Varied transcriptional efficiencies of multiple Arabidopsis U6 small nuclear RNA genes

Arabidopsis U6 small nuclear RNA (snRNA) promoters are those transcribed by RNA polymerase III, but all the core elements for transcriptional initiation are located in the 5'promoter region. Previously, three Arabidopsis U6 snRNA genes (U6-1, U6-26, and U6-29) were identified. Herein, we have further identified three new U6 loci (U6-4, U6-5, and U6-6) in the Arabidopsis genome. Alignment of these revealed that the upstream sequence element and TATA elements were contained in six U6 promoters. In addition, a unique, highly conserved element named the CAT element was observed in the promoter region. To understand the expression patterns of these U6 genes in Arabidopsis, we fused these promoters to the DNA segment of beta-glucuronidase and then transferred these six constructs into Arabidopsis. Real-time reverse transcription-polymerase chain reaction analysis of these fused transcripts indicated that the newly identified U6 genes are active in Arabidopsis and that the U6-26 promoter seems to have higher transcriptional activity in leaf, stem, flower and silique. These results help to understand the function of these U6 snRNAs in Arabidopsis.