Transcription of the sea urchin U6 gene in vitro requires a TATA-like box, a proximal sequence element, and sea urchin USF, which binds an essential E box

How to Recruit the Correct RNA Polymerase? Lessons from snRNA Genes

Nuclear eukaryotic genomes are transcribed by three related RNA polymerases (Pol), which transcribe distinct gene sets. Specific Pol recruitment is achieved through selective core promoter recognition by basal transcription factors (TFs). Transcription by an inappropriate Pol appears to be rare and to generate mostly unstable products. A collection of short noncoding RNA genes [for example, small nuclear RNA (snRNA) or 7SK RNA genes], which play essential roles in processes such as maturation of RNA molecules or control of Pol II transcription elongation, possess highly similar core promoters, and yet are transcribed for some by Pol II and for others by Pol III as a result of small promoter differences. Here we discuss the mechanisms of selective Pol recruitment to such promoters.

TBP recruitment to the U1 snRNA gene promoter is disrupted by substituting a U6 proximal sequence element A (PSEA) for the U1 PSEA

Transcription of Drosophila U1 or U6 snRNAs by RNA polymerases II and III respectively requires a unique approximately 21 base-pair promoter element termed the proximal sequence element A (PSEA) recognized by the snRNA activating protein complex (DmSNAPc). A five-nucleotide substitution that changed the U1 PSEA to a U6 PSEA inactivated the U1 promoter. Chromatin immunoprecipitation assays indicated this substitution did not affect DmSNAPc DNA binding but instead interfered with SNAPc recruitment of TBP to the TATA-less U1 promoter. These findings support a model wherein sequence differences between the U1 and U6 PSEAs induce distinct DmSNAPc conformational states involved in RNA polymerase selectivity.

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

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.

The Drosophila U1 and U6 gene proximal sequence elements act as important determinants of the RNA polymerase specificity of small nuclear RNA gene promoters in vitro and in vivo

Transcription of genes coding for metazoan spliceosomal snRNAs by RNA polymerase II (U1, U2, U4, U5) or RNA polymerase III (U6) is dependent upon a unique, positionally conserved regulatory element referred to as the proximal sequence element (PSE). Previous studies in the organism Drosophila melanogaster indicated that as few as three nucleotide differences in the sequences of the U1 and U6 PSEs can play a decisive role in recruiting the different RNA polymerases to transcribe the U1 and U6 snRNA genes in vitro. Those studies utilized constructs that contained only the minimal promoter elements of the U1 and U6 genes in an artificial context. To overcome the limitations of those earlier studies, we have now performed experiments that demonstrate that the Drosophila U1 and U6 PSEs have functionally distinct properties even in the environment of the natural U1 and U6 gene 5'-flanking DNAs. Moreover, assays in cells and in transgenic flies indicate that expression of genes from promoters that contain the "incorrect" PSE is suppressed in vivo. The Drosophila U6 PSE is incapable of recruiting RNA polymerase II to initiate transcription from the U1 promoter region, and the U1 PSE is unable to recruit RNA polymerase III to transcribe the U6 gene.

The proximal sequence element (PSE) plays a major role in establishing the RNA polymerase specificity of Drosophila U-snRNA genes

Most small nuclear RNA (snRNA) genes are transcribed by RNA polymerase II, but some (e.g., U6) are transcribed by RNA polymerase III. In vertebrates a TATA box at a fixed distance downstream of the proximal sequence element (PSE) acts as a dominant determinant for recruiting RNA polymerase III to U6 gene promoters. In contrast, vertebrate snRNA genes that contain a PSE but lack a TATA box are transcribed by RNA polymerase II. In plants, transcription of both classes of snRNA genes requires a TATA box in addition to an upstream sequence element (USE), and polymerase specificity is determined by the spacing between these two core promoter elements. In these examples, the PSE (or USE) is interchangeable between the two classes of snRNA genes. Here we report the surprising finding that the Drosophila U1 and U6 PSEs cannot functionally substitute for each other; rather, determination of RNA polymerase specificity is an intrinsic property of the PSE sequence itself. The alteration of two or three base pairs near the 3'-end of the U1 and U6 PSEs was sufficient to switch the RNA polymerase specificity of Drosophila snRNA promoters in vitro. These findings reveal a novel mechanism for achieving RNA polymerase specificity at insect snRNA promoters.

Effect of the nuclear factors EmBP1 and viviparous1 on the transcription of the Em gene in HeLa nuclear extracts

Templates constructed from the wheat Em and maize rab28 promoters are efficiently and accurately transcribed in the well-characterized cell-free transcription system prepared from HeLa nuclei. Deletion analysis of the Em promoter indicates that a G-box (CACGTG) element (Em1b) is required for transcription. USF, a Myc transcription factor in HeLa nuclear extracts, activates transcription by binding to Em1b, as shown by the ability of an antibody raised against USF to inhibit transcription and to interfere with Em1b complex formation in an electrophoretic mobility shift assay. The addition of the recombinant Viviparous1 protein from maize to HeLa nuclear extracts specifically stimulated transcription of the Em promoter but was dependent on the presence of USF in the extract. In USF-depleted extracts, the addition of recombinant EmBP1, a basic leucine zipper transcription factor from wheat, activated transcription through Em1b as well as from a similar G-box in the adenovirus major late promoter. Our study demonstrates that the basic transcriptional apparatus in HeLa nuclear extract supports transcription from plant promoters and can be used to assay the function of certain plant nuclear proteins, thereby helping to determine their effects on transcription.

Identification of developmentally regulated sea urchin U5 snRNA genes

A PCR approach was used to isolate repeated U5 small nuclear RNA (snRNA) genes from the sea urchin Lytechinus variegatus. A 1.3 kb repeat, LvU5.0, and three other variants, LvU5.1-U5.3, that differ in the coding region and in the proximal sequence element (PSE) region were isolated. Southern Blot analysis indicate that the U5 snRNA genes, unlike other embryonically expressed snRNA genes (U1, U2 and U6), are not found in a simple tandem repeat, but instead, exist in several heterogeneous clusters each with a small number of genes. The U5 PSE has limited sequence similarity with the other sea urchin PSEs. However, when used in a mobility shift assay the U5 PSE forms a protein/DNA complex that is very similar to the complex formed with the U6 PSE. An RNase protection assay used to monitor the accumulation of U5 snRNA during development shows that at least two U5 variants are coordinately expressed during embryogenesis.

The RNA polymerase I promoter-activating factor CPBF is functionally and immunologically related to the basic helix-loop-helix-zipper DNA-binding protein USF

Analysis of the core promoter sequence of the mammalian ribosomal RNA genes revealed an E-box-like sequence (CACGCTG) to which the upstream stimulatory factor (USF) binds. Because the core promoter binding factor (CPBF) binds specifically to the core promoter sequence of the ribosomal RNA gene (Liu, Z., and Jacob, S. T. (1994) J. Biol. Chem. 269, 16618-16626) and resembles USF in some respects, we explored the potential relationship between USF and CPBF. Competition electrophoretic mobility shift assay using labeled core promoter probe and several unlabeled competitor oligonucleotides showed that USF can indeed bind to the core promoter and that only those oligonucleotides with an E-box sequence could compete in the promoter-protein complex formation characteristic of CPBF. This complex formation was thermostable, a unique property of USF. Furthermore, antibodies raised against USF cross-reacted with the 44-kDa component of rat CPBF. To prove further the relationship between CPBF and USF, we examined the effects of the unlabeled USF and ribosomal gene core promoter oligonucleotides on polymerase (pol) I and pol II transcription. Both oligonucleotides inhibited rDNA transcription as well as transcription from the adenovirus major late promoter. Only the oligonucleotides that contain the E-box sequence competed in the transcription. These data indicate that the promoter sequence of mammalian ribosomal RNA gene contains an USF-binding site, that the 44-kDa polypeptide of CPBF is related to the 44/43-kDa polypeptide of human USF, and that USF or USF-related protein can transactivate both pol I and pol II promoters.