High-resolution transcription atlas of the mitotic cell cycle in budding yeast.
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.
Granovskaia
Marina V
MV
EMBL - European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr, Heidelberg, Germany. mgranovsk@gmail.com
Jensen
Lars J
LJ
Ritchie
Matthew E
ME
Toedling
Joern
J
Ning
Ye
Y
Bork
Peer
P
Huber
Wolfgang
W
Steinmetz
Lars M
LM
D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D016681:Genome, Fungal / Q000235:genetics*; D023281:Genomics / Q000379:methods; D008938:Mitosis / Q000235:genetics*; D016372:RNA, Antisense / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*
D016372:RNA, Antisense; D022661:RNA, Untranslated