A high-resolution map of transcription in the yeast genome

Abstract

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...

Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions

“…1 C in that reference. TSS locations in S. cerevisiae were derived from David et al (39) in the manner described in Vaillant et al (40).…”

Transcription termination by nuclear RNA polymerases

“…The Nrd1 complex has wider functions in gene expression, especially in the synthesis/processing of CUTs. CUTs are short noncoding RNAs (300-600 nt) that were first detected by genome-wide microarray analysis in yeast strains defective for RNA nuclear degradation (Kapranov et al 2005;Wyers et al 2005;David et al 2006;Davis and Ares 2006). In strains defective for the nuclear exosome protein Rrp6, CUTs with a defined 59-end and heterogenous 39-ends accumulate.…”

The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci

“…There have been independent experiments using complementary sequencing technologies that have also detected large amounts of previously unidentified transcription (Carninci et al 2005). Genome tiling arrays have also been used for transcript mapping in a variety of different organisms besides human: Arabidopsis thaliana (Yamada et al 2003), Drosophila melanogaster , Manak et al 2006, Saccharomyces cerevisiae (David et al 2006), and Oryza sativa (Li et al 2006).…”