There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide 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.
Proc Natl Acad Sci U S A 2006;103:5320-5
高密度オリゴヌクレオチドタイリングアレイ(High-density oligonucleotide tiling array)を利用することで、酵母(Saccharomyces cerebisiae)の完全なゲノムの両方のストランドのRNAの発現量を調べた。本研究では、コーディングとノンコーディングの転写物の発現レベル、境界、構造を特定した。全部でゲノムの85％が栄養のある培地(in rich media)において発現していた。期待していた転写物とは別に、オペロン様転写物、遺伝子の近傍の転写物、同一の遺伝子の異なった部分から異なったレベルで発現している複雑な転写構造をもつ遺伝子などを発見した。