Enhancer sequences and the regulation of gene transcription

Müller, Michael M.; Gerster, Thomas; Schaffner, Walter

doi:10.1111/j.1432-1033.1988.tb14306.x

Cited by 151 publications

(61 citation statements)

References 211 publications

(43 reference statements)

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“…Binding of those factors results in a synergistic activation of transcription, i.e. the intact enhancer displays a distinct activity in comparison with the individual elements (reviewed in Mü ller et al, 1988;Tjian and Maniatis, 1994). In conclusion, we find that the homologous NRSE/RE-1 sequence is the sole regulatory element necessary and sufficient for neuron-specific expression of the synapsin I gene.…”

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confidence: 66%

Neuron-specific Gene Expression of Synapsin I

Schoch

Cibelli

Thiel

1996

Journal of Biological Chemistry

133

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The synapsins are a family of neuron-specific phosphoproteins that selectively bind to small synaptic vesicles in the presynaptic nerve terminal. The human synapsin I gene was functionally analyzed to identify control elements directing the neuron-specific expression of synapsin I. By directly measuring the mRNA transcripts of a reporter gene, we demonstrate that the proximal region of the synapsin I promoter is sufficient for directing neuron-specific gene expression. This proximal region is highly conserved between mouse and human. Deletion of a putative binding site for the zinc finger protein, neuron-restrictive silencer factor/RE-1 silencing transcription factor (NRSF/REST), abolished neuron-specific expression of the reporter gene almost entirely, allowing constitutively acting elements of the promoter to direct expression in a non-tissue-specific manner. These constitutive transcriptional elements are present as a bipartite enhancer, consisting of the region upstream (nucleotides ؊422 to ؊235) and downstream (nucleotides ؊199 to ؊143) of the putative NRSF/REST-binding site. The latter contains a motif identical to the cAMP response element. Both regions are not active or are only weakly active in promoting transcription on their own and show no tissue-specific preference. From these data we conclude that neuron-specific expression of synapsin I is accomplished by a negative regulatory mechanism via the NRSF/REST binding motif.The synapsins are a family of neuronal phosphoproteins that coat the cytoplasmic surface of small synaptic vesicles (Thiel, 1993). This family consists of four proteins, synapsin Ia and synapsin Ib (collectively termed synapsin I) and synapsin IIa and synapsin IIb (collectively termed synapsin II). Synapsins I and II are generated via alternative splicing from two different genes (Sü dhof et al., 1989). Molecular cloning of bovine, human, and rat synapsins revealed striking homologies in the aminoterminal 420 amino acids of all four synapsins. The major difference between synapsins I and II lies in the C-terminal domain of the synapsin I isoforms. This domain contains clusters of basic amino acids as well as two recognition sites for Ca 2ϩ

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confidence: 66%

Neuron-specific Gene Expression of Synapsin I

Schoch

Cibelli

Thiel

1996

Journal of Biological Chemistry

133

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“…This does not occur with enhancers of polymerase II transcription (30) but is difficult to rule out experimentally in our tandem contruct. In any case, this possibility has little impact on the model presented below.…”

Section: Discussionmentioning

confidence: 88%

“…On integration into the URA3 locus, these genes were transcribed by RNA polymerase I. A single enhancer effectively stimulated transcription of both genes by 10-to 30-fold, even when it was located upstream of both or downstream of both. Two enhancers had roughly additive effects.…”

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confidence: 99%

Unusual enhancer function in yeast rRNA transcription.

Johnson

Warner

1989

Mol. Cell. Biol.

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The rRNA genes in most eucaryotic organisms are present in a tandem array. There is substantial evidence that transcription of one of these genes may not be independent of transcription of others. In particular, in the yeast Saccharomyces cerevisiae, the enhancer of rRNA transcription that lies 2.2 kilobases 5' of the transcription initiation site is at least partly within the upstream transcription unit. The transcription by RNA polymerase II of a wide variety of genes is profoundly influenced by cis-acting short-nucleotide sequences called enhancer elements that can lie upstream or downstream of the transcription unit, at a distance of up to several kilobases. In many cases, the enhancer elements bind protein factors that are necessary for enhancer function. Although a number of models have been proposed (reviewed in reference 30), a clear understanding of enhancer function is not at hand.Two features distinguish rRNA genes from other genes in the eucaryotic cell. They are transcribed by a specific enzyme, RNA polymerase I, and they are arranged in a tandem array. This unique genetic structure has led to speculation that transcription of an individual gene is not independent of transcription of the neighboring genes; e.g., termination at one transcription unit may lead directly to initiation at the neighboring downstream promoter (7,12,15, 26).We have identified a sequence element, specific for RNA polymerase I, that has many of the characteristics of an RNA polymerase II enhancer (9, 10). In this paper, we explore aspects of the function of RNA polymerase I and its enhancer to ask about the parallels between polymerase I and polymerase II enhancers and about the importance of the tandemness of rRNA genes to polymerase I activity.Transcription by RNA polymerase I has been reviewed recently (38). The spacers between individual rRNA transcription units vary in length from 2 kilobase pairs (kb) (yeasts) to >30 kb (mammals). Within them are found a variety of sequence elements that influence the level of transcription. In Xenopus laevis, for example, these include several copies of a sequence closely related to the promoter, dubbed spacer promoters (6,7,22,23,29,33), each followed by about 10 copies of a 60-to 81-base-pair (bp) repeat, that behave in some respects like enhancer elements (22,23,29). The spacer promoters are curious because although they can give rise to transcripts and can stimulate transcription from an adjacent real promoter (6,7,29), the transcription from the spacer promoter seems not to be involved in this stimulation (7,25). Repetitive elements, some related to the promoter, have also been found in the nontranscribed spacer * Corresponding author. t Present address:

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“…There are many wellcharacterized examples of enhancers controlling eukaryotic cellular and viral genes (3)(4)(5). Although initially defined in eukaryotes, regulation of transcription from distant sites has been observed for many prokaryotic promoters (6,7).…”

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confidence: 99%

DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter.

Porter

Kustu

et al. 1990

Proc. Natl. Acad. Sci. U.S.A.

245

168

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The NtrC protein activates transcription of the ginA operon of enteric bacteria by stimulating the formation of stable "open" complexes by RNA polymerase (oMholoenzyme form). To regulate the ginA promoter, NtrC binds to sites that have the properties of transcriptional enhancers: the sites will function far from the promoter and in an orientation-independent fashion. To investigate the mechanism of enhancer function, we have used electron microscopy to visualize the interactions of purified NtrC and RNA polymerase with their DNA binding sites and with each other. Under conditions that allow the formation of open complexes, about 30% of DNA molecules carry both RNA polymerase and NtrC bound to their specific sites. Of these, about 15% form looped structures in which NtrC and the RNA polymerase-promoter complex are in contact. The length of the looped DNA is that predicted from the spacing that was engineered between the enhancer and the ginA promoter (390 base pairs). As expected for activation intermediates, the looped structures disappear when RNA polymerase is allowed to transcribe the DNA. We conclude that the NtrC enhancer functions by means of a direct association between DNA-bound NtrC and RNA polymerase (DNA-looping model). Association of DNA-bound proteins appears to be the major mechanism by which different types of site-specific DNA transactions are localized and controlled.Enhancer sequences have been defined by their function in activating transcription from relatively long distances in an orientation-independent manner (1, 2). There are many wellcharacterized examples of enhancers controlling eukaryotic cellular and viral genes (3-5). Although initially defined in eukaryotes, regulation of transcription from distant sites has been observed for many prokaryotic promoters (6, 7). The site for positive regulation of the glnA operon of enteric bacteria is a particularly well-defined example of a prokaryotic enhancer (8-10). To investigate the mechanism of enhancer action, we have studied the activation of transcription from the glnA promoter by the NtrC enhancer-binding protein.Three principal models have been proposed for enhancer action (11-13). In the first, the regulatory protein (or RNA polymerase) associates with the DNA at the enhancer site and then traverses the DNA to the start site for RNA synthesis (entry-site or scanning model) (1,14). In the second model, the enhancer-binding protein facilitates transcription by initiating a change in DNA structure that is propagated from the enhancer site to the promoter (e.g., a site-specific DNA topoisomerase) (15). In the third model, the enhancerbound regulatory protein stimulates transcription by a direct protein-protein interaction with RNA polymerase at the promoter site (or with other proteins that contact polymerase) (DNA-looping model) (11-13, 16).The DNA-looping model for enhancer action has been considered attractive for several reasons. The interaction between DNA-bound proteins has been for some time an established principle for contr...

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Enhancer sequences and the regulation of gene transcription

Cited by 151 publications

References 211 publications

Neuron-specific Gene Expression of Synapsin I

Neuron-specific Gene Expression of Synapsin I

Unusual enhancer function in yeast rRNA transcription.

DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter.

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