Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
Epigenetics Chromatin. 2018 Jun 29;11(1):37. doi: 10.1186/s13072-018-0205-1.
DNA methylation is one of the main epigenetic mechanisms for the regulation of gene expression in eukaryotes. In the standard model, methylation in gene promoters has received the most attention since it is generally associated with transcriptional silencing. Nevertheless, recent studies in human tissues reveal that methylation of the region downstream of the transcription start site is highly informative of gene expression. Also, in some cell types and specific genes it has been found that methylation of the first intron, a gene feature typically rich in enhancers, is linked with gene expression. However, a genome-wide, tissue-independent, systematic comparative analysis of the relationship between DNA methylation in the first intron and gene expression across vertebrates has not been explored yet.
The most important findings of this study are: (1) using different tissues from a modern fish, we show a clear genome-wide, tissue-independent quasi-linear inverse relationship between DNA methylation of the first intron and gene expression. (2) This relationship is conserved across vertebrates, since it is also present in the genomes of a model pufferfish, a model frog and different human tissues. Among the gene features, tissues and species interrogated, the first intron's negative correlation with the gene expression was most consistent. (3) We identified more tissue-specific differentially methylated regions (tDMRs) in the first intron than in any other gene feature. These tDMRs have positive or negative correlation with gene expression, indicative of distinct mechanisms of tissue-specific regulation. (4) Lastly, we identified CpGs in transcription factor binding motifs, enriched in the first intron, the methylation of which tended to increase with the distance from the first exon-first intron boundary, with a concomitant decrease in gene expression.
Our integrative analysis clearly reveals the important and conserved role of the methylation level of the first intron and its inverse association with gene expression regardless of tissue and species. These findings not only contribute to our basic understanding of the epigenetic regulation of gene expression but also identify the first intron as an informative gene feature regarding the relationship between DNA methylation and gene expression where future studies should be focused.
DNA 甲基化是真核生物中基因表达调控的主要表观遗传机制之一。在标准模型中，由于启动子中的甲基化通常与转录沉默有关，因此受到了最多的关注。然而，人类组织中的最近研究表明，转录起始位点下游区域的甲基化高度反映基因表达。此外，在一些细胞类型和特定基因中，已经发现第一内含子的甲基化与基因表达有关，第一内含子是富含增强子的基因特征。然而，在脊椎动物中，尚未进行全基因组、组织独立、系统比较分析第一内含子中的 DNA 甲基化与基因表达之间关系的研究。
本研究的最重要发现是：（1）使用现代鱼类的不同组织，我们在全基因组范围内显示了第一内含子的 DNA 甲基化与基因表达之间清晰的、组织独立的准线性负相关关系。（2）这种关系在脊椎动物中是保守的，因为它也存在于模式河豚、模式青蛙和不同人类组织的基因组中。在所研究的基因特征、组织和物种中，第一内含子与基因表达之间的负相关关系最为一致。（3）我们在第一内含子中鉴定出了比其他任何基因特征都多的组织特异性差异甲基化区域（tDMR）。这些 tDMR 与基因表达呈正相关或负相关，表明存在不同的组织特异性调控机制。（4）最后，我们在转录因子结合基序中鉴定出富含第一内含子的 CpG 位点，其甲基化程度随着与第一外显子-第一内含子边界的距离增加而增加，同时基因表达降低。
我们的综合分析清楚地揭示了第一内含子的甲基化水平及其与基因表达的负相关关系的重要性和保守性，无论组织和物种如何。这些发现不仅有助于我们对基因表达的表观遗传调控的基本理解，而且还确定了第一内含子作为一个有关 DNA 甲基化与基因表达之间关系的信息丰富的基因特征，未来的研究应集中于此。
