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.tiling array ͉ transcriptone survey ͉ gene architecture ͉ segmentation ͉ antisense regulation P roteins constitute most structural and functional components of cells. The assumption has been that protein-encoding genes are also the main controllers of cellular processes. Recent evidence challenges this assumption, suggesting a wide-spread involvement of noncoding RNA in regulation, including through the activity of untranslated regions of mRNAs (1), antisense transcripts (2, 3), and isolated noncoding RNAs such as microRNA that control transcript levels or their translation (4).High-resolution transcriptome analysis in higher eukaryotes using tiling arrays has improved ORF annotations and exonintron predictions and discovered many new transcripts of currently unknown function (5-7). However, these studies have encountered challenges, due to noise, limited resolution, lack of strand-specific signal, and drawbacks in the analysis methods (8). Sequencing of cloned cDNAs has also revealed a high level of transcriptional complexity, including the presence of many new transcripts, alternative promoter usage, splicing, and polyadenylation, as well as the presence of many sense-antisense transcript pairs (3, 9). However, because of the cost and labor of large-scale sequencing, this approach has been limited. Therefore, there is a need to develop high-throughput, precise, and high-re...

Budding yeast noncoding RNAs (ncRNAs) are pervasively transcribed during mitosis, and some regulate mitotic protein-coding genes. However, little is known about ncRNA expression during meiotic development. Using high-resolution profiling we identified an extensive meiotic ncRNA expression program interlaced with the protein-coding transcriptome via sense/antisense transcript pairs, bidirectional promoters, and ncRNAs that overlap the regulatory regions of genes. Meiotic unannotated transcripts (MUTs) are mitotic targets of the conserved exosome component Rrp6, which itself is degraded after the onset of meiosis when MUTs and other ncRNAs accumulate in successive waves. Diploid cells lacking Rrp6 fail to initiate premeiotic DNA replication normally and cannot undergo efficient meiotic development. The present study demonstrates a unique function for budding yeast Rrp6 in degrading distinct classes of meiotically induced ncRNAs during vegetative growth and the onset of meiosis and thus points to a critical role of differential ncRNA expression in the execution of a conserved developmental program.

A high resolution strand-specific transcriptional atlas of the budding yeast mitotic cell cycle, including both mRNA and non-coding RNA profiles.