The abscissa represents the extent of the DMRs in base pairs. The dashed and dotted lines correspond for the median and mean respectively b) Distribution of the Differentially Methylated Regions per chromosome without normalization (ignoring chromosome length).
Mentions: As for the distribution of the DMRs’ length, as shown in Fig 3a, we found the average was 1,215 with extreme values of 80 and 13,200 base pairs, respectively. Approximately more than 55% of the DMRs were less than 1,000 bp and only one percent of the DMRs accounted for fragments longer than 4,000 bp. Fig 3b illustrates the number of DMRs per chromosome. Due to the large number of unassigned locations in the chicken genome, the random chromosome accounted for 222 regions, followed by chromosome one with 172 DMRs. Chromosomes 16, 22 and 25 had the lowest numbers of DMRs with values of 5, 5 and 6, correspondingly.

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