The methylomes of six bacteria.
The methylomes of six bacteria.
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DOI：
10.1093/nar/gks891
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发表时间：
2012-12
影响因子：
14.9
通讯作者：
Roberts RJ
中科院分区：
文献类型：
--
作者：
Murray IA;Clark TA;Morgan RD;Boitano M;Anton BP;Luong K;Fomenkov A;Turner SW;Korlach J;Roberts RJ
六种细菌基因组，金属还原地杆菌 GS-15、色盐杆菌、布雷氏弧菌 1C-10、蜡样芽孢杆菌 ATCC 10987、空肠弯曲杆菌亚种。空肠弯曲菌 81-176 和空肠弯曲菌 NCTC 11168 之前均已使用其他平台进行过测序，现在使用单分子实时 (SMRT) 测序进行重新测序，专门分析其甲基化组。在每种情况下，都发现了许多新的 N6-甲基腺嘌呤 (m6A) 和 N4-甲基胞嘧啶 (m4C) 甲基化模式，并指定了负责这些甲基化模式的 DNA 甲基转移酶 (MTase)。在 15 个案例中，无需进一步亚克隆即可将 MTase 基因与 MTase 识别序列进行匹配。两个 I 型限制系统需要亚克隆来区分其识别序列，而四个在天然生物体中不表达的 MTase 基因则被亚克隆以测试活力和识别序列。其中两个被证明是活跃的。没有尝试从 SMRT® 测序数据中检测 5-甲基胞嘧啶 (m5C) 识别基序，因为这种修饰使用当前方法会产生较弱的信号。然而，所有预测的 m6A 和 m4C MTase 均被明确检测到。这项研究表明，在传统测序方法中添加 SMRT 测序可以提供有关基因组的大量有用的功能信息，不仅显示哪些 MTase 基因处于活跃状态，还揭示了它们的识别序列。
Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and C. jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their methylomes. In every case a number of new N6-methyladenine (m6A) and N4-methylcytosine (m4C) methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for those methylation patterns were assigned. In 15 cases, it was possible to match MTase genes with MTase recognition sequences without further sub-cloning. Two Type I restriction systems required sub-cloning to differentiate their recognition sequences, while four MTase genes that were not expressed in the native organism were sub-cloned to test for viability and recognition sequences. Two of these proved active. No attempt was made to detect 5-methylcytosine (m5C) recognition motifs from the SMRT® sequencing data because this modification produces weaker signals using current methods. However, all predicted m6A and m4C MTases were detected unambiguously. This study shows that the addition of SMRT sequencing to traditional sequencing approaches gives a wealth of useful functional information about a genome showing not only which MTase genes are active but also revealing their recognition sequences.
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影响因子：
48
作者：
Flusberg, Benjamin A.;Webster, Dale R.;Lee, Jessica H.;Travers, Kevin J.;Olivares, Eric C.;Clark, Tyson A.;Korlach, Jonas;Turner, Stephen W.
通讯作者：
Turner, Stephen W.
影响因子：
4.4
作者：
LOVLEY, DR;PHILLIPS, EJP
通讯作者：
PHILLIPS, EJP
影响因子：
48
作者：
Gibson, Daniel G.;Young, Lei;Smith, Hamilton O.
通讯作者：
Smith, Hamilton O.
影响因子：
14.9
作者：
BROOKS, JE;BLUMENTHAL, RM;GINGERAS, TR
通讯作者：
GINGERAS, TR
影响因子：
14.9
作者：
BHAGWAT, AS;MCCLELLAND, M
通讯作者：
MCCLELLAND, M