Correlating gene promoters and expression in gene disruption experiments
19
Citation
21
Reference
10
Related Paper
Citation Trend
Abstract:
Finding putative transcription factor binding sites in the upstream sequences of similarly expressed genes has recently become a subject of intensive studies. In this paper we investigate how much gene expression regulation can be attributed to the presence of various binding sites in the gene promoters by correlating the binding sites and the changes in gene expression resulting from gene disruptions (e.g. knockouts).We have developed a data analysis method for comparing mRNA measurements of gene disruption experiments with information about gene promoters. The method was applied to a well-known dataset to uncover correlations between known transcription factor binding site motifs in the upstream regions of all S. cerevisiae genes and the gene expression changes in various gene disruption experiments. The possible explanations of the correlations were categorized and analyzed using e.g. expression cascades. Several correlations turned out to be consistent with existing biological knowledge while some new ones suggest themselves for further study.The resulting tables are available at http://www.cs.helsinki.fi/u/kpalin/CorrDisrupt/.Keywords:
DNA binding site
Gene prediction
Gene knockout
This chapter deals with natural and synthetic promoters frequently used in yeast. It describes principles and strategies exploited to produce synthetic promoters and their cognate transcription factors. The chapter points out the essential structural and functional features of yeast promoters. It highlights some examples of both regulated and constitutive natural yeast promoters. The characterization of these sequences allowed for the identification of structural and functional features that are exploited to build synthetic promoters and heterologous transcription factors. Modification of the binding affinity between the transcription factor and its cognate transcription factor binding site (TFBS) results in promoter strength modulation. The chapter discusses two main groups of synthetic promoters. One includes modified versions of natural promoters, and the other contains hybrid promoters. The chapter also describes Saccharomyces cerevisiae promoters. The characterization of S. cerevisiae promoters began by using them to drive expression of reporter genes.
Transcription
DNA binding site
Cite
Citations (5)
Transcription factors regulate gene expression by binding to specific cis-regulatory elements in gene promoters. Although DNA sequences that serve as transcription-factor binding sites have been characterized and associated with the regulation of numerous genes, the principles that govern the design and evolution of such sites are poorly understood.Using the comprehensive mapping of binding-site locations available in Saccharomyces cerevisiae, we examined possible factors that may have an impact on binding-site design. We found that binding sites tend to be shorter and fuzzier when they appear in promoter regions that bind multiple transcription factors. We further found that essential genes bind relatively fewer transcription factors, as do divergent promoters. We provide evidence that novel binding sites tend to appear in specific promoters that are already associated with multiple sites.Two principal models may account for the observed correlations. First, it may be that the interaction between multiple factors compensates for the decreased specificity of each specific binding sequence. In such a scenario, binding-site fuzziness is a consequence of the presence of multiple binding sites. Second, binding sites may tend to appear in promoter regions that are subject to low selective pressure, which also allows for fuzzier motifs. The latter possibility may account for the relatively low number of binding sites found in promoters of essential genes and in divergent promoters.
DNA binding site
Transcription
Cite
Citations (70)
Summary Our limited understanding of plant promoters does not allow us to recognize any core promoter elements for the majority of plant promoters. To understand the promoter architecture of Arabidopsis, we used the combined approach of in silico detection of novel core promoter elements and large‐scale determination of transcription start sites (TSSs). To this end, we developed a novel methodology for TSS identification, using a combination of the cap‐trapper and massively parallel signature sequencing methods. This technique, CT–MPSS, allowed us to identify 158 237 Arabidopsis TSS tags corresponding to 38 311 TSS loci, which provides an opportunity for quantitative analysis of plant promoters. The expression characteristics of these promoters were analyzed with respect to core promoter elements detected by our in silico analyses, revealing that Arabidopsis promoters contain two main types of elements with exclusive characteristics, the TATA type and the GA type. The TATA‐type promoters tend to be associated with the Y Patch and the Inr motif, and cause high expression with sharp‐peak TSS clusters. By contrast, the GA type produces broad‐type TSS clusters. Unlike mammalian promoters, plant promoters are not associated with CpG islands. However, plant‐specific GA‐type promoters share some characteristics with mammalian CpG‐type promoters.
TATA box
Cite
Citations (109)
Cite
Citations (14)
Fine-tuning of the expression of genes is crucial for cell factory construction. Promoters are the most important tools to control gene expression. However, native promoters are often limited by their transcriptional ability. In this study, we sought to overcome the limitations of native promoters in Saccharomyces cerevisiae through the construction of hybrid promoter libraries for both constitutive promoters and promoters induced by diauxic shift. A series of hybrid constitutive promoters were constructed by combing the upstream activation sequences and changing the core promoter elements. The transcriptional capacity of the strongest promoter was 2-fold higher than that of the yeast native TEF1 promoter. Aside from the constitutive promoters, hybrid promoters that were induced in the post-diauxic phase were also constructed. These promoters had low transcriptional ability during growth on glucose and automatically activated upon growth with a diauxic shift. The strength of these promoters was also increased by replacing the core promoter with strong core promoters. Our study provides a series of constitutive and diauxic shift-induced promoters with a broad range of transcriptional capacity and will facilitate synthetic biology and metabolic engineering application.
Cite
Citations (16)
Heterologous
Transcription
RNA polymerase II
Cite
Citations (43)
Bidirectional promoters lie between adjacent genes, which are transcribed from opposite strands of DNA. The functional mechanisms underlying the activation of bidirectional promoters are currently uncharacterised. To define the core promoter elements of bidirectional promoters in human, we mapped motifs for TATA, INR, BRE, DPE, INR, as well as CpG-islands. We found a consistently high correspondence between C+G content, CpG-island presence and an average expression level increasing the median level for all genes in bidirectional promoters. These CpG-rich promoters showed discrete initiation patterns rather than broad regions of transcription initiation, as are typically seen for CpG-island promoters. CpG-islands encompass both TSSs within bidirectional promoters, providing an explanation for the symmetrical co-expression patterns of many of these genes. In contrast, TATA motifs appear to be asymmetrically positioned at one TSS or the other. Our findings demonstrate that bidirectional promoters utilize a variety of core promoter elements to initiate transcription. CpG-islands dominate the regulatory landscape of this group of promoters.
CpG site
Transcription
TATA box
Cite
Citations (67)
In the cyanobacterium Anabaena sp. strain PCC 7120 (also known as Nostoc sp. strain PCC 7120), a zinc-responsive operon (all4725-all4721) has been described, which contains 4 distinct promoters. The two most upstream ones bind Zur with high affinity, whereas the other two do not or do so with a very low affinity. In this paper, a detailed characterization of the four promoters is presented, showing that all four were induced by metal depletion, and they were constitutively derepressed in a zur mutant, despite the two downstream promoters not being direct targets for this regulator. Crucially, induction by metal depletion of the two downstream promoters was abrogated when transcription initiated at the upstream promoters was interrupted by a polar insertion midway in the operon. In contrast, insertion of a nitrogen-responsive promoter at a roughly similar position provoked the two downstream promoters to adopt a regulatory pattern mimicking that of the inserted promoter. Thus, regulation of the two downstream promoters is apparently influenced by transcription from promoters upstream. Evidence is presented indicating that the activity of the two downstream promoters is kept basal in Anabaena by repression. A regulatory model compatible with these results is proposed, where promoters controlled by repression in bacterial operons may be subjected to a hierarchical regulation depending on their position in the operon. According to this model, internal promoters may respond to stimuli governing the activity of promoters upstream by an indirect regulation and to specific stimuli by a direct regulation.
Transcription
Cite
Citations (13)
YY1
Transcription
Cite
Citations (36)
This study supplements earlier received experimental data using modern databases. Previously tumor-specific activity of several human native and chimeric promoters was demonstrated. Here we compared tumor-specific promoters with promoters of housekeeping genes by the presence of recognition profiles for transcription factors in DNA sequences of the promoters. A number of transcription factor recognition profiles have been identified, the presence of which in promoters may indicate the tumor specificity of the promoters. Transcription factors which may directly regulate promoters of genes involved in cell proliferation and carcinogenesis were revealed by pathway analysis. The results of the study may help in studying the peculiarities of gene transcription in tumors and in the search for or the creation of tumor-specific promoters for cancer gene therapy.
Housekeeping gene
Transcription
Cite
Citations (0)