%0 Generic
%A Granovskaia, Marina
%D 2008
%F heidok:8447
%K genomics , transcriptome , microarrays , yeast ,  cell cycle
%R 10.11588/heidok.00008447
%T Genome-wide characterization of the Complex Trancriptome Architecture of S.cerevisiae with tiling arrays
%U https://archiv.ub.uni-heidelberg.de/volltextserver/8447/
%X Recent genome-wide transcriptome analysis in humans, Drosophila, Arabidopsis and yeast challenged the old notion of fundamental aspects of gene regulation, providing evidence that protein-encoding genes are not the only agents controlling cellular processes. Non-coding RNAs comprising untranslated regions of protein coding genes, antisense transcripts of annotated genes, micro RNAs and small interfering RNAs present another tier in gene regulation, enabling integration and networking of complex suites of gene activity. Sophisticated RNA signaling networks operate in higher eukaryotes, enabling gene to gene communication and regulation of chromatin structure, DNA methylation, transcription, translation, RNA silencing and stability, and coordinate multiple tasks of the whole cellular system. Fundamental mechanisms and structure of such control architecture remained largely obscure due to limitations of available approaches, such as noise in the data, strand–unspecific transcription analysis and difficulties in functional follow-up opportunities in higher eukaryotes.  To address the complexity of transcriptome architecture we undertook the genome-wide transcriptome study in a simpler genome of S.cerevisiae with the help of a new tiling array. We have shown that 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 non-annotated 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. Overall our study revealed complexity of yeast transcriptional architecture calling for additional annotation of the genome and putting forward an important role for RNA-mediated regulation.  An attractive model for the study of the genome-wide RNA-mediated regulation of gene activity in yeast is mitotic cell cycle, which has been extensively studied over past decade and is therefore a well characterized system. Mitosis is associated with important physiological changes in the cell and diverse biological events depend on this periodicity. To ensure the proper functioning of the mechanisms that maintain order during cell division about 800 genes of diverse GO categories are coordinately regulated in a periodic manner coincident with the cell cycle. This includes genes involved in DNA replication, budding, glycosylation, nuclear division, control of mRNA transcription, responsiveness to external stimuli and subcellular localization of proteins.  Several genome-wide studies have been done to catalogue cell cycle-regulated genes with the help of early expression arrays. Given the high resolution of our technique, profiling genome-wide periodic expression with the tiling arrays allowed taking a step forward to prove the existence of RNA-mediated regulation of transcription. Using two methods of synchronization, I have monitored cell-cycle dependent transcription for more than 3 complete cell cycles. I have identified about ~600 periodic ORFs. In consent with previous studies on transcriptional regulation during specific mitotic phases, I have shown prevalence of periodic expression of annotated genes in three distinct periods of cell cycle progression: late G1/S transition, G2/M transition and exit of M phase of mitosis. Moreover, I have shown antisense transcription throughout the cell cycle phases. Out of ~260 antisense transcripts that we discovered, 37 display periodic patterns; half of them are expressed coincidentally with peak expression intensity of cell cycle-regulated ORFs, whereas the other half peaks at the periods of relaxation of the transcriptional machinery, which drives phase transition. Cycling antisense has been registered opposite several important cell cycle regulators.  Additionally, periodic novel isolated transcripts were detected in the dataset, which may represent non-annotated ncRNAs involved in regulation of mitosis or regulated by cell cycle controlling genes.