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Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity.

Hernandez G, Valafar F, Stumph WE - Nucleic Acids Res. (2006)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA.

ABSTRACT
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 approximately 21 bp PSEA and approximately 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.

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Alignment and analysis of snRNA gene promoters of B.mori. Color-coding, symbolism and derivation of consensus sequences are as explained in the legends of Figures 2 and 3.
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fig6: Alignment and analysis of snRNA gene promoters of B.mori. Color-coding, symbolism and derivation of consensus sequences are as explained in the legends of Figures 2 and 3.

Mentions: The B.mori PSEAs from the Pol II-transcribed snRNA genes are well conserved over a region of at least 24 bp from position −3 to position 21 (upper section of Figure 6). Also well-conserved are five nucleotides that lie at positions that correspond to the location of the D.melanogaster PSEB.


Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity.

Hernandez G, Valafar F, Stumph WE - Nucleic Acids Res. (2006)

Alignment and analysis of snRNA gene promoters of B.mori. Color-coding, symbolism and derivation of consensus sequences are as explained in the legends of Figures 2 and 3.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1761439&req=5

fig6: Alignment and analysis of snRNA gene promoters of B.mori. Color-coding, symbolism and derivation of consensus sequences are as explained in the legends of Figures 2 and 3.
Mentions: The B.mori PSEAs from the Pol II-transcribed snRNA genes are well conserved over a region of at least 24 bp from position −3 to position 21 (upper section of Figure 6). Also well-conserved are five nucleotides that lie at positions that correspond to the location of the D.melanogaster PSEB.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA.

ABSTRACT
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 approximately 21 bp PSEA and approximately 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.

Show MeSH