Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays.
Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays.
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DOI：
10.1186/gb-2010-11-7-r71
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发表时间：
2010
期刊：
影响因子：
12.3
通讯作者：
Nantel A
中科院分区：
文献类型：
--
作者：
Sellam A;Hogues H;Askew C;Tebbji F;van Het Hoog M;Lavoie H;Kumamoto CA;Whiteway M;Nantel A
与其他模式生物相比，尽管致病性酵母菌白色念珠菌具有临床相关性，但尚未进行全面分析以提供其基于计算机的基因组注释的实验支持。我们已经进行了全基因组的实验注释，以准确地揭示致病性酵母C。白色念珠菌使用链特异性高密度平铺阵列。从在与C.白念珠菌的致病性，包括生物膜，实验室培养的酵母菌和血清诱导的菌丝，以及从小鼠盲肠分离的细胞。这项工作提供了一个全基因组的实验验证了大量的预测ORF的转录没有被其他方法检测到。此外，我们鉴定了2,000多个新的转录片段，包括新的ORF和外显子，非编码RNA（ncRNA）以及令人信服的反义基因转录案例。我们还表征了表达的ORF的5'和3' UTR，并确定具有长5'UTR的基因在控制丝状生长的调节功能中显著富集。此外，我们还发现端粒附近的基因组区域含有一组表达的ncRNA。为了验证和确认新的ncRNA候选者，我们采用了一种迭代策略，结合了RNA聚合酶I，II和III的不同亚基的全基因组占用率和表达数据。这种综合方法允许鉴定不同的ncRNA家族。总之，我们提供了一个全面的表达图谱，涵盖了相关的C。除了发现新的ORF和非编码遗传元件之外，还发现了白色念珠菌的致病发育阶段。
Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. We have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. RNAs were purified from cells growing under conditions relevant to C. albicans pathogenicity, including biofilm, lab-grown yeast and serum-induced hyphae, as well as cells isolated from the mouse caecum. This work provides a genome-wide experimental validation for a large number of predicted ORFs for which transcription had not been detected by other approaches. Additionally, we identified more than 2,000 novel transcriptional segments, including new ORFs and exons, non-coding RNAs (ncRNAs) as well as convincing cases of antisense gene transcription. We also characterized the 5' and 3' UTRs of expressed ORFs, and established that genes with long 5' UTRs are significantly enriched in regulatory functions controlling filamentous growth. Furthermore, we found that genomic regions adjacent to telomeres harbor a cluster of expressed ncRNAs. To validate and confirm new ncRNA candidates, we adapted an iterative strategy combining both genome-wide occupancy of the different subunits of RNA polymerases I, II and III and expression data. This comprehensive approach allowed the identification of different families of ncRNAs. In summary, we provide a comprehensive expression atlas that covers relevant C. albicans pathogenic developmental stages in addition to the discovery of new ORF and non-coding genetic elements.
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DOI：
10.1073/pnas.0700327104
发表时间：
2007-07-10
影响因子：
11.1
作者：
Hsu, Min;McEachern, Michael J.;Lue, Neal F.
通讯作者：
Lue, Neal F.
影响因子：
56.9
作者：
Azzalin, Claus M.;Reichenbach, Patrick;Lingner, Joachim
通讯作者：
Lingner, Joachim
影响因子：
56.9
作者：
Bertone, P;Stolc, V;Snyder, M
通讯作者：
Snyder, M
影响因子：
2.6
作者：
Bertone, P;Gerstein, M;Snyder, M
通讯作者：
Snyder, M
影响因子：
2.5
作者：
Guillemette, T;Sellam, A;Simoneau, P
通讯作者：
Simoneau, P