In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene regulation and DNA replication. Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 90 micrometers (0.09 mm) of 30 nm diameter chromatin fibers.
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.
Histone acetyltransferase KAT2A is an enzyme that in humans is encoded by the KAT2A gene.
TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa, also known as TAF9, is a protein that in humans is encoded by the TAF9 gene.
Transcription initiation factor TFIID subunit 12 is a protein that in humans is encoded by the TAF12 gene.
Transcription initiation factor TFIID subunit 4 is a protein that in humans is encoded by the TAF4 gene.
Transcription initiation factor TFIID subunit 2 is a protein that in humans is encoded by the TAF2 gene.
Transcription initiation factor TFIID subunit 10 is a protein that in humans is encoded by the TAF10 gene.
Transcription initiation factor TFIID subunit 11 also known as TAFII28, is a protein that in humans is encoded by the TAF11 gene.
Transcription initiation protein SPT3 homolog is a protein that in humans is encoded by the SUPT3H gene.
TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L is an enzyme that in humans is encoded by the TAF5L gene.
TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L is an enzyme that in humans is encoded by the TAF6L gene.
Cryptic unstable transcripts (CUTs) are a subset of non-coding RNAs (ncRNAs) that are produced from intergenic and intragenic regions. CUTs were first observed in S. cerevisiae yeast models and are found in most eukaryotes. Some basic characteristics of CUTs include a length of around 200–800 base pairs, a 5' cap, poly-adenylated tail, and rapid degradation due to the combined activity of poly-adenylating polymerases and exosome complexes. CUT transcription occurs through RNA Polymerase II and initiates from nucleosome-depleted regions, often in an antisense orientation. To date, CUTs have a relatively uncharacterized function but have been implicated in a number of putative gene regulation and silencing pathways. Thousands of loci leading to the generation of CUTs have been described in the yeast genome. Additionally, stable uncharacterized transcripts, or SUTs, have also been detected in cells and bear many similarities to CUTs but are not degraded through the same pathways.
The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.
Gene gating is a phenomenon by which transcriptionally active genes are brought next to nuclear pore complexes (NPCs) so that nascent transcripts can quickly form mature mRNA associated with export factors. Gene gating was first hypothesised by Günter Blobel in 1985. It has been shown to occur in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster as well as mammalian model systems.
The transactivation domain or trans-activating domain (TAD) is a transcription factor scaffold domain which contains binding sites for other proteins such as transcription coregulators. These binding sites are frequently referred to as activation functions (AFs). TADs are named after their amino acid composition. These amino acids are either essential for the activity or simply the most abundant in the TAD. Transactivation by the Gal4 transcription factor is mediated by acidic amino acids, whereas hydrophobic residues in Gcn4 play a similar role. Hence, the TADs in Gal4 and Gcn4 are referred to as acidic or hydrophobic, respectively.
The Gal4 transcription factor is a positive regulator of gene expression of galactose-induced genes. This protein represents a large fungal family of transcription factors, Gal4 family, which includes over 50 members in the yeast Saccharomyces cerevisiae e.g. Oaf1, Pip2, Pdr1, Pdr3, Leu3.
Spt-Ada-Gcn5 acetyltransferase (SAGA) complex is a multicomponent regulator of acetylation. It has been found that this complex is highly conserved between different organisms, such as humans, Drosophila, and yeast. This 15 subunit complex has been best characterized for its histone acetyltransferase activity (HAT). The acetylating activity has been found to occur in the lysine residues of the N-terminal tails of H3 and H2 histones. It has been found recently that this activity is actually a deubiquitination of a monoubiquitin that occurs in residue Lys 123 of the H2b histone and the acetylation of the H3 histone. The histone acetylation is mediated by the GCN5 histone acetyl transferase, while the deubiquitinating activity is mediated by a deubiquitinating module (DUBm), which is composed of 4 proteins, Ubp8 ubiquitin hydrolase, Sgf11, Sus1, and Sgf73. This DUB module is an independently folding subcomplex that is connected to the C-terminal tail of Sgf 73, Sgf73, as well as Sus1, also have a role in facilitating SAGA complex's role in nuclear export by binding to components of the nuclear pore complex. Even though Ubp8 has ubiquitin specific hydrolase (USP) domain, the protein remains inactive unless it is in complex with the other 3 DUBm proteins.
Kevin Struhl is an American biochemist and academic who works at Harvard Medical School as the David Wesley Gaiser Professor of Biological Chemistry and Molecular Pharmacology.
