Genome-wide identification and characterization of replication origins by deep sequencing.
Genome-wide identification and characterization of replication origins by deep sequencing.
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DOI：
10.1186/gb-2012-13-4-r27
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发表时间：
2012-04-24
期刊：
影响因子：
12.3
通讯作者：
Rhind N
中科院分区：
文献类型：
--
作者：
Xu J;Yanagisawa Y;Tsankov AM;Hart C;Aoki K;Kommajosyula N;Steinmann KE;Bochicchio J;Russ C;Regev A;Rando OJ;Nusbaum C;Niki H;Milos P;Weng Z;Rhind N
DNA 复制起始于真核基因组中的不同起源，但定义这些位点的基因组特征尚不清楚。我们采用了实验和生物信息学相结合的方法来识别和表征三种远缘裂殖酵母的复制起点：粟酒裂殖酵母、八孢裂殖酵母和日本裂殖酵母。使用单分子深度测序构建无扩增的高分辨率复制图谱，我们定位了起源并鉴定了预测起源功能的序列基序。然后，我们通过对相应物种的单核小体 DNA 进行深度测序来绘制核小体占据图谱，发现起源往往占据核小体耗尽的区域。指定起源的序列在进化上是可塑的，具有在粟酒裂殖酵母和八孢链球菌中发挥作用的低复杂性核小体排除序列，以及在日本沙门氏菌中发挥作用的反式作用核小体排除蛋白的结合位点。此外，复制时间的染色体尺度变化是保守的，与起源位置无关，并且通过不同于已知的异染色质对起源功能的影响的机制。这些结果与一个模型一致，在该模型中，起源只是基因组中核小体耗尽的区域，对起源识别复合物具有最高的亲和力。这种方法为理解真核生物中定义 DNA 复制起点的机制提供了一般策略。
DNA replication initiates at distinct origins in eukaryotic genomes, but the genomic features that define these sites are not well understood. We have taken a combined experimental and bioinformatic approach to identify and characterize origins of replication in three distantly related fission yeasts: Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Using single-molecule deep sequencing to construct amplification-free high-resolution replication profiles, we located origins and identified sequence motifs that predict origin function. We then mapped nucleosome occupancy by deep sequencing of mononucleosomal DNA from the corresponding species, finding that origins tend to occupy nucleosome-depleted regions. The sequences that specify origins are evolutionarily plastic, with low complexity nucleosome-excluding sequences functioning in S. pombe and S. octosporus, and binding sites for trans-acting nucleosome-excluding proteins functioning in S. japonicus. Furthermore, chromosome-scale variation in replication timing is conserved independently of origin location and via a mechanism distinct from known heterochromatic effects on origin function. These results are consistent with a model in which origins are simply the nucleosome-depleted regions of the genome with the highest affinity for the origin recognition complex. This approach provides a general strategy for understanding the mechanisms that define DNA replication origins in eukaryotes.
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影响因子：
21.3
作者：
Feng, Wenyi;Collingwood, David;Boeck, Max E;Fox, Lindsay A;Alvino, Gina M;Fangman, Walton L;Raghuraman, Mosur K;Brewer, Bonita J
通讯作者：
Brewer, Bonita J
影响因子：
7
作者：
Cayrou, Christelle;Coulombe, Philippe;Mechali, Marcel
通讯作者：
Mechali, Marcel
影响因子：
10.5
作者：
Eaton, Matthew L.;Galani, Kyriaki;MacAlpine, David M.
通讯作者：
MacAlpine, David M.
影响因子：
2.6
作者：
Aoki, Keita;Nakajima, Reiko;Niki, Hironori
通讯作者：
Niki, Hironori
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS