Plant 7SL RNA genes belong to type 4 of RNA polymerase III‐ dependent genes that are composed of mixed promoters

Abstract

SummaryThe genes transcribed by RNA polymerase III (pol III) display a great diversity in terms of promoter structure and are placed in four groups accordingly. Type 3 subset of pol III genes has promoter elements which reside entirely upstream of the coding region of the gene whereas type 4 consists of genes with mixed promoters that enclose intra-and extragenic regulatory sequences. Plant 7SL RNA genes have been previously classified as type 3 of pol III genes requiring an upstream sequence element and a canonical TATA box for transcriptional activity in transfected plant protoplasts. We have identified two novel functional control regions within the coding region of an Arabidopsis 7SL RNA gene (At7SL-1) that resemble tRNA gene-specific A and B boxes with respect to sequence and position. Single and multiple nucleotide substitutions in either of these regions resulted in a pronounced reduction of transcription activity in tobacco nuclear extract that was not caused by a decreased stability as shown by decay kinetics of wild type and mutant RNA transcripts. These findings suggest that plant 7SL RNA genes should be actually placed in type 4 of pol III-transcribed genes. As a consequence of substantially different upstream promoters utilized by plant and human pol III, in vitro transcription of 7SL RNA genes in heterologous systems is severely impaired. A chimeric human 7SL RNA gene that contains the 5¢ flanking region up to position )300 of At7SL-1 is yet transcribed with a reduced efficiency in tobacco extract when compared with the plant wild-type gene, supporting the notion that internal regulatory elements contribute to full activity.

Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription

“…By contrast, addition of tagetin (0.5 U/μl), a Pol III‐specific inhibitor, completely abolished transcription from all three templates. tRNA and 7SL RNA have previously been established as Pol III genes in Drosophila , human, and plants (Ullu and Weiner, 1985; Takada et al , 2000; Yukawa et al , 2005). Interestingly, snoRNAs have been reported to rely on either Pol II or Pol III for transcription (Antal et al , 2000; Kiss, 2002; Harismendy et al , 2003; Roberts et al , 2003; Moqtaderi and Struhl, 2004).…”

“…In the case of snoRNA:314 gene, it appears that significant gene‐external sequences and promoter elements may be necessary for transcriptional initiation as in vitro transcription experiments with promoter deletions of the snoRNA:314 template revealed that at least ∼250 bp upstream of the putative transcription start site are essential for efficient initiation. This suggests that the promoter structure of snoRNA:644 gene may resemble tRNAs whereas that of snoRNA:314 is more similar to the 7SL RNA gene in plants wherein both gene‐external and ‐internal sequence elements play a role in directing transcriptional initiation (Yukawa et al , 2005). Interestingly, under our in vitro transcription system, the snoRNA:644 template produced larger amounts of transcripts than the snoRNA:314 template.…”

Arabidopsis Pol II-Dependent in Vitro Transcription System Reveals Role of Chromatin for Light-InduciblerbcSGene Transcription

“…Plasmids pAt7SL1, pAtU2.2, pAtU3CP, and pBAU6-28 include Arabidopsis 7SL RNA, U2 snRNA, U3 snoRNA, and U6 snRNA gene promoters, respectively Yukawa et al, 2005;Yukawa et al, 2013). Plasmids pNS10, pNtYI, and pGNPS include tobacco (Nicotiana tabacum) promoters from rbcS (Ntss23), tRNA Tyr , and b-1,3-glucanase genes, respectively (Mazur and Chui, 1985;Stange and Beier, 1986;Yukawa et al, 2001).…”

“…to transcribe b-1, 3-glucanase gene, and light-harvesting chlorophyll a/bbinding protein (lhcb1) genes; Hasegawa et al, 2003b), and Pol III (e.g. to transcribe tRNA genes, U3 snoRNA genes, U6 snRNA gene, 7SL RNA genes, SINE retroposon, and 5S rRNA genes; Akama et al, 1998;Arnaud et al, 2001;Cloix et al, 2002;Hasegawa et al, 2003a;Mathieu et al, 2003;Yukawa et al, 2005;Dieci et al, 2006;Yukawa et al, 2011). However, the BY-2 cells are nonphotosynthetic.…”

Arabidopsis Non-Coding RNA Regulation in Abiotic Stress Responses

“…Specifically, AtR18 was not processed into a smaller fragment and no small open reading frames (sORFs) were included. Short interspersed elements (SINEs) and 7SL (signal recognition particle) RNA for protein trafficking are known as Pol III-derived RNA, with exception of the canonical functional RNA [73,74]. …”