scispace - formally typeset
Search or ask a question
Topic

Upstream activating sequence

About: Upstream activating sequence is a research topic. Over the lifetime, 1633 publications have been published within this topic receiving 100112 citations.


Papers
More filters
Journal ArticleDOI
TL;DR: Gal4 has been shown to activate the GAL1/10 upstream activation sequence upon Galactose catabolism as mentioned in this paper, which is the first detectable factor to be recruited to GAL 1/10 downstream activation sequence.
Abstract: Transcription activators are necessary for the precise regulation of gene expression in response to a variety of cellular signals. Many eukaryotic activators directly or indirectly facilitate recruitment of the transcription machinery to a promoter by enhancing the binding of chromatin remodeling factors, by counteracting the action of specific repressors, and/or by directly interacting with the transcription machinery (23, 26, 41). Acidic activating regions are common in eukaryotes and typically contain one or more critical hydrophobic residues and an abundance of acidic side chains. Strong acidic activators can be as short as 30 residues and are relatively insensitive to mutagenesis, and truncations of the activation regions result in a progressive loss of activity (20, 28). These results suggest that acidic activators do not fold into a typical structured protein domain. In agreement with this proposal, structural studies of the activators c-myc, CREB, and VP16 demonstrated that these activating regions are unstructured in the absence of an interacting partner (30, 42, 47). Sequence comparisons, the isolation of activators from random sequences, mutagenesis, and selection for mutations which increase function have not revealed any obvious similarity among the primary sequences of acidic activators, apart from being rich in acidic and hydrophobic residues (13, 19, 28). A central question in gene regulation is how these diverse activators function to stimulate transcription through the common set of factors comprising the transcription machinery. Yeast Gal4, one of the first known acidic activators, is responsible for the regulation of genes involved in galactose catabolism (41). In the absence of galactose, Gal4 is inhibited by the repressor Gal80. Upon the addition of galactose, Gal4 is released from this repression by the activation of Gal3, which blocks the repressive function of Gal80 (27). Gal4 contains an N-terminal DNA binding and dimerization domain (residues 1 to 147), an N-terminal activating region (residues 148 to 196), and a C-terminal activating region (residues 768 to 881) (28). The most acidic part of the C-terminal activating region (residues 840 to 881) is the minimal segment required for strong activator function in vivo (28). The Gal4 activator functions to stimulate transcription in all eukaryotes tested, from yeast to humans, and activates transcription when fused to a heterologous DNA binding domain (5, 41). The Gal4 DNA binding domain has no activation activity when separated from the activating regions, although mutations within this domain have been reported to reduce activation in vivo (12). Many direct activation targets of Gal4 have been proposed, based on a variety of biochemical, genetic, and molecular studies. In vivo assays have demonstrated that the acetyltransferase/coactivator complex SAGA, which is required for Gal4 induction, is the first detectable factor to be recruited to the GAL1/10 upstream activation sequence upon galactose induction (3, 7). In agreement with these studies, in vivo fluorescent resonance energy transfer (FRET) assays suggest that Gal4 and the SAGA subunit Tra1 are in close proximity only after induction (4). In vitro protein-protein interaction studies have demonstrated binding of Gal4 to TATA-binding protein (TBP), TFIIB, Swi/Snf, Mediator, and SAGA (1, 22, 37, 51). In Mediator, Gal4 binds to the Srb10 and Gal11 subunits, binding Gal11 in two separate regions. Other acidic activators such as yeast Gcn4 have also been found to interact with numerous polypeptides in vitro (6, 15, 35). The short nonconserved sequences of acidic activators, coupled with the observed in vitro binding of many polypeptides, raise the question of how these factors specifically recognize their relevant targets. Nearly every general transcription factor and coactivator complex has been proposed as a direct activator target, but in only a few cases has the functional relevance of these interactions been demonstrated (4, 6, 16, 18, 39, 49). One limitation of many previous studies is that the activator targets were not defined in functional transcription complexes, but instead were identified using isolated factors or individual subunits of large complexes. For this work, we used site-specific photo-cross-linkers inserted within the Gal4 C-terminal activating region to identify polypeptides in close proximity to the activator while the activator stimulates transcription. This approach revealed six polypeptides that cross-link to the activating region. Three of these polypeptides (Tra1, Gal11, and Taf12) are subunits of four complexes previously implicated in gene regulation, namely, Mediator, SAGA, NuA4, and TFIID. Remarkably, these three cross-linking targets were also identified in a cross-linking assay with the acidic activator Gcn4 (17). Thus, two activators with unrelated sequences interact with the same set of three targets during transcription activation. Unexpectedly, we found that Ste12, which is itself a gene-specific transcription factor, is also a specific target of Gal4. Functional studies demonstrate that these Gal4 cross-linking targets make differential contributions to activation by Gal4.

131 citations

Journal ArticleDOI
TL;DR: The present studies identify regulators which are required to promote transcription from both human c-myc promoters, P1 and P2, and have a role in determining their relative activities in vivo.
Abstract: Transcription of the human proto-oncogene c-myc is governed by two tandem principal promoters, termed P1 and P2. In general, the downstream promoter, P2, is predominant, which is in contrast to the promoter occlusion phenomenon usually observed in genes containing tandem promoters. A shift in human c-myc promoter usage has been observed in some tumor cells and in certain physiological conditions. However, the mechanisms that regulate promoter usage are not well understood. The present studies identify regulators which are required to promote transcription from both human c-myc promoters, P1 and P2, and have a role in determining their relative activities in vivo. A novel regulatory region located 101 bp upstream of P1 was characterized and contains five tandem repeats of the consensus sequence CCCTCCCC (CT element). The integrity of the region containing all five elements is required to promote transcription from P1 and for maximal activity from P2 in vivo. A single copy of this same element, designated CT-I2, also appears in an inverted orientation 53 bp upstream of the P2 transcription start site. This element has an inhibitory effect on P1 transcription and is required for P2 transcription. The transcription factor Sp1 was identified as the factor that binds specifically to the tandem CT elements upstream of P1 and to the CT-I2 element upstream of P2. In addition, the recently cloned zinc finger protein ZF87, or MAZ, was also able to bind these same elements in vitro. The five tandem CT elements can be functionally replaced by a heterologous enhancer that only in the absence of CT-I2 reverses the promoter usage, similar to what is observed in the translocated c-myc allele of Burkitt's lymphoma cells.

131 citations

Journal ArticleDOI
TL;DR: It is concluded that basal Mediator is a novel general transcription factor of RNA polymerase II that is essential in crude but not in purified systems.
Abstract: Human Mediator complexes have been described as important bridging factors that enhance the effect of activators in purified systems and in chromatin. Here we report a novel basal function of a human Mediator complex. A monoclonal antibody was generated that depleted the majority of Mediator components from crude cell extracts. The removal of human Mediator abolished transcription by RNA polymerase II. This was observed on all genes tested, on TATA-containing and TATA-less promoters, both in the presence and absence of activators. To identify the relevant complex a combined biochemical and immunopurification protocol was applied. Two variants termed Mediator and basal Mediator were functionally and structurally distinguished. Basal Mediator function relies on additional constraints, which is reflected in the observation that it is essential in crude but not in purified systems. We conclude that basal Mediator is a novel general transcription factor of RNA polymerase II.

131 citations

Journal ArticleDOI
TL;DR: In B-lymphoma cells, a 37-amino-acid EBNA-2 domain previously identified to be essential for transformation was nearly as strong a transcriptional activator as the activating domain of herpes simplex virus trans-inducing factor VP16.
Abstract: Epstein-Barr virus nuclear protein 2 (EBNA-2) increases mRNA levels of specific viral and cellular genes through direct or indirect effects on upstream regulatory elements. The EBNA-2 domains essential for these effects have been partially defined and correlate with domains important for B-cell growth transformation. To determine whether EBNA-2 has a direct transcriptional activating domain, gene fusions between the DNA-binding domain of GAL4 and EBNA-2 were tested in CHO and B-lymphoma cells for the ability to activate transcription from target plasmids containing GAL4 recognition sites upstream of an adenovirus or murine mammary tumor virus promoter. In B-lymphoma cells, a 37-amino-acid EBNA-2 domain previously identified to be essential for transformation was nearly as strong a transcriptional activator as the activating domain of herpes simplex virus trans-inducing factor VP16. A quadradecapeptide had about 25% of the activating activity of the longer peptide. This first evidence that EBNA-2 directly activates transcription should facilitate the identification of nuclear factors with which EBNA-2 interacts in transactivation and transformation.

131 citations

Journal ArticleDOI
TL;DR: It is proposed that Mediator is released quickly from promoters after phosphorylation of Ser5 by Kin28 (CDK7), which also allows for RNAPII to escape from the promoter.
Abstract: Mediator is an essential, broadly utilized eukaryotic transcriptional co-activator. How and what it communicates from activators to RNA polymerase II (RNAPII) remains an open question. Here we performed genome-wide location profiling of Saccharomyces cerevisiae Mediator subunits. Mediator is not found at core promoters but rather occupies the upstream activating sequence (UAS), upstream of the pre-initiation complex. In the absence of Kin28 (CDK7) kinase activity, or in cells where the RNAPII C-terminal domain (CTD) is mutated to replace Ser5 with alanines, however, Mediator accumulates at core promoters together with RNAPII. We propose that Mediator is quickly released from promoters upon Ser5 phosphorylation by Kin28 (CDK7), which also allows for RNAPII to escape from the promoter.

129 citations


Network Information
Related Topics (5)
Regulation of gene expression
85.4K papers, 5.8M citations
88% related
Peptide sequence
84.1K papers, 4.3M citations
87% related
Transcription factor
82.8K papers, 5.4M citations
87% related
RNA
111.6K papers, 5.4M citations
86% related
Mutant
74.5K papers, 3.4M citations
86% related
Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20232
20223
20218
20206
20196
20186