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Genome-wide profiling of untranslated regions by paired-end ditag sequencing reveals unexpected transcriptome complexity in yeast

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Abstract

The identification of structural and functional elements encoded in a genome is a challenging task. Although the transcriptome of budding yeast has been extensively analyzed, the boundaries and untranslated regions of yeast genes remain elusive. To address this least-explored field of yeast genomics, we performed a transcript profiling analysis through paired-end ditag (PET) approach coupled with deep sequencing. With 562,133 PET sequences we accurately defined the boundaries and untranslated regions of 3,409 ORFs, suggesting many yeast genes have multiple transcription start sites (TSSs). We also identified 85 previously uncharacterized transcripts either in intergenic regions or from the opposite strand of reported genomic features. Furthermore, our data revealed the extensive 3′ end heterogeneity of yeast genes and identified a novel putative motif for polyadenylation. Our results indicate the yeast transcriptome is more complex than expected. This study would serve as an invaluable resource for elucidating the regulation and evolution of yeast genes.

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Acknowledgments

We thank Kim Nasmyth (University of Oxford, UK) for kindly providing the yeast strain used in this study. We are also indebted to Ting Ni (Duke University Medical Center) for technical assistance. This work was supported by Longhua Medicial Project of State Clinical Research Center of TCM in Longhua Hospital (LYTD-21 and JDZX2012123), State Key Development Program for Basic Research of China (2010CB529205 and 2013CB967402) and National Natural Science Foundation of China (91019004 and 91229123).

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Authors and Affiliations

  1. Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China

    Ya-Ni Kang, Daniel M. Czajkowsky, Zhifeng Shao & Xiaodong Zhao

  2. Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China

    Deng-Pan Lai & Ting-ting Shen

  3. Biomolecular Function Discovery Division, Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), 30 Biopolis Street, Singapore, 138671, Singapore

    Hong Sain Ooi

  4. The College of Life Sciences, Northwest University, Xi’an, 710069, China

    Yao Kou & Jing Tian

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  1. Ya-Ni Kang
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  2. Deng-Pan Lai
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  9. Xiaodong Zhao
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Correspondence to Xiaodong Zhao.

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Communicated by S. Hohmann.

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Kang, YN., Lai, DP., Ooi, H.S. et al. Genome-wide profiling of untranslated regions by paired-end ditag sequencing reveals unexpected transcriptome complexity in yeast. Mol Genet Genomics 290, 217–224 (2015). https://doi.org/10.1007/s00438-014-0913-6

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  • DOI: https://doi.org/10.1007/s00438-014-0913-6

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