Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees.
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.
Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA. douglasr@wayne.edu.
Pablo
P
Cingolani
Xiaoyi
X
Cao
Radhika S
RS
Khetani
Chieh-Chun
CC
Chen
Melissa
M
Coon
Alya'a
A
Sammak
Aliccia
A
Bollig-Fischer
Susan
S
Land
Yun
Y
Huang
Matthew E
ME
Hudson
Mark D
MD
Garfinkel
Sheng
S
Zhong
Gene E
GE
Robinson
Douglas M
DM
Ruden
D044503:5-Methylcytosine / Q000031:analogs & derivatives; D000349:Africa; D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D001516:Bees / Q000235:genetics*; D001522:Behavior, Animal; D018899:CpG Islands / Q000235:genetics*; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics*; D005060:Europe; D005091:Exons / Q000235:genetics; D005786:Gene Expression Regulation; D017344:Genes, Insect / Q000235:genetics; D006722:Honey; D007438:Introns / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013447:Sulfites
D022821:RNA Splice Sites; D012333:RNA, Messenger; D013447:Sulfites; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; C042345:hydrogen sulfite