Derks Martijn F L, Schachtschneider Kyle M, Madsen Ole, Schijlen Elio, Verhoeven Koen J F, van Oers Kees
Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.
Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
BMC Genomics. 2016 May 4;17:332. doi: 10.1186/s12864-016-2653-y.
Studies on vertebrate DNA methylomes have revealed a regulatory role of tissue specific DNA methylation in relation to gene expression. However, it is not well known how tissue-specific methylation varies between different functional and structural components of genes and genomes. Using whole-genome bisulfite sequencing data we here describe both CpG and non-CpG methylation profiles of whole blood and brain tissue in relation to gene features, CpG-islands (CGIs), transposable elements (TE), and their functional roles in an ecological model species, the great tit (Parus major).
We show that hypomethylation at the transcription start site (TSS) is enriched in genes with functional classes that relate directly to processes specific to each tissue type. We find that 6877 (~21 %) of the CGIs are differentially methylated between blood and brain, of which 1186 and 2055 are annotated to promoter and intragenic regions, respectively. We observe that CGI methylation in promoter regions is more conserved between tissues compared to CGI methylation in intra and inter-genic regions. Differentially methylated CGIs in promoter and intragenic regions are overrepresented in genomic loci linked to development, suggesting a distinct role for CGI methylation in regulating expression during development. Additionally, we find significant non-CpG methylation in brain but not in blood with a strong preference for methylation at CpA dinucleotide sites. Finally, CpG hypermethylation of TEs is significantly stronger in brain compared to blood, but does not correlate with TE activity. Surprisingly, TEs showed significant hypomethylation in non-CpG contexts which was negatively correlated with TE expression.
The discovery that TSS methylation levels are directly linked to functional classes related to each tissue provides new insights in the regulatory role of DNA-methylation patterns. The dominant sequence motifs for brain non-CpG methylation, similar to those found in mammals, suggests that a conserved non-CpG regulatory mechanism was already present in the amniote ancestor. The negative correlation between brain non-CpG methylation and TE activity (not found for CpG methylation) suggests that non-CpG is the dominant regulatory form of methylation in TE silencing.
对脊椎动物DNA甲基化组的研究揭示了组织特异性DNA甲基化与基因表达相关的调控作用。然而，目前尚不清楚组织特异性甲基化在基因和基因组的不同功能和结构成分之间如何变化。利用全基因组亚硫酸氢盐测序数据，我们在此描述了全血和脑组织中与基因特征、CpG岛（CGI）、转座元件（TE）相关的CpG和非CpG甲基化图谱，以及它们在生态模式物种大山雀（Parus major）中的功能作用。
我们发现转录起始位点（TSS）的低甲基化在与每种组织类型特有的过程直接相关的功能类别基因中富集。我们发现，6877个（约21%）CGI在血液和大脑之间存在差异甲基化，其中1186个和2055个分别注释在启动子和基因内区域。我们观察到，与基因内和基因间区域的CGI甲基化相比，启动子区域的CGI甲基化在不同组织之间更为保守。启动子和基因内区域差异甲基化的CGI在与发育相关的基因组位点中过度富集，表明CGI甲基化在发育过程中调控基因表达方面具有独特作用。此外，我们发现大脑中存在显著的非CpG甲基化，而血液中没有，且强烈倾向于在CpA二核苷酸位点甲基化。最后，与血液相比，大脑中转座元件的CpG高甲基化明显更强，但与转座元件活性无关。令人惊讶的是，转座元件在非CpG环境中表现出显著的低甲基化，这与转座元件表达呈负相关。
转录起始位点甲基化水平与各组织相关功能类别直接相关这一发现，为DNA甲基化模式的调控作用提供了新见解。大脑非CpG甲基化的主要序列基序与在哺乳动物中发现的相似，这表明羊膜动物祖先中已经存在保守的非CpG调控机制。大脑非CpG甲基化与转座元件活性之间的负相关（CpG甲基化未发现此现象）表明，非CpG是转座元件沉默中甲基化的主要调控形式。
