1 3 Mol Genet Genomics (2015) 290:217–224 DOI 10.1007/s00438-014-0913-6 ORIGINAL PAPER Genome‑wide profiling of untranslated regions by paired‑end ditag sequencing reveals unexpected transcriptome complexity in yeast Ya‑Ni Kang · Deng‑Pan Lai · Hong Sain Ooi · Ting‑ting Shen · Yao Kou · Jing Tian · Daniel M. Czajkowsky · Zhifeng Shao · Xiaodong Zhao Received: 28 April 2014 / Accepted: 1 September 2014 / Published online: 12 September 2014 © Springer-Verlag Berlin Heidelberg 2014 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 com- plex than expected. This study would serve as an invalu- able resource for elucidating the regulation and evolution of yeast genes. Keywords PET sequencing · Untranslated region · Budding yeast · Transcriptome Introduction The untranslated regions of specific mRNA play important roles in post-transcriptional gene regulation and have func- tional relevance to diverse biological processes in various cell types (Hughes 2006). Through the interaction between the regulatory elements and their binding proteins UTRs can modulate gene expression by influencing cytoplasmic localization, translation efficiency, nuclear export and sta- bility. For example, translational efficiency of some yeast genes with alternative 5′UTRs varies by 80-fold in vivo (Rojas-Duran and Gilbert 2012). Many efforts have been made to separately charac- terize either 5′ or 3′UTRs of yeast genes (Ozsolak et al. 2010; Zhang and Dietrich 2005). However, these studies could not provide the information of transcription start and termination sites of each transcript, which is hard to accurately interpret their functional relevance. Although a moderate full-length cDNA sequencing analysis identi- fied many yeast genes with distinct 5′UTR variants (Miura et al. 2006), the full extent of yeast transcriptome com- plexity has long been underappreciated. Very recently, a yeast transcriptome profiling report revealed extensive transcriptional heterogeneity (Pelechano et al. 2013). We 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 tran- script 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 tran- scripts either in intergenic regions or from the opposite strand of reported genomic features. Furthermore, our data Communicated by S. Hohmann. Electronic supplementary material The online version of this article (doi:10.1007/s00438-014-0913-6) contains supplementary material, which is available to authorized users. Y.-N. Kang · D. M. Czajkowsky · Z. Shao · X. Zhao (*) Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China e-mail: xiaodongzhao@sjtu.edu.cn D.-P. Lai · T. Shen Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China H. S. Ooi Biomolecular Function Discovery Division, Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671, Singapore Y. Kou · J. Tian The College of Life Sciences, Northwest University, Xi’an 710069, China