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| Content | |
| Description | yeast transcription factor sequence specificities. |
| Contact | |
| Research center | University of Toronto |
| Laboratory | Department of Molecular Genetics and Banting |
| Authors | Carl G de Boer |
| Primary citation | de Boer & al. (2012) [1] |
| Release date | 2011 |
| Access | |
| Website | http://yetfasco.ccbr.utoronto.ca/ |
YeTFaSCo (The Yeast Transcription Factor Specificity Compendium) is a database of transcription factors for Saccharomyces cerevisiae. [1]
In molecular biology, a transcription factor (TF) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The function of TFs is to regulate—turn on and off—genes in order to make sure that they are expressed in the desired cells at the right time and in the right amount throughout the life of the cell and the organism. Groups of TFs function in a coordinated fashion to direct cell division, cell growth, and cell death throughout life; cell migration and organization during embryonic development; and intermittently in response to signals from outside the cell, such as a hormone. There are up to 1600 TFs in the human genome. Transcription factors are members of the proteome as well as regulome.
In molecular biology, the TATA box is a sequence of DNA found in the core promoter region of genes in archaea and eukaryotes. The bacterial homolog of the TATA box is called the Pribnow box which has a shorter consensus sequence.
Histone acetyltransferases (HATs) are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl-CoA to form ε-N-acetyllysine. DNA is wrapped around histones, and, by transferring an acetyl group to the histones, genes can be turned on and off. In general, histone acetylation increases gene expression.
RNA polymerase 1 is, in higher eukaryotes, the polymerase that only transcribes ribosomal RNA, a type of RNA that accounts for over 50% of the total RNA synthesized in a cell.
RNA polymerase II is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription.
Two-hybrid screening is a molecular biology technique used to discover protein–protein interactions (PPIs) and protein–DNA interactions by testing for physical interactions between two proteins or a single protein and a DNA molecule, respectively.
The yeast Saccharomyces cerevisiae is a simple single-celled eukaryote with both a diploid and haploid mode of existence. The mating of yeast only occurs between haploids, which can be either the a or α (alpha) mating type and thus display simple sexual differentiation. Mating type is determined by a single locus, MAT, which in turn governs the sexual behaviour of both haploid and diploid cells. Through a form of genetic recombination, haploid yeast can switch mating type as often as every cell cycle.
Transcription factor II Human is an important protein complex, having roles in transcription of various protein-coding genes and DNA nucleotide excision repair (NER) pathways. TFIIH first came to light in 1989 when general transcription factor-δ or basic transcription factor 2 was characterized as an indispensable transcription factor in vitro. This factor was also isolated from yeast and finally named as TFIIH in 1992.
Mediator is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. It was discovered in 1990 in the lab of Roger D. Kornberg, recipient of the 2006 Nobel Prize in Chemistry. Mediator complexes interact with transcription factors and RNA polymerase II. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase.
GATA transcription factors are a family of transcription factors characterized by their ability to bind to the DNA sequence "GATA".
Nuclear transcription factor Y subunit alpha is a protein that in humans is encoded by the NFYA gene.
Myocyte-specific enhancer factor 2A is a protein that in humans is encoded by the MEF2A gene. MEF2A is a transcription factor in the Mef2 family. In humans it is located on chromosome 15q26. Certain mutations in MEF2A cause an autosomal dominant form of coronary artery disease and myocardial infarction.
Mitochondrial transcription factor A, abbreviated as TFAM or mtTFA, is a protein that in humans is encoded by the TFAM gene.
Cofactor of BRCA1, also known as COBRA1, is a human gene that encodes NELF-B.
Transcription factor Sp4 is a protein that in humans is encoded by the SP4 gene.
Dimethyladenosine transferase 1, mitochondrial; Transcription factor B1, mitochondrial is a mitochondrial enzyme that in is encoded by the TFB1M gene.
POLRMT is a symbol of RNA polymerase mitochondrial
Pho4 is a protein with a basic helix-loop-helix (bHLH) transcription factor. It is found in S. cerevisiae and other yeasts. It functions as a transcription factor to regulate phosphate responsive genes located in yeast cells. The Pho4 protein homodimer is able to do this by binding to DNA sequences containing the bHLH binding site 5'-CACGTG-3'. This sequence is found in the promoters of genes up-regulated in response to phosphate availability such as the PHO5 gene.
YEASTRACT is a curated repository of more than 48000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references. It also includes the description of about 300 specific DNA binding sites for more than a hundred characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains more than 7100 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks.
Gcn4 is a transcription factor and a “master regulator” for gene expression which regulates close to one tenth of the yeast genome. In a study by Razaghi et al, amino acid starvation activated the transcription factor Gcn4p, resulting in transcriptional induction of almost all genes involved in amino acid biosynthesis, including HIS4. Thus involvement of Gcn4 in regulation of both histidinol dehydrogenase HIS4 and interferon gamma hIFNγ was hypothesised as a scenario explaining the increased level of hIFNγ under amino acid starvation.
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