A distant enhancer element is required for polymerase III transcription of a U6 RNA gene

Bark, Christina; Weller, P A; Zabielski, J.; Janson, L.; Pettersson, Ulf

doi:10.1038/328356a0

Cited by 103 publications

(65 citation statements)

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“…An octamer motif has been observed in the same orientation at this approximate location for mouse and Xenopus U6 genes (Hoffman et al 1986;Bark et al 1987;Krol et al 1987). Moreover, the transcription of mouse and Xenopus U6 RNA in Xenopus oocytes was responsive to the presence of a distal, octamer-containing sequence, and DNase I footprinting showed protection of the octamer motif {Bark et al 1987; Carbon et al 1987).…”

Section: Discussionmentioning

confidence: 96%

Upstream elements required for efficient transcription of a human U6 RNA gene resemble those of U1 and U2 genes even though a different polymerase is used.

Kunkel¹,

Pederson²

1988

Genes Dev.

154

142

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U6 small nuclear RNA is transcribed by a different polymerase than U1-U5 RNAs, likely to be RNA polymerase III. Transcription from human U6 gene deletion-substitution templates in a HeLa S100 extract delineated the 5' border of a control element lying between 67 and 43 bp upstream from the initiation site. This region matches the location of, and shows considerable sequence similarity with, the proximal control element of U1 and U2 RNA genes, which are transcribed by RNA polymerase II. Transfection of human 293 cells with 5'-flanking deletion-substitution mutants of a U6 maxigene revealed a dominant control element between 245 and 149 bp upstream of the transcription start site. An octamer motif was found in this region in an inverted orientation relative to that of the human U1 and U2 RNA gene enhancers but in the same orientation as a human U4 RNA gene, the transcript of which functions together with U6 RNA in a single small nuclear ribonucleoprotein (snRNP) particle. The human U2 gene enhancer joined to the U6 maxigene was able to functionally replace the U6 distal control element(s).

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Section: Discussionmentioning

confidence: 96%

Upstream elements required for efficient transcription of a human U6 RNA gene resemble those of U1 and U2 genes even though a different polymerase is used.

Kunkel¹,

Pederson²

1988

Genes Dev.

154

142

View full text Add to dashboard Cite

show abstract

“…One way to overcome this problem was to increase the dose of the shRNA by enhancing the promoter activity. Some snRNAs are synthesized by Pol II, whereas others are synthesized by Pol III, and they share similar enhancer elements (Bark et al 1987;Carbon et al 1987;Das et al 1988;Kunkel and Pederson 1988;Mattaj et al 1988;Lobo and Hernandez 1989). Hence, a Pol II enhancer might be able to enhance the Pol III transcription.…”

Section: Introductionmentioning

confidence: 99%

Hybrid Cytomegalovirus-U6 Promoter-based Plasmid Vectors Improve Efficiency of RNA Interference in Zebrafish

Zhu

Xiong

et al. 2008

Mar Biotechnol

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Short hairpin RNA (shRNA) directed by RNA polymerase III (Pol III) or Pol II promoter was shown to be capable of silencing gene expression, which should permit analyses of gene functions or as a potential therapeutic tool. However, the inhibitory effect of shRNA remains problematic in fish. We demonstrated that silencing efficiency by shRNA produced from the hybrid construct composed of the CMV enhancer or entire CMV promoter placed immediately upstream of a U6 promoter. When tested the exogenous gene, silencing of an enhanced green fluorescent protein (EGFP) target gene was 89.18±5.06% for CMVE-U6 promoter group and 88.26 ± 6.46% for CMV-U6 promoter group. To test the hybrid promoters driving shRNA efficiency against an endogenous gene, we used shRNA against no tail (NTL) gene. When vectorized in the zebrafish, the hybrid constructs strongly repressed NTL gene expression. The NTL phenotype occupied 52.09± 3.06% and 51.56±3.68% for CMVE-U6 promoter and CMV-U6 promoter groups, respectively. The NTL gene expression reduced 82.17±2.96% for CMVE-U6 promoter group and 83.06±2.38% for CMV-U6 promoter group. We concluded that the CMV enhancer or entire CMV promoter locating upstream of the U6-promoter could significantly improve inhibitory effect induced by the shRNA for both exogenous and endogenous genes compared with the CMV promoter or U6 promoter alone. In contrast, the two hybrid promoter constructs had similar effects on driving shRNA.

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“…111 transcription (Bark et al, 1987;Carbon et al, 1987) and the stimulation of viral-DNA replication (Pruijn et al, 1986;Pruijn et al, 1987;Verrijzer et al, 1990a). The participation of Oct-1 at these regulatory elements is dependent on the presence of a highly conserved motif that has been defined as an octamer, ATGCAAAT (Parslow et al, 1984), or as a decamer, ATGCAAATNA (Falkner and Zachau, 1984;Falkner et al, 1986), that represents a core binding site for this protein.…”

mentioning

confidence: 99%

Broad binding‐site specificity and affinity properties of octamer 1 and brain octamer‐binding proteins

Bendall

Sturm

Danoy

et al. 1993

European Journal of Biochemistry

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The ubiquitous Pit‐1‐Oct‐1‐Unc‐1 (POU)‐domain protein octamer 1 (Oct‐1) has been observed to bind specifically to a number of degenerate and dissimilar sequences. We have used antibodies directed against a C‐terminal Oct‐1 peptide to immunoselect binding sequences for HeLa cell Oct‐1 from random‐sequence oligonucleotides and we describe the isolation of binding sequences of considerable heterogeneity. Although our consensus alignment indicated a 9‐bp TATGCAAAT motif with AT‐rich flanking sequences, this binding motif is not immediately obvious in the population of sequences and no clone actually contained this sequence. Screening these Oct‐1‐binding sequences with a mouse whole‐brain extract demonstrated that the neuronal octamer‐binding proteins exhibit similar but distinct DNA sequence specificities. Unlike the reported selection of binding sequences for other transcription factors, the dependence of Oct‐1‐binding affinity upon sequence did not correspond tightly to the degree of conservation at particular positions of the consensus sequence. Our results suggest that either base‐specific hydrogen bonding is not the only major determinant of binding affinity and specificity, or that Oct‐1 binding to some sequences is mechanistically different from its binding to an octamer. These results exemplify the potential to overlook binding sites for some factors by searching gene sequences with a consensus nucleotide sequence.

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A distant enhancer element is required for polymerase III transcription of a U6 RNA gene

Cited by 103 publications

References 0 publications

Upstream elements required for efficient transcription of a human U6 RNA gene resemble those of U1 and U2 genes even though a different polymerase is used.

Upstream elements required for efficient transcription of a human U6 RNA gene resemble those of U1 and U2 genes even though a different polymerase is used.

Hybrid Cytomegalovirus-U6 Promoter-based Plasmid Vectors Improve Efficiency of RNA Interference in Zebrafish

Broad binding‐site specificity and affinity properties of octamer 1 and brain octamer‐binding proteins

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