In the human small nuclear RNA (snRNA) promoters, the presence of a TATA box recognized by the TATA box-binding protein (TBP) determines the selection of RNA polymerase III over RNA polymerase II. The RNA polymerase II snRNA promoters are, therefore, good candidates for TBP-independent promoters. We show here, however, that TBP activates transcription from RNA polymerase II snRNA promoters through a non-TATA box element, the snRNA proximal sequence element (PSE), as part of a new snRNA-activating protein complex (SNAPc). In contrast to the previously identified TBP-containing complexes SL1, TFIID, and TFIIIB, which appear dedicated to transcription by a single RNA polymerase, SNAP c is also essential for RNA polymerase III transcription from the U6 snRNA promoter. The U6 initiation complex appears to contain two forms of TBP, one bound to the TATA box and one bound to the PSE as a part of SNAPc, suggesting that multiple TBP molecules can have different functions within a single promoter. In eukaryotes, transcription is carried out by three different RNA polymerases, none of which can recognize its target promoters directly. Instead, promoter elements are first recognized by specific transcription factors that then recruit the correct RNA polymerase. Because RNA polymerase I, II, and III promoters are generally very different in structure, it has long been assumed that RNA polymerase specificity is achieved through the binding of very distinct sets of transcription factors. Although it is now well established that the TATA box binding protein [TBP) participates in transcription from TATA-containing and TATA-less promoters by all three RNA polymerases, it does so as part of distinct complexes that are each dedicated to transcription by a single RNA polymerase (for review, see Hernandez 1993). Thus, SL1 (Comai et al. 1992), TFIID (for review, see Sawadogo and Sentenac 1990;Roeder 1991; Pugh and Tjian 1992;Zawel and Reinberg 1992,1993), and TFIIIB (Lobo et al. 1992;Simmen et al. 1992b;Taggart et al. 1992; White and Jackson 1992) participate in transcription by RNA polymerases I, II, and III, respectively.The promoters of human small nuclear RNA (snRNA) genes are very similar in structure even though some of them are recognized by RNA polymerase II whereas others are recognized by RNA polymerase III. They therefore serve as a model to study how RNA polymerase specificity is achieved. The human U1 and U2 snRNA promoters are recognized by RNA polymerase II and consist essentially of two elements: A proximal sequence element (PSE) located upstream of position -40, which is essential and sufficient to direct basal levels of transcription, and a distal sequence element (DSE) located upstream of position -200, which serves as a transcriptional enhancer and is characterized by the presence of an octamer motif (for review, see Dahlberg and Lund 1988;Hernandez 1992). The human U6 snRNA promoter, which is recognized by RNA polymerase III, differs from most other RNA polymerase III promoters in that it does not contain any esse...
Although the human U2 and U6 snRNA genes are transcribed by different RNA polymerases (i.e., RNA polymerases II and III, respectively), their promoters are very similar in structure. Both contain a proximal sequence element (PSE) and an octamer motif-containing enhancer, and these elements are interchangeable between the two promoters. The RNA polymerase III specificity of the U6 promoter is conferred by a single A/T-rich element located around position -25. Mutation of the A/T-rich region converts the U6 promoter into an RNA polymerase II promoter, whereas insertion of the A/T-rich region into the U2 promoter converts that promoter into an RNA polymerase III promoter. We show that this A/T-rich element can be replaced by a number of TATA boxes derived from mRNA promoters transcribed by RNA polymerase II with little effect on RNA polymerase III transcription. Furthermore, the cloned RNA polymerase II transcription factor TFIID both binds to the U6 A/T-rich region and directs accurate RNA polymerase III transcription in vitro. Mutations in the U6 A/T-rich region that convert the U6 promoter into an RNA polymerase II promoter also abolish TFIID binding. Together, these observations suggest that in the human snRNA promoters, unlike in mRNA promoters, binding of TFIID directs the assembly of RNA polymerase III transcription complexes, whereas the lack of TFIID binding results in the assembly of RNA polymerase II snRNA transcription complexes.[Key Words: RNA polymerases II and III; snRNA genes; TATA box; proximal sequence element; transcription factor TFIID] Received April 15, 1991; revised version accepted May 21, 1991.The vertebrate small nuclear RNA (snRNA) genes U1-U6 are members of a growing gene family that also includes the H1 and MRP/Th RNA genes. These genes share two characteristics. First, they encode short, nonpolyadenylated RNAs that are involved in the processing of other RNA molecules. The snRNAs U1, U2, and U4-U6 are involved in mRNA splicing (see Steitz et al. 1988); U3 is involved in rRNA processing (Kass et al. 1990; Savino and Gerbi 1990); H1 RNA is the RNA component of RNase P (Baer et al. 1989;Bartkiewicz et al. 1989); and MRP/Th RNA is the RNA component of RNase MRP, an endoribonuclease that cleaves the mitochondrial RNA primer for mitochondrial replication (Chang andClayton 1987, 1989;Gold et al. 1989). Because of this common characteristic and by analogy to tRNAs and mRNAs, whose names refer to their functions, we refer to these RNAs as pRNAs, for processor RNAs, and to their genes as pRNA genes (Hernandez 1991). Second, these genes share common cis-acting transcriptional elements, although some, including the U1-U5 pRNA genes, are transcribed by RNA polymerase II, whereas others, including the U6, H1, and MRP/Th pRNA genes, are transcribed by RNA polymerase III (for review, see Dahlberg and Lund 1988; Hernandez 1991). As a result, RNA polymerase II and III pRNA promoter elements are more similar to each other than to either RNA polymerase II mRNA promoter elements or RNA polymerase III pro...
A 6.9 kilobase Eco R1 fragment containing genes for two U1 RNAs has been isolated from a library of mouse DNA. The two genes code for an RNA which is very similar, if not identical, to mouse U1b RNA as judged by S1 nuclease mapping. This RNA is one base longer than the mouse U1a RNA, human U1 RNA, and rat U1 RNA and differs in six nucleotide substitutions from rat U1 RNA. The two genes are five kilobases apart and the U1 RNAs are coded for on opposite strands of the DNA with the 5' ends juxtaposed. The sequences flanking the genes are identical for 700 bases 5' to the gene and at least 80 bases 3' to the gene.
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