Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees

BMC Genomics

Research Article

Mark D Garfinkel¹  Melissa Coon²  Alya’a Sammak²  Susan Land²  Douglas M Ruden³  Pablo Cingolani⁴  Aliccia Bollig-Fischer⁵  Sheng Zhong⁶  Chieh-Chun Chen⁶  Xiaoyi Cao⁶  Radhika S Khetani⁶  Matthew E Hudson⁷  Gene E Robinson⁸  Yun Huang⁹ 

[1] Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA;Department of Obstetrics and Gynecology, Wayne State University, 48201, Detroit, MI, USA;Department of Obstetrics and Gynecology, Wayne State University, 48201, Detroit, MI, USA;Institute of Environmental Health Sciences, Wayne State University, 48201, Detroit, MI, USA;Department of Obstetrics and Gynecology, Wayne State University, 48201, Detroit, MI, USA;School of Computer Science & Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada;Department of Oncology, Wayne State University, 48201, Detroit, MI, USA;Institute for Genomic Biology, University of Illinois, 61801, Urbana, IL, USA;Institute for Genomic Biology, University of Illinois, 61801, Urbana, IL, USA;Department of Crop Sciences, University of Illinois, 61801, Urbana, IL, USA;Institute for Genomic Biology, University of Illinois, 61801, Urbana, IL, USA;Department of Entomology, University of Illinois, 61801, Urbana, IL, USA;Neuroscience Program, University of Illinois, 61801, Urbana, IL, USA;La Jolla Institute for Allergy & Immunology, 92037, La Jolla, CA, USA;

关键词: Honey Bees;    DNA methylation;    DNA hydroxymethylation;    Epigenetics;   

DOI  :  10.1186/1471-2164-14-666

 received in 2013-01-11, accepted in 2013-09-22,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundPrevious 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.ResultsWe 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.ConclusionsCytosine 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.

【 授权许可】

Unknown   
© Cingolani et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.