Open Access Highly Accessed Research

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Marina V Granovskaia1, Lars J Jensen12, Matthew E Ritchie34, Joern Toedling5, Ye Ning6, Peer Bork1, Wolfgang Huber15 and Lars M Steinmetz1*

  • * Corresponding author: Lars M Steinmetz larsms@embl.de

  • † Equal contributors

Author Affiliations

1 EMBL - European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr. 1, D-69117 Heidelberg, Germany

2 Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark

3 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

4 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia

5 EMBL - European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

6 Plant Biochemistry Lab, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark

For all author emails, please log on.

Genome Biology 2010, 11:R24  doi:10.1186/gb-2010-11-3-r24

Published: 1 March 2010

Abstract

Background

Extensive transcription of non-coding RNAs has been detected in eukaryotic genomes and is thought to constitute an additional layer in the regulation of gene expression. Despite this role, their transcription through the cell cycle has not been studied; genome-wide approaches have only focused on protein-coding genes. To explore the complex transcriptome architecture underlying the budding yeast cell cycle, we used 8 bp tiling arrays to generate a 5 minute-resolution, strand-specific expression atlas of the whole genome.

Results

We discovered 523 antisense transcripts, of which 80 cycle or are located opposite periodically expressed mRNAs, 135 unannotated intergenic non-coding RNAs, of which 11 cycle, and 109 cell-cycle-regulated protein-coding genes that had not previously been shown to cycle. We detected periodic expression coupling of sense and antisense transcript pairs, including antisense transcripts opposite of key cell-cycle regulators, like FAR1 and TAF2.

Conclusions

Our dataset presents the most comprehensive resource to date on gene expression during the budding yeast cell cycle. It reveals periodic expression of both protein-coding and non-coding RNA and profiles the expression of non-annotated RNAs throughout the cell cycle for the first time. This data enables hypothesis-driven mechanistic studies concerning the functions of non-coding RNAs.