Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming.
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming.
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DOI：
10.1038/nbt.1530
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发表时间：
2009-04
影响因子：
46.9
通讯作者：
Zhang, Kun
中科院分区：
文献类型：
--
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
目前的DNA甲基化检测方法在确定大量基因组靶标的灵活性和效率方面存在局限性。我们报告了一种专门捕获基因组目标的任意子集的方法，用于单分子亚硫酸盐测序，用于单核苷酸分辨率下DNA甲基化的数字量化。设计了一套约30,000个挂锁探针，用于评估人类12号染色体、20号染色体和34个选定区域上2,020个CpG岛上约66,000个CpG位点的甲基化。为了研究与去分化相关的表观遗传学差异，我们比较了三个人类成纤维细胞系和八个人类多能干细胞系的甲基化。在所有被研究的品系中，染色体范围的甲基化模式是相似的，但胞嘧啶甲基化在多能细胞中比在成纤维细胞中略普遍。诱导多能干细胞(IPS)似乎比胚胎干细胞表现出更多的甲基化。我们在成纤维细胞和多能细胞中发现了288个不同的甲基化区域。这种有针对性的方法对于分析大基因组中的DNA甲基化特别有用。
Current DNA methylation assays are limited in the flexibility and efficiency of characterizing a large number of genomic targets. We report a method to specifically capture an arbitrary subset of genomic targets for single-molecule bisulfite sequencing for digital quantification of DNA methylation at single-nucleotide resolution. A set of ~30,000 padlock probes was designed to assess methylation of ~66,000 CpG sites within 2,020 CpG islands on human chromosome 12, chromosome 20, and 34 selected regions. To investigate epigenetic differences associated with dedifferentiation, we compared methylation in three human fibroblast lines and eight human pluripotent stem cell lines. Chromosome-wide methylation patterns were similar among all lines studied, but cytosine methylation was slightly more prevalent in the pluripotent cells than in the fibroblasts. Induced pluripotent stem (iPS) cells appeared to display more methylation than embryonic stem cells. We found 288 regions methylated differently in fibroblasts and pluripotent cells. This targeted approach should be particularly useful for analyzing DNA methylation in large genomes.
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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：
64.8
作者：
Mueller, Franz-Josef;Laurent, Louise C.;Kostka, Dennis;Ulitsky, Igor;Williams, Roy;Lu, Christina;Park, In-Hyun;Rao, Mahendra S.;Shamir, Ron;Schwartz, Philip H.;Schmidt, Nils O.;Loring, Jeanne F.
通讯作者：
Loring, Jeanne F.
影响因子：
9.8
作者：
Rakyan, VK;Hildmann, T;Beck, S
通讯作者：
Beck, S
影响因子：
64.8
作者：
Park, In-Hyun;Zhao, Rui;Daley, George Q.
通讯作者：
Daley, George Q.
影响因子：
7
作者：
Khulan, Batbayar;Thompson, Reid F.;Greally, John M.
通讯作者：
Greally, John M.