Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks.
Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks.
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DOI：
10.1371/journal.pgen.1002440
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发表时间：
2012-01
期刊：
影响因子：
4.5
通讯作者：
Kono T
中科院分区：
文献类型：
--
作者：
Kobayashi H;Sakurai T;Imai M;Takahashi N;Fukuda A;Yayoi O;Sato S;Nakabayashi K;Hata K;Sotomaru Y;Suzuki Y;Kono T
DNA甲基化的全基因组动态变化对于哺乳动物的生殖细胞发育和基因组印记是必不可少的。在这里，我们报告单碱基分辨率DNA甲基化和转录组的小鼠生殖细胞，使用全基因组鸟枪亚硫酸氢盐测序和cDNA测序（mRNA-seq）生成的地图。卵母细胞基因组显示mRNA转录水平和转录区域甲基化之间存在显著正相关。精子基因组几乎完全覆盖甲基化，除了在CpG丰富的区域，并显示出显着的基因表达和启动子甲基化之间的负相关。因此，这些甲基化图谱揭示了卵母细胞和精子在DNA甲基化的程度和分布方面存在很大差异。此外，卵母细胞和精子甲基化组的比较确定了卵母细胞和精子中超过1，600个CpG岛的差异甲基化（种系差异甲基化区域，gDMR），以及已知的印记控制区域（ICR）。这些差异甲基化的DNA序列中约有一半似乎至少部分抵抗着床前发育过程中发生的整体DNA去甲基化。在不存在Dnmt 3L的情况下，既没有观察到大多数卵母细胞甲基化的gDMR的甲基化，也没有观察到基因内甲基化。在卵母细胞中，也存在全基因组低甲基化和特定逆转录转座子的部分甲基化，同时维持全局基因表达。沿着在基因内区域鉴定出许多依赖于Dnmt 3L的gDMR，本研究结果表明卵母细胞甲基化可分为2种类型：依赖于Dnmt 3L的甲基化，这是母体甲基化印记所必需的;和不依赖于Dnmt 3L的甲基化，这可能是内源性逆转录病毒DNA沉默所必需的。目前的数据提供了全新的观点评价生殖细胞中的表观遗传标记。在哺乳动物中，生殖细胞特异性甲基化模式和基因组印记是通过卵子发生和精子发生中的大规模从头DNA甲基化建立的。这些步骤是正常生殖细胞分化和胚胎发育所必需的;然而，目前的DNA甲基化分析仅为我们提供了生殖细胞甲基化组的部分图像。据我们所知，这是第一项以单碱基分辨率生成小鼠生殖细胞DNA甲基化组和转录组综合图谱的研究。这些甲基化图谱揭示了卵母细胞和精子基因组中全基因组相反的DNA甲基化模式以及甲基化与基因表达水平之间的差异相关性。此外，我们的研究结果表明卵母细胞中存在2种类型的甲基化模式：（i）转录区域的甲基化，这可能是建立母体甲基化印记和正常胚胎发生所必需的，以及（ii）逆转录病毒甲基化，这可能是逆转录转座子沉默和正常卵子发生所必需的。我们相信，这项工作的扩展将导致更好地了解生殖细胞中的表观遗传重编程和基因调控的作用。
Genome-wide dynamic changes in DNA methylation are indispensable for germline development and genomic imprinting in mammals. Here, we report single-base resolution DNA methylome and transcriptome maps of mouse germ cells, generated using whole-genome shotgun bisulfite sequencing and cDNA sequencing (mRNA-seq). Oocyte genomes showed a significant positive correlation between mRNA transcript levels and methylation of the transcribed region. Sperm genomes had nearly complete coverage of methylation, except in the CpG-rich regions, and showed a significant negative correlation between gene expression and promoter methylation. Thus, these methylome maps revealed that oocytes and sperms are widely different in the extent and distribution of DNA methylation. Furthermore, a comparison of oocyte and sperm methylomes identified more than 1,600 CpG islands differentially methylated in oocytes and sperm (germline differentially methylated regions, gDMRs), in addition to the known imprinting control regions (ICRs). About half of these differentially methylated DNA sequences appear to be at least partially resistant to the global DNA demethylation that occurs during preimplantation development. In the absence of Dnmt3L, neither methylation of most oocyte-methylated gDMRs nor intragenic methylation was observed. There was also genome-wide hypomethylation, and partial methylation at particular retrotransposons, while maintaining global gene expression, in oocytes. Along with the identification of the many Dnmt3L-dependent gDMRs at intragenic regions, the present results suggest that oocyte methylation can be divided into 2 types: Dnmt3L-dependent methylation, which is required for maternal methylation imprinting, and Dnmt3L-independent methylation, which might be essential for endogenous retroviral DNA silencing. The present data provide entirely new perspectives on the evaluation of epigenetic markers in germline cells. In mammals, germ-cell–specific methylation patterns and genomic imprints are established throughout large-scale de novo DNA methylation in oogenesis and spermatogenesis. These steps are required for normal germline differentiation and embryonic development; however, current DNA methylation analyses only provide us a partial picture of germ cell methylome. To the best of our knowledge, this is the first study to generate comprehensive maps of DNA methylomes and transcriptomes at single base resolution for mouse germ cells. These methylome maps revealed genome-wide opposing DNA methylation patterns and differential correlation between methylation and gene expression levels in oocyte and sperm genomes. In addition, our results indicate the presence of 2 types of methylation patterns in the oocytes: (i) methylation across the transcribed regions, which might be required for the establishment of maternal methylation imprints and normal embryogenesis, and (ii) retroviral methylation, which might be essential for silencing of retrotransposons and normal oogenesis. We believe that an extension of this work would lead to a better understanding of the epigenetic reprogramming in germline cells and of the role for gene regulations.
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影响因子：
46.9
作者：
Ball, Madeleine P.;Li, Jin Billy;Gao, Yuan;Lee, Je-Hyuk;LeProust, Emily M.;Park, In-Hyun;Xie, Bin;Daley, George Q.;Church, George M.
通讯作者：
Church, George M.
影响因子：
46.9
作者：
Deng, Jie;Shoemaker, Robert;Xie, Bin;Gore, Athurva;LeProust, Emily M.;Antosiewicz-Bourget, Jessica;Egli, Dieter;Maherali, Nimet;Park, In-Hyun;Yu, Junying;Daley, George Q.;Eggan, Kevin;Hochedlinger, Konrad;Thomson, James;Wang, Wei;Gao, Yuan;Zhang, Kun
通讯作者：
Zhang, Kun
影响因子：
21.3
作者：
De La Fuente, Rabindranath;Baumann, Claudia;Muegge, Kathrin
通讯作者：
Muegge, Kathrin
影响因子：
56.9
作者：
Bourc'his, D;Xu, GL;Bestor, TH
通讯作者：
Bestor, TH
影响因子：
10.5
作者：
Chotalia, Mita;Smallwood, Sebastien A.;Kelsey, Gavin
通讯作者：
Kelsey, Gavin