Details:

Alternative Title:
BMC Genomics
Publisher's site:
http://dx.doi.org/10.1186/1471-2164-14-666
Personal Author:
Cingolani, Pablo ; Cao, Xiaoyi ; Khetani, Radhika S ; Chen, Chieh-Chun ; Coon, Melissa ; ... More +
Cingolani, Pablo ; Cao, Xiaoyi ; Khetani, Radhika S ; Chen, Chieh-Chun ; Coon, Melissa ; Sammak, Alya’a ; Bollig-Fischer, Aliccia ; Land, Susan ; Huang, Yun ; Hudson, Matthew E ; Garfinkel, Mark D ; Zhong, Sheng ; Robinson, Gene E ; Ruden, Douglas M Less -
Description:
Background

Previous whole-genome shotgun bisulfite sequencing experiments showed that DNA cytosine methylation in the honey bee (Apis mellifera) is almost exclusively at CG dinucleotides in exons. However, the most commonly used method, bisulfite sequencing, cannot distinguish 5-methylcytosine from 5-hydroxymethylcytosine, an oxidized form of 5-methylcytosine that is catalyzed by the TET family of dioxygenases. Furthermore, some analysis software programs under-represent non-CG DNA methylation and hydryoxymethylation for a variety of reasons. Therefore, we used an unbiased analysis of bisulfite sequencing data combined with molecular and bioinformatics approaches to distinguish 5-methylcytosine from 5-hydroxymethylcytosine. By doing this, we have performed the first whole genome analyses of DNA modifications at non-CG sites in honey bees and correlated the effects of these DNA modifications on gene expression and alternative mRNA splicing.

Results

We confirmed, using unbiased analyses of whole-genome shotgun bisulfite sequencing (BS-seq) data, with both new data and published data, the previous finding that CG DNA methylation is enriched in exons in honey bees. However, we also found evidence that cytosine methylation and hydroxymethylation at non-CG sites is enriched in introns. Using antibodies against 5-hydroxmethylcytosine, we confirmed that DNA hydroxymethylation at non-CG sites is enriched in introns. Additionally, using a new technique, Pvu-seq (which employs the enzyme PvuRts1l to digest DNA at 5-hydroxymethylcytosine sites followed by next-generation DNA sequencing), we further confirmed that hydroxymethylation is enriched in introns at non-CG sites.

Conclusions

Cytosine hydroxymethylation at non-CG sites might have more functional significance than previously appreciated, and in honey bees these modifications might be related to the regulation of alternative mRNA splicing by defining the locations of the introns.


Subject:
[+]
Alternative Splicing
Animals
Bees
Behavior, Animal
CpG Islands
Cytosine
DNA Methylation
Exons
Gene Expression Regulation
Genes, Insect
Honey
Introns
Reproducibility Of Results
RNA, Messenger
RNA Splice Sites
Sequence Analysis, DNA
Sulfites

Source:
BMC Genomics. 2013; 14:666.
Pubmed ID:
24079845
Pubmed Central ID:
PMC3850688
Document Type:
Journal Article
Funding:
1DP10D006416/DP/NCCDPHP CDC HHS/United States ; AI44432/AI/NIAID NIH HHS/United States ; ES012933/ES/NIEHS NIH HHS/United States ; ES021983/ES/NIEHS NIH HHS/United States ; P30 CA022453/CA/NCI NIH HHS/United States ; ... More +
1DP10D006416/DP/NCCDPHP CDC HHS/United States ; AI44432/AI/NIAID NIH HHS/United States ; ES012933/ES/NIEHS NIH HHS/United States ; ES021983/ES/NIEHS NIH HHS/United States ; P30 CA022453/CA/NCI NIH HHS/United States ; R01 ES012933/ES/NIEHS NIH HHS/United States ; R21 ES021983/ES/NIEHS NIH HHS/United States Less -
Place as Subject:
Africa ; Europe
Africa ; Europe Less -
Collection(s):
CDC Public Access
Main Document Checksum:
[+]
urn:sha256:9dd957ec32cd37d41bce5b7e2f27d75941ec0ec83f25713c2cb5987499af0a86
File Type:

Supporting Files

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