Nucleic Acids Research Advance Access originally published online on December 5, 2006
Nucleic Acids Research 2007 35(1):21-34; doi:10.1093/nar/gkl982
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Nucleic Acids Research, 2007, Vol. 35, No. 1 21-34
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Genomics |
Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity
1 Department of Chemistry and Biochemistry, San Diego State University 5500 Campanile Drive, San Diego, CA 92182-1030, USA 2 Department of Computer Science, San Diego State University 5500 Campanile Drive, San Diego, CA 92182-1030, USA
*To whom correspondence should be addressed. Tel: +1 619 594 5575; Fax: +1 619 594-4634; Email: wstumph{at}sciences.sdsu.edu
Received September 2, 2006. Revised October 25, 2006. Accepted October 27, 2006.
In animals, most small nuclear RNAs (snRNAs) are synthesized by RNA polymerase II (Pol II), but U6 snRNA is synthesized by RNA polymerase III (Pol III). In Drosophila melanogaster, the promoters for the Pol II-transcribed snRNA genes consist of 
21 bp PSEA and 8 bp PSEB. U6 genes utilize a PSEA but have a TATA box instead of the PSEB. The PSEAs of the two classes of genes bind the same protein complex, DmSNAPc. However, the PSEAs that recruit Pol II and Pol III differ in sequence at a few nucleotide positions that play an important role in determining RNA polymerase specificity. We have now performed a bioinformatic analysis to examine the conservation and divergence of the snRNA gene promoter elements in other species of insects. The 5' half of the PSEA is well-conserved, but the 3' half is divergent. Moreover, within each species positions exist where the PSEAs of the Pol III-transcribed genes differ from those of the Pol II-transcribed genes. Interestingly, the specific positions vary among species. Nevertheless, we speculate that these nucleotide differences within the 3' half of the PSEA act similarly to induce conformational alterations in DNA-bound SNAPc that result in RNA polymerase specificity.
Present address: Genaro Hernandez Jr, Biomedical Informatics Stanford Medical Informatics, Medical School Office Building, Room X-215, 251 Campus Drive, Stanford, CA 94305-5479, USA
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