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A high-resolution map of transcription in the yeast genome

机译：酵母基因组中高分辨率的转录图

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摘要

There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genomewide survey of transcription in a well annotated genome will help relate transcriptional complexity to function. By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts. A total of 85% of the genome is expressed in rich media. Apart from expected transcripts, we found operon-like transcripts, transcripts from neighboring genes not separated by intergenic regions, and genes with complex transcriptional architecture where different parts of the same gene are expressed at different levels. We mapped the positions of 3' and 5' UTRs of coding genes and identified hundreds of RNA transcripts distinct from annotated genes. These nonannotated transcripts, on average, have lower sequence conservation and lower rates of deletion phenotype than protein coding genes. Many other transcripts overlap known genes in antisense orientation, and for these pairs global correlations were discovered: UTR lengths correlated with gene function, localization, and requirements for regulation; antisense transcripts overlapped 3' UTRs more than 5' UTRs; UTRs with overlapping antisense tended to be longer; and the presence of antisense associated with gene function. These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation.
机译：真核生物基因组有大量转录，蛋白质编码基因无法解释。注释清晰的基因组中的转录全基因组高分辨率调查将有助于将转录复杂性与功能联系起来。通过使用高密度寡核苷酸切片阵列对酿酒酵母完整基因组的两条链上的RNA表达进行定量，本研究确定了编码和非编码转录本的边界，结构和水平。共有85％的基因组在丰富的培养基中表达。除了预期的转录本外，我们还发现了操纵子样转录本，未被基因间区域分隔的邻近基因的转录本以及具有复杂转录结构的基因，其中同一基因的不同部分以不同的水平表达。我们绘制了编码基因的3'和5'UTR的位置，并确定了数百个与注释基因不同的RNA转录本。与蛋白质编码基因相比，这些未注释的转录本平均具有较低的序列保守性和较低的缺失表型发生率。许多其他转录物以反义方向与已知基因重叠，并且对于这些对，发现了全局相关性：UTR长度与基因功能，定位和调节要求相关；反义转录本与3'UTR重叠超过5'UTR；反义词重叠的UTR往往更长；以及与基因功能相关的反义的存在。这些发现可能暗示反义转录在啤酒酵母中的调节作用。而且，数据表明，即使是经过充分研究的基因组，其转录复杂性也远远超出了当前的注释范围。

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