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Evolution of cis-regulatory elements in yeast de novo and duplicated new genes

Zing Tsung-Yeh Tsai123, Huai-Kuang Tsai24*, Jen-Hao Cheng2, Chih-Hsu Lin5, Yuan-Fan Tsai6 and Daryi Wang5*

Author affiliations

1 Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan

2 Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan

3 Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 112, Taiwan

4 Research Center for Information Technology Innovation, Academia Sinica, Taipei, 115, Taiwan

5 Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan

6 Department of Social and Regional Development, National Taipei University of Education, Taipei, 106, Taiwan

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Citation and License

BMC Genomics 2012, 13:717  doi:10.1186/1471-2164-13-717

Published: 21 December 2012



New genes that originate from non-coding DNA rather than being duplicated from parent genes are called de novo genes. Their short evolution time and lack of parent genes provide a chance to study the evolution of cis-regulatory elements in the initial stage of gene emergence. Although a few reports have discussed cis-regulatory elements in new genes, knowledge of the characteristics of these elements in de novo genes is lacking. Here, we conducted a comprehensive investigation to depict the emergence and establishment of cis-regulatory elements in de novo yeast genes.


In a genome-wide investigation, we found that the number of transcription factor binding sites (TFBSs) in de novo genes of S. cerevisiae increased rapidly and quickly became comparable to the number of TFBSs in established genes. This phenomenon might have resulted from certain characteristics of de novo genes; namely, a relatively frequent gain of TFBSs, an unexpectedly high number of preexisting TFBSs, or lower selection pressure in the promoter regions of the de novo genes. Furthermore, we identified differences in the promoter architecture between de novo genes and duplicated new genes, suggesting that distinct regulatory strategies might be employed by genes of different origin. Finally, our functional analyses of the yeast de novo genes revealed that they might be related to reproduction.


Our observations showed that de novo genes and duplicated new genes possess mutually distinct regulatory characteristics, implying that these two types of genes might have different roles in evolution.

De novo gene; Regulatory evolution; TFBS turnover; Promoter architecture