Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software.

Alessandro Sardu,Laura Treu,Stefano Campanaro

doi:10.1186/1471-2164-15-1045

Abstract

BackgroundRNA-seq studies have an important role for both large-scale analysis of gene expression and for transcriptome reconstruction. However, the lack of software specifically developed for the analysis of the transcriptome structure in lower eukaryotes, has so far limited the comparative studies among different species and strains.ResultsIn order to fill this gap, an innovative software called ORA (Overlapped Reads Assembler) was developed. This software allows a simple and reliable analysis of the transcriptome structure in organisms with a low number of introns. It can also determine the size and the position of the untranslated regions (UTR) and of polycistronic transcripts. As a case study, we analyzed the transcriptional landscape of six S. cerevisiae strains in two different key steps of the fermentation process. This comparative analysis revealed differences in the UTR regions of transcripts. By extending the transcriptome analysis to yeast species belonging to the Saccharomyces genus, it was possible to examine the conservation level of unknown non-coding RNAs and their putative functional role.ConclusionsBy comparing the results obtained using ORA with previous studies and with the transcriptome structure determined with other software, it was proven that ORA has a remarkable reliability. The results obtained from the training set made it possible to detect the presence of transcripts with variable UTRs between S. cerevisiae strains. Finally, we propose a regulatory role for some non-coding transcripts conserved within the Saccharomyces genus and localized in the antisense strand to genes involved in meiosis and cell wall biosynthesis.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1045) contains supplementary material, which is available to authorized users.

Highlights

RNA-seq studies have an important role for both large-scale analysis of gene expression and for transcriptome reconstruction
The transcriptome assembly software ORA is a reference-based assembler taking RNA-seq reads aligned on a reference genome as input
Since it is known that only 5% of S. cerevisiae genes have introns, in most cases these gaps are due to biases in the sequencing process [27]

Summary

Introduction

RNA-seq studies have an important role for both large-scale analysis of gene expression and for transcriptome reconstruction. S. cerevisiae was one of the first species in which transcriptome reconstruction using tiling arrays and RNA-seq was evaluated [8,9,10] These studies allowed both a detailed determination of the transcriptome structure and the identification of entirely new classes of Despite the high number of genomic studies, pivotal aspects of the transcriptome structure, such as its structural variability among different strains, have not been considered at all. The same is true for the presence of non-coding transcripts in other species belonging to the Saccharomyces genus The reason for this bias in literature studies is that the gene expression analysis performed on the same strain under different growth conditions is technically affordable, while the comparison of gene expression between different strains is more difficult. Arrays designed on a reference strain can be used for transcriptome analysis on other strains (or species), but this procedure can lead to biases in gene expression due to differences in the genomic sequences that can influence array hybridization

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Conclusion