BC1 RNA: Transcriptional Analysis of a Neural Cell-Specific RNA Polymerase III Transcript

Abstract

Rodent BC1 RNA represents the first example of a neural cell-specific RNA polymerase III (Pol III) transcription product. By developing a rat brain in vitro system capable of supporting Pol III-directed transcription, we showed that the rat BC1 RNA intragenic promoter elements, comprising an A box element and a variant B box element, as well as its upstream region, containing octamer-binding consensus sequences and functional TATA and proximal sequence element sites, are necessary for transcription. The BC1 B box, lacking the invariant A residue found in the consensus B boxes of tRNAs, represents a functionally related and possibly distinct promoter element. The transcriptional activity of the BC1 B box element is greatly increased, in both a BC1 RNA and a chimeric tRNA Leu gene construct, when the BC1 5 flanking region is present and is appropriately spaced. Moreover, a tRNA consensus B-box sequence can efficiently replace the BC1 B box only if the BC1 upstream region is removed. These interactions, identified only in a homologous in vitro system, between upstream Pol II and intragenic Pol III promoters suggest a mechanism by which the tissue-specific BC1 RNA gene and possibly other Pol III-transcribed genes can be regulated.Rodent BC1 RNA is a small, developmentally regulated, cytoplasmic RNA present in the somatic and dendritic compartments of a distinct subset of central and peripheral nervous system neurons (59, 60). This neural cell-specific RNA is most likely functional, since the single-copy rat BC1 RNA gene, which evolved from a tRNA Ala molecule (10, 36), and its neural cell-specific expression pattern have been conserved in rodents for at least 55 million years (10,35,36,38). It has been hypothesized that this nontranslated RNA, as part of a ribonucleoprotein complex, plays a role in the pre-or posttranslational events in neural postsynaptic compartments (60).Neural cell-specific BC1 RNA represents a unique model for transcriptional studies in that it is transcribed by RNA polymerase III (Pol III). While RNA Pol III is responsible for the synthesis of most small cytoplasmic and some small nuclear RNAs (reviewed in references 6 and 18), only a few genes are known to be transcribed by this enzyme in either a tissuespecific or developmentally specific manner. Examples include the oocyte-specific and somatic 5S RNA genes of Xenopus laevis (4), the tRNA Ala gene of Bombyx mori (41,56), and the primate neural cell-specific BC200 RNA (37, 63).The initial studies on Pol III-transcribed (class III) genes defined highly conserved intragenic sequences as being both necessary and sufficient for transcription (3,11,15,17,20,24,49,52). These intragenic promoters are present in the majority of class III genes, including tRNA, adenovirus VA RNA, and the Epstein-Barr virus EBER RNA genes, as well as certain repetitive sequences, and contain two noncontiguous domains, the A and B boxes (reviewed in references 6 and 18). It is now evident that (i) numerous Pol III genes require (in addition to their intragenic promoters...

RNA Transport in Dendrites: Acis-Acting Targeting Element Is Contained within Neuronal BC1 RNA

“…This observation, together with the fact that BC1 RNA is an RNA polymerase III transcript (Martignetti and Brosius, 1995), raises the question of whether the BC1-targeting element (BTE) is shared by mRNAs (i.e., RNA polymerase II transcripts) that have been localized to dendrites. To address this question, we compared the BC1 5Ј sequence with sequences of dendritic and nondendritic mRNAs.…”

Gene duplication and neofunctionalization: POLR3G and POLR3GL

“…When considering loci significantly occupied either in the liver or in Hepa 1-6 cells or in both, we uncovered another 136 loci (indicated in column D of Supplemental Table S3), including one Rn5s locus on chromosome 6, outside of the cluster of Rn5s genes on chromosome 8, and encoding a divergent 5S RNA; the Bc1_Mm_scRNA locus, encoding Bc1 RNA, a transcript previously described as neural-specific (Martignetti and Brosius 1995) and corresponding to human BCYRN1 (BC200) (Martignetti and Brosius 1993); 14 Rn4.5s loci; 95 SINEs, most of them from the B2 family; and 25 NA loci (Fig. 3B).…”

Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription

“…TATA-like elements were proposed for the vTRNA1-1, -2, -3, the 7SL1 and 2 genes, eBeR genes (eTAB) 138 and the mouse analog of the BCYRN1 gene. 121,122,140 Sequences at similar positions in vTRNA2-1 and TRNAU1 genes are shown. A stimulatory influence of a SP1 binding site on in vitro transcription of the eBeR2 gene was shown.…”