Yeast Systems Biology

Volume 759 of the series Methods in Molecular Biology pp 107-123


Genome-Wide Transcriptome Analysis in Yeast Using High-Density Tiling Arrays

  • Lior DavidAffiliated withDepartment of Animal Sciences, R.H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem
  • , Sandra Clauder-MünsterAffiliated withGenome Biology Unit, EMBL
  • , Lars M. SteinmetzAffiliated withGenome Biology Unit, EMBL Email author 

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In the last decade, it became clear that transcription goes far beyond that of protein-coding genes. Most RNA molecules are transcribed from intergenic regions or introns and exhibit much variability in size, expression level, secondary structure, and evolutionary conservation. While for several types of non-coding RNAs some cellular functions have been reported, like for micro-RNAs and small nucleolar RNAs, for most others no indications of function or regulation have so far been found. Therefore, the RNA population inside a cell is diverse and cryptic and, thus, demands powerful methods to study its composition, abundance, and structure. DNA oligonucleotide microarrays have proven to be of great utility to study transcription of genes in various organisms. Recently, due to advancement in microarray technology, tiling microarrays that extend transcription measurement to genomic regions beyond protein-coding genes were designed for several species. The Saccharomyces cerevisiae yeast tiling array contains overlapping probes across the full genomic sequence, with consecutive probes starting every 8 bp on average on each strand, enabling strand-specific measurement of transcription from a full eukaryotic genome. Here, we describe the methods used to extract yeast RNA, convert it into first-strand cDNA, fragment, and label it for hybridization to the tiling array. This protocol will enable researchers not only to study which genes are expressed and to what levels, but also to identify non-coding RNAs and to study the structure of transcripts including their untranslated regions, alternative start, stop, and processing sites. This information will allow understanding their roles inside cells.

Key words

Tiling microarray transcription gene expression gene structure non-coding RNA whole-genome microarray strand-specific transcription cDNA yeast