Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing.
Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing.
复制标题
使用降低的表示硫酸盐测序来映射斑马鱼脑甲基甲基。
DOI：
10.4161/epi.25797
复制
发表时间：
2013-09
期刊：
影响因子：
3.7
通讯作者：
Nakagawa S
中科院分区：
文献类型：
--
作者：
Chatterjee A;Ozaki Y;Stockwell PA;Horsfield JA;Morison IM;Nakagawa S
还原型亚硫酸氢盐测序（RRBS）已用于分析哺乳动物基因组（如人、小鼠和大鼠）中的DNA甲基化模式。斑马鱼的甲基化组，一个重要的动物模型，尚未在碱基对分辨率使用RRBS的特点。因此，我们通过产生成年斑马鱼脑的四个单核苷酸分辨率DNA甲基化组来评估RRBS在该模式生物中的技术。我们进行了几次模拟，以显示在不同的在硅片上减少代表性的斑马鱼基因组中的片段的分布和富集的CpG。四个RRBS大脑文库产生了9800万个测序读数，并且比同等的人类RRBS文库具有更高的多重定位频率。斑马鱼的甲基化组表明，与人类的甲基化组相比，斑马鱼基因组中存在更高的整体DNA甲基化。斑马鱼肝脏的RRBS证实了这一观察结果。高覆盖度的CpG二核苷酸在CpG岛海岸中比在CpG岛核心中更富集。我们发现45%的定位的CpG位于基因体中，7%位于基因启动子中。该分析提供了一个路线图，用于产生可重复的碱基对水平甲基化的斑马鱼使用RRBS和我们的研究结果提供了第一个证据，RRBS是一个合适的技术，在斑马鱼的全球甲基化分析。
Reduced representation bisulfite sequencing (RRBS) has been used to profile DNA methylation patterns in mammalian genomes such as human, mouse and rat. The methylome of the zebrafish, an important animal model, has not yet been characterized at base-pair resolution using RRBS. Therefore, we evaluated the technique of RRBS in this model organism by generating four single-nucleotide resolution DNA methylomes of adult zebrafish brain. We performed several simulations to show the distribution of fragments and enrichment of CpGs in different in silico reduced representation genomes of zebrafish. Four RRBS brain libraries generated 98 million sequenced reads and had higher frequencies of multiple mapping than equivalent human RRBS libraries. The zebrafish methylome indicates there is higher global DNA methylation in the zebrafish genome compared with its equivalent human methylome. This observation was confirmed by RRBS of zebrafish liver. High coverage CpG dinucleotides are enriched in CpG island shores more than in the CpG island core. We found that 45% of the mapped CpGs reside in gene bodies, and 7% in gene promoters. This analysis provides a roadmap for generating reproducible base-pair level methylomes for zebrafish using RRBS and our results provide the first evidence that RRBS is a suitable technique for global methylation analysis in zebrafish.
登录
查看更多内容
DOI：
10.1016/j.bbrc.2008.09.044
发表时间：
2008-11-28
影响因子：
3.1
作者：
Igarashi, Jun;Muroi, Satomi;Kawashima, Hiroyuki;Wang, Xiaofei;Shinojima, Yui;Kitamura, Eiko;Oinuma, Toshinori;Nemoto, Norimichi;Song, Fei;Ghosh, Srimoyee;Held, William A.;Nagase, Hiroki
通讯作者：
Nagase, Hiroki
影响因子：
12.3
作者：
Akalin A;Kormaksson M;Li S;Garrett-Bakelman FE;Figueroa ME;Melnick A;Mason CE
通讯作者：
Mason CE
影响因子：
4.5
作者：
Gertz J;Varley KE;Reddy TE;Bowling KM;Pauli F;Parker SL;Kucera KS;Willard HF;Myers RM
通讯作者：
Myers RM
影响因子：
--
作者：
Chatterjee A;Rodger EJ;Stockwell PA;Weeks RJ;Morison IM
通讯作者：
Morison IM
影响因子：
16
作者：
Bock, Christoph;Beerman, Isabel;Lien, Wen-Hui;Smith, Zachary D.;Gu, Hongcang;Boyle, Patrick;Gnirke, Andreas;Fuchs, Elaine;Rossi, Derrick J.;Meissner, Alexander
通讯作者：
Meissner, Alexander