Abstract
A bidirectional promoter is a region along a strand of DNA that regulates the expression of two genes flanking the region. Each of these genes is transcibed in a direction that points away from the other gene; two such genes are said to be in a head-to-head configuration. We search the UCSC List of Known Genes and GenBank Expressed Sequence Tag (EST) data for pairs of genes in such a configuration in order to identify new bidirectional promoters.
The EST data constitutes a larger and more intricate dataset than the UCSC List of Known Genes. However, working with EST data presents a challenge, as the EST database may be highly redundant and may also contain overlapping ESTs. To deal with these problems, we have developed an algorithm to identify bidirectional promoters based on the above data sources; the algorithm is capable of handling redundant ESTs, and also ESTs that overlap or disagree in orientation.
This analysis resulted in the identification of thousands of new candidate head-to-head gene pairs, corroborated the 5’ ends of many known human genes, revealed new 5’ exons of previously characterized genes, and in some cases identified novel genes. Further analyses yielded evidence for coordinate expression of genes in a head-to-head configuration, and examined the prevalence of bidirectional promoters in different biological pathways.
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References
Trinklein, N.D., et al.: An Abundance of Bidirectional Promoters in the Human Genome. Genome Res. 14(1), 62–66 (2004), http://www.genome.org/cgi/content/abstract/14/1/62 , doi:10.1101/gr.1982804
Benson, D.A., et al.: GenBank: update. Nucl. Acids Res. 32, D23–26 (2004), http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D23
Hsu, F., et al.: The UCSC Known Genes. Bioinformatics 22(9), 1036–1046 (2006), http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/9/1036
Kim, T.H., et al.: A high-resolution map of active promoters in the human genome. Nature 436, 876–880 (2005), doi:10.1038/nature03877
Su, A.I., et al.: A gene atlas of the mouse and human protein-encoding transcriptomes. PNAS 101(16), 6062–6067 (2004), http://www.pnas.org/cgi/content/abstract/101/16/6062 , doi:10.1073/pnas.0400782101
Adachi, N., Lieber, M.R.: Bidirectional gene organization: a common architectural feature of the human genome. Cell 109(7), 807–809 (2002)
Zhao, Q., et al.: A mitochondrial specific stress response in mammalian cells. The EMBO Journal 21, 4411–4419 (2002)
Joshi-Tope, G., et al.: Reactome: a knowledgebase of biological pathways. Nucl. Acids Res. 33, D428–432 (2005), http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_1/D428
Beissbarth, T., Speed, T.P.: GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20(9), 1464–1465 (2004), http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/9/1464
Chen, C., et al.: Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22. PNAS 99(5), 2930–2935 (2002), http://www.pnas.org/cgi/content/abstract/99/5/2930 , doi:10.1073/pnas.052692099
Cooper, S.J., et al.: Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res. 16(1), 1–10 (2006), http://www.genome.org/cgi/content/abstract/16/1/1 , doi:10.1101/gr.4222606
Trinklein, N.D., et al.: Identification and Functional Analysis of Human Transcriptional Promoters. Genome Res. 13(2), 308–312 (2003), http://www.genome.org/cgi/content/abstract/13/2/308 , doi:10.1101/gr.794803
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Yang, M.Q., Elnitski, L.L. (2007). Invited Talk: A Computational Study of Bidirectional Promoters in the Human Genome. In: Măndoiu, I., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2007. Lecture Notes in Computer Science(), vol 4463. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72031-7_33
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DOI: https://doi.org/10.1007/978-3-540-72031-7_33
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