A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.
A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.
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DOI：
10.1371/journal.pgen.1000946
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发表时间：
2010-05-13
期刊：
影响因子：
4.5
通讯作者：
Keich U
中科院分区：
文献类型：
--
作者：
Liachko I;Bhaskar A;Lee C;Chung SC;Tye BK;Keich U
真核染色体从多个复制来源启动DNA合成。启动DNA合成的机制是高度保守的，但复制起始蛋白结合的位置已经明显分化。功能比较基因组学是研究复制起源进化的一种明显方法。然而，到目前为止，酿酒酵母复制起始图是唯一可用的基因组图。使用计算预测和功能验证相结合的迭代方法，我们已经生成了克鲁维酵母DNA复制起点的高分辨率全基因组图谱。与其他酵母菌或后生动物不同，乳酸克雷伯氏菌自主复制序列(KlARs)含有一个50bp的共识基序，暗示着一种二聚体结构。这个基序是启动所必需的，并且在很大程度上足以启动，并被用来可靠地鉴定为乳酸钾基因组所预测的多达156个非重复基因间ARS中的145个。尽管在基因组大小上相似，但乳酸克雷伯氏菌的ARS数量是其远亲酿酒酵母的一半。比较基因组分析表明，乳酸克雷伯菌和酿酒酵母中的ARSs优先定位于非共线基因间隔区，将ARSs与加速进化变化的位点联系在一起。在真核生物中，DNA复制是一种进化保守、细胞周期调控、时空协调的机制。它是由起源识别复合体(ORC)与多个复制起点结合而启动的。虽然ORC高度保守，但其DNA结合特异性和复制起始点的初级序列却不是。比较功能基因组学是解决复制起源的位置保守和染色体决定因素问题的一种明显的方法。然而，到目前为止，酿酒酵母是唯一拥有完整的全基因组复制起源图的真核生物，这张图花了30年的时间才编制完成。我们设计了一种迭代方法，通过直接克隆复制起始点来结合计算预测和功能验证，有效地识别出高分辨率、接近完整的乳酸克鲁维酵母复制起始点。比较这两个酵母基因组图谱提供了关于这两个远缘酵母物种的DNA元件和复制起始点的位置保守的丰富信息。这种方法通常适用于构建与可分析的生物功能相关的进化保守序列的高分辨率基因组图。对所有生物功能的全基因组研究来说，快速生成未表征基因组的全面功能图是至关重要的。
Eukaryotic chromosomes initiate DNA synthesis from multiple replication origins. The machinery that initiates DNA synthesis is highly conserved, but the sites where the replication initiation proteins bind have diverged significantly. Functional comparative genomics is an obvious approach to study the evolution of replication origins. However, to date, the Saccharomyces cerevisiae replication origin map is the only genome map available. Using an iterative approach that combines computational prediction and functional validation, we have generated a high-resolution genome-wide map of DNA replication origins in Kluyveromyces lactis. Unlike other yeasts or metazoans, K. lactis autonomously replicating sequences (KlARSs) contain a 50 bp consensus motif suggestive of a dimeric structure. This motif is necessary and largely sufficient for initiation and was used to dependably identify 145 of the up to 156 non-repetitive intergenic ARSs projected for the K. lactis genome. Though similar in genome sizes, K. lactis has half as many ARSs as its distant relative S. cerevisiae. Comparative genomic analysis shows that ARSs in K. lactis and S. cerevisiae preferentially localize to non-syntenic intergenic regions, linking ARSs with loci of accelerated evolutionary change. DNA replication is an evolutionarily conserved, cell cycle–regulated, spatially and temporally coordinated mechanism in eukaryotes. It is initiated by the binding of the Origin Recognition Complex (ORC) to multiple replication origins. While the ORC is highly conserved, its DNA binding specificity and the primary sequences of replication origins are not. Comparative functional genomics is an obvious approach to addressing questions about the positional conservation and chromosomal determinants of replication origins. However, to date, Saccharomyces cerevisiae is the only eukaryote with a complete genome-wide replication origin map, one which took three decades to compile. We have devised an iterative approach, combining computational prediction and functional validation by direct cloning of replication origins that efficiently identifies a high resolution, near complete repertoire of replication origins in Kluyveromyces lactis. Comparing these two yeast genome maps provides a wealth of information about the DNA elements and positional conservation of replication origins in these two distantly related yeast species. This approach is generally applicable to the construction of high-resolution genome maps of evolutionarily conserved sequences associated with assayable biological functions. Rapid generation of comprehensive functional maps of uncharacterized genomes is critical to whole genome studies of all biological functions.
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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：
4.5
作者：
Donato JJ;Chung SC;Tye BK
通讯作者：
Tye BK
影响因子：
1.6
作者：
Gogel, E;Langst, G;Grummt, F
通讯作者：
Grummt, F
影响因子：
5.3
作者：
DESHPANDE, AM;NEWLON, CS
通讯作者：
NEWLON, CS
DOI：
10.1073/pnas.77.11.6329
发表时间：
1980-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
CHAN, CSM;TYE, BK
通讯作者：
TYE, BK