Small Nuclear RNA Genes: a Model System to Study Fundamental Mechanisms of Transcription

Abstract

The human small nuclear RNA (snRNA) 1 genes, which encode snRNAs that are involved in RNA processing reactions such as mRNA splicing, serve as prototypes for a family of genes whose promoters are characterized by the presence of a proximal sequence element (PSE) and a distal sequence element (DSE). From a transcription point of view, this family of genes is highly interesting because all of its members have very similar promoters, even though some of them are transcribed by RNA polymerase (pol) II and others by pol III. As a result, the snRNA genes have served as a model system to explore how RNA polymerase specificity is determined and, in general, to compare the pol II and III transcription machineries. This has led to the concept that the pol II and III transcription machineries use common factors, the best known of which is the TATA box binding protein (TBP). In addition, the relative simplicity of these promoters has also made them an attractive system to study how transcriptional activators perform their function. Fig. 1 shows the structures of snRNA promoters from Homo sapiens (Hs), Arabidopsis thaliana (At), and Drosophila melanogaster (Dm) and serves to illustrate the remarkable fact that although snRNA promoters have diverged during evolution, the close similarity between those recognized by pol II and those recognized by pol III has been conserved. In fact, in each of the examples in Fig. 1, RNA polymerase specificity can be changed by altering a single parameter, indicated in red on the figure. The Structure of snRNA PromotersIn the human genes, the U1 and U2 snRNA promoters serve as the prototypic pol II snRNA promoters, and the U6 snRNA promoter serves as the prototypic pol III snRNA promoter (see Ref. 1 for a review). The human pol II snRNA core promoters contain only one essential element, the PSE, whereas the pol III snRNA core promoters consist of two elements, the PSE and a TATA box located at a fixed distance downstream. The DSE serves to enhance transcription from the core promoter. Both the DSE and the PSE can be interchanged between pol II and III snRNA promoters with no effect on RNA polymerase specificity, which is determined by the presence or absence of the TATA box. The A. thaliana pol II and III snRNA promoters contain an upstream sequence element (USE) and a TATA box, which are both interchangeable between the pol II and III snRNA promoters. RNA polymerase specificity is determined in this case by the exact spacing between the USE and the TATA box, which is 33-34 base pairs (bp) and 23-24 bp in the pol II and III snRNA promoters, respectively (2).The D. melanogaster pol II snRNA promoters contain two elements referred to as the PSEA and the PSEB spaced by 8 bp, and the pol III snRNA promoters contain a PSEA and a TATA box spaced by 12 bp. The PSEA is quite conserved in various pol II and III snRNA promoters, but positions 19 and 20 of the 21-bp elements are always g/aG in the pol II and TC in the pol III snRNA promoters. RNA polymerase specificity is determined by the precise sequ...

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

“…They were manually compared with previously published sequence elements. We visually compared the MEME -patterns with the upstream elements in related species from the following literature sources: [26] (general motifs), [14,82,2,38] (human), [36,5] (chicken), [53] (insects), [77] (Bombyx mori), [81] (Strongylocentrotus purpuratus), [84] (Caenorhabditis elegans).…”

“…The classical snRNA-specific PSE and TATA elements that have been described in detail for several vertebrates [26,14] are highly conserved. This appers to be an exception rather than the rule, however: the snRNA upstream elements are highly diverse across metazoa.…”

A loxP-Containing pol II Promoter for RNA Interference is Reversibly Regulated by Cre Recombinase

“…1A). [27][28][29][30] Thus, we assumed that the substitution of a loxP site for 34bp of the sequence present between the PSE and the +1 would neither affect transcription nor selection of the initiation site (Fig. 1C).…”

Evolutionary patterns of non-coding RNAs

“…Some snoRNAs, however, are transcribed directly from monocistronic or poly-cistronic genes, notably the U3, U8, and U13 snoRNAs. These share their promoter structure with a group of non-coding RNAs that contains the spliceosomal RNAs and the U7 RNA which is involved in histone mRNA processing [151]. In vertebrates almost all snoRNAs are encoded in introns of a specific subclass of pol-II transcripts, the TOP genes, whose promoter elements determine a specific ratio of snoRNA and mRNA production [77].…”