Alternative titles; symbols
Other entities represented in this entry:
HGNC Approved Gene Symbol: TAF1
SNOMEDCT: 1237420004, 698279003;
Cytogenetic location: Xq13.1 Genomic coordinates (GRCh38): X:71,366,357-71,530,525 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| Xq13.1 | Dystonia-Parkinsonism, X-linked | 314250 | X-linked recessive | 3 |
| Intellectual developmental disorder, X-linked syndromic 33 | 300966 | X-linked recessive | 3 |
Transcription factor IID (TFIID) is a DNA-binding protein complex required for RNA polymerase II (see POLR2A; 180660)-mediated transcription of many, if not all, protein-encoding genes in eukaryotic cells. Other general transcription factors are TFIIA (600519, 600520), TFIIB (189963), TFIIE (189962, 189964), TFIIF (189968), TFIIG/J, and TFIIH (189972). TFIID plays a key role in initiation, since it binds to the TATA element to form a complex that nucleates the assembly of the other components into a preinitiation complex and that may be stable through multiple rounds of transcription. TAF1, or TAFII250, is the largest subunit of TFIID. Other protein subunits of TFIID include TATA box-binding protein (TBP; 600075) and numerous other TBP-associated factors (TAFs; see 600475). TFIID is thought to interact with TFIIA, which may stabilize its binding, and with TFIIB, which is the next factor to enter the complex.
By somatic cell hybridization, Jha and Ozer (1977) found synteny of human HGPRT (308000) on the X chromosome and a human gene correcting for a temperature-sensitive defect in DNA synthesis in a particular mouse cell line. Jha et al. (1980) assigned the gene, which they called BA2R, to Xq13-q27. Schwartz et al. (1977, 1979) found that a temperature-sensitive mutation in hamster cells (BHK21) was also X-linked and could be complemented by the human X chromosome. Sekiguchi et al. (1987) studied a temperature-sensitive mutant isolated from the hamster cell line BHK21/13, which cannot progress into S phase at 39.5 degrees C, following release from isoleucine deprivation. (The original description of this mutant cell line was given by Nishimoto et al. (1982).) The mutant cells were transfected with high molecular weight DNA from human cells, and several human DNA bands were found to be conserved through 3 cycles of transformation to temperature resistance. A 70-kb human DNA band was mapped to the region Xpter-q21 by study of human-mouse hybrid cells.
Sekiguchi et al. (1988) cloned the X-linked gene that corrects the defect in the temperature-sensitive hamster cell line. They isolated the gene, which they called CCG1, from a secondary ts(+) transformant using DNA-mediated gene transfer of total human DNA and a cosmid vector. The isolated cDNA complemented a temperature-sensitive mutation with a clear defect in the G1 phase, the most important phase for the control of cell proliferation. The cloned genomic cDNA was 5.3 kb long and had an open reading frame of 4,662 bp, encoding a protein of almost 180 kD. Sekiguchi et al. (1991) showed that the previously cloned cDNA for the CCG1 gene was a truncated form; authentic CCG1 cDNA is 6.0 kb and encodes a protein with a molecular mass of 210 kD.
Ruppert et al. (1993) described the cloning, expression, and properties of the 250-kD subunit of transcription factor IID, TAFII250, which was found to be identical to CCG1 (see also Hisatake et al. (1993)).
By screening human fetal brain, leukocyte, and placenta cDNA libraries using a PCR-based enrichment method, followed by RT-PCR of caudate nucleus RNA, Nolte et al. (2003) identified 8 splice variants of TAF1 containing novel 3-prime exons, which they referred to as DYT3 transcripts. Six of the variants contain previously identified TAF1 coding exons at their 5-prime ends, whereas 2 of the variants contain only novel 3-prime exons.
Herzfeld et al. (2007) stated that the first 38 exons of the TAF1 gene encode the highly conserved 250-kD subunit of TFIID. By RT-PCR of human fetal brain and caudate nucleus, they identified several alternatively spliced transcripts that initiated with exon 26, skipped exon 38, and contained some of the 3-prime exons reported by Nolte et al. (2003). These 3-prime exons encode sequences not included in the 250-kb subunit.
Nolte et al. (2003) stated that the TAF1 gene contains at least 38 exons, and they identified 5 additional downstream exons. Herzfeld et al. (2007) called these 5 downstream exons d1 through d5. Their analysis suggested that these downstream exons are much younger than the first 38 highly conserved exons and were added approximately 30 million years ago. In the region upstream from exon d2, Herzfeld et al. (2007) identified a TATA-less promoter within a CpG island that contains an initiator element and binding sites for several putative transcription factors, including a functional Ikaros (see 603023)-binding site.
Brown et al. (1989) assigned the human CCG1 gene, which complements the temperature-sensitive hamster cell cycle mutations BN462 and ts13, to Xq11-q13 by study of somatic cell hybrids segregating portions of various X-autosome translocations. Derry and Barnard (1989) showed that the mouse equivalent, Ccg1, is located on the X chromosome. They determined its position relative to 7 other X-linked gene markers. Very close linkage was found to the gene for the alpha subunit of phosphorylase kinase of muscle (PHKA1; 311870), and the locus was found to be situated between the androgen receptor locus proximally and the phosphoroglycerate kinase locus distally. Assuming conservation of gene order, this supports the location of the human CCG1 locus on Xq, probably in the region Xq11-q13. This location is consistent with the positioning of the gene 7 Mb from pter on the megabase scale presented by Nelson et al. (1995).
The largest subunit of human TFIID, TAFII250, contains serine/threonine kinase domains that can autophosphorylate and transphosphorylate the large subunit of the basal factor TFIIF (Dikstein et al., 1996). O'Brien and Tjian (1998) identified the regions of the N-terminal kinase domain (amino acids 1-414) necessary for kinase activity and examined its function in vivo. Point mutations within 2 patches of amino acids in the kinase domain decrease both autophosphorylation and transphosphorylation activities. The TAFII250-bearing mutations within the N-terminal kinase domain exhibited a significantly reduced ability to rescue ts13 cells that express a temperature-sensitive TAFII250. Moreover, transcription from the cyclin A and cdc2 promoters became impaired when cotransfected with TAFII250 containing inactive forms of the N-terminal kinase domain.
Jacobson et al. (2000) demonstrated that the TFIID 250-kD subunit contains 2 tandem bromodomain modules that bind selectively to multiply acetylated histone H4 peptides. The 2.1-angstrom crystal structure of the double bromodomain reveals 2 side-by-side, 4-helix bundles with a highly polarized surface charge distribution. Each bundle contains an N(epsilon)-acetyllysine-binding pocket at its center, which results in a structure ideally suited for recognition of diacetylated histone H4 tails. Jacobson et al. (2000) concluded that TFIID may be targeted to specific chromatin-bound promoters and may play a role in chromatin recognition.
Acetylation of p53 (TP53; 191170) in response to DNA damage enhances its ability to bind DNA and recruit transcriptional coactivators to p53-responsive promoters. Li et al. (2007) showed that acetylation of lys373 and lys382 on p53 led to their direct interaction with the tandem bromodomains of TAF1. p53 recruited TAF1 to a distal p53-binding site on the p21 (CDKN1A; 116899) promoter prior to the DNA looping that brings TAF1 to the TATA box-containing core promoter.
Using peptide arrays, Flynn et al. (2015) found that, in addition to acetylated lysine (Kac), TAF1 recognized butyrylated lysine (Kbu) in histone. A 'gatekeeper' tyrosine in the bromodomain of TAF1 was responsible for this expanded acyl recognition. In addition, the second bromodomain of TAF1 could recognize histone with crotonylated lysine (Kcr).
Transcription Factor IID
Starr and Hawley (1991) and Lee et al. (1991) demonstrated that, unlike most sequence-specific DNA-binding proteins, TFIID interacts primarily within the minor groove of the DNA helix. Binding of TFIID appears to be the first step in the formation of a transcription-competent complex, followed by TFIIB, RNA polymerase II, and the remaining factors. TFIID may also serve to link the control of transcription to the cell cycle.
High levels of gene transcription by RNA polymerase II depend on high rates of transcription initiation and reinitiation. Initiation requires recruitment of the complete transcription machinery to a promoter, a process facilitated by activators and chromatin remodeling factors. Reinitiation is thought to occur through a different pathway. After initiation, a subset of the transcription machinery remains at the promoter, forming a platform for assembly of a second transcription complex. Yudkovsky et al. (2000) described the isolation of a reinitiation intermediate in yeast that includes transcription factors TFIID, TFIIA, TFIIH, TFIIE, and Mediator (see 602984). This intermediate can act as a scaffold for formation of a functional reinitiation complex. Formation of this scaffold is dependent on ATP and TFIIH. In yeast, the scaffold is stabilized in the presence of the activator Gal4-VP16, but not Gal4-AH, suggesting a new role for some activators and Mediator in promoting high levels of transcription.
Christova and Oelgeschlager (2002) found that TFIID can act as a 'bookmark' to identify previously active genes for rapid reactivation after cell division. Both TFIID and TFIIB remained associated with active gene promoters during condensation of chromatin and mitosis in asynchronous and mitotic human cell populations, whereas RNA polymerase II was displaced, and NC2 (see 601482) was displaced from some, but not all, gene promoters. Christova and Oelgeschlager (2002) concluded that TFIID-promoter complexes can withstand condensation of chromatin into transcriptionally silent chromosomes and therefore could propagate cell type-specific gene expression patterns through cell division.
Downstream core promoter elements (DPE) are regulatory sequences that add diversity to the promoter architecture of RNA polymerase II-transcribed genes. Despite a functional correlation between the presence of TFIID and DPE, Lewis et al. (2005) found that TFIID was insufficient for DPE-specific transcription in HeLa cells. Using a functional transcription assay coupled with conventional biochemistry, they found that protein kinase CK2 (see CSNK2A1; 115440), in conjunction with the coactivator PC4 (600503), established DPE-specific transcription.
Trimethylation of histone H3 (see 602810) at lys4 (H3K4me3) is a hallmark of active human promoters. Using stable isotope labeling by amino acids in cell culture (SILAC)-based proteomic screening, Vermeulen et al. (2007) showed that TFIID bound directly to H3K4me3 via the plant homeodomain (PHD) of the TFIID subunit TAF3 (606576). Selective loss of H3K4me3 reduced transcription from and TFIID binding to a subset of promoters in vivo. Equilibrium binding assays and competition experiments indicated that the TAF3 PHD finger was highly selective for H3K4me3. In transient assays, TAF3 could act as a transcriptional activator in a PHD finger-dependent manner. Asymmetric dimethylation of H3 at arg2 selectively inhibited binding of TFIID to H3K4me3, whereas acetylation of H3 at lys9 and lys14 potentiated interaction of TFIID with H3K4me3. Vermeulen et al. (2007) concluded that there is crosstalk between histone modifications and TFIID.
Pijnappel et al. (2013) showed that knockdown of the TFIID complex affects the pluripotent circuitry in mouse embryonic stem (ES) cells and inhibits reprogramming of fibroblasts. TFIID subunits and OSKM factors Oct4 (164177), Sox2 (184429), Klf4 (602253), and Myc (190080) form a feed-forward loop to induce and maintain a stable transcription state. Notably, transient expression of TFIID subunits greatly enhanced reprogramming. Pijnappel et al. (2013) concluded that TFIID is critical for transcription factor-mediated reprogramming.
Cryoelectron Microscopy
Papai et al. (2010) used cryoelectron microscopy to determine the architecture of nucleoprotein complexes composed of TFIID, TFIIA (see 600519), the transcriptional activator RAP1 (605061), and yeast enhancer-promoter DNA. These structures revealed the mode of binding of RAP1 and TFIIA to TFIID, as well as a reorganization of TFIIA induced by its interaction with RAP1. Papai et al. (2010) proposed that this change in position increases the exposure of TATA box-binding protein within TFIID, consequently enhancing its ability to interact with the promoter. A large RAP1-dependent DNA loop forms between the activator-binding site and the proximal promoter region. This loop is topologically locked by a TFIIA-RAP1 protein bridge that folds over the DNA. These results highlighted the role of TFIIA in transcriptional activation, defined the molecular mechanism for enhancer-promoter communication, and provided structural insights into the pathways of intramolecular communication that convey transcription activation signals through the TFIID complex.
Patel et al. (2018) used cryoelectron microscopy, chemical crosslinking mass spectrometry, and biochemical reconstitution to determine the complete molecular architecture of TFIID and defined the conformational landscape of TFIID in the process of loading TATA box-binding protein (TBP; 600075) onto promoter DNA. The structural analysis revealed 5 structural states of TFIID in the presence of TFIIA and promoter DNA, showing that the initial binding of TFIID to the downstream promoter positions the upstream DNA and facilitates scanning of TBP for a TATA box and the subsequent engagement of the promoter. Patel et al. (2018) concluded that their findings provided a mechanistic model for the specific loading of TBP by TFIID onto the promoter.
Crystal Structure
Flynn et al. (2015) found that the crystal structure of TAF1 complexed with Kbu adopted a conformation similar to that of BRD9 (618465) complexed with Kbu. However, the structure of the TAF1-Kcr complex revealed that the crotonyl group displaced 2 conserved structural water molecules from their usual positions and produced a significantly altered network of 5 rather than 6 water molecules.
X-linked Dystonia-Parkinsonism
X-linked dystonia-parkinsonism (XDP; 314250) is characterized by severe progressive torsion dystonia followed by parkinsonism. Its prevalence is particularly high (5.24 in 100,000) on Panay Island, Philippines. Makino et al. (2007) performed genomic sequencing of the complete XDP locus, designated DYT3, on Xq13.1 in a search for disease-specific mutations. The study included 67 Filipino individuals (20 affected males) from 16 families residing in Panay. The authors found a disease-specific SVA (short interspersed nuclear element, variable number of tandem repeats, and Alu composite) retrotransposon insertion in an intron of the TAF1, which encodes the largest component of the transcription factor IID (TFIID) complex. Studies of XDP postmortem brain showed significantly decreased expression levels of TAF1 and of the dopamine receptor D2 gene (DRD2; 126450) in the caudate nucleus. Makino et al. (2007) also identified an abnormal pattern of DNA methylation in the retrotransposon in the genome from the patient's caudate, which could account for decreased expression of TAF1. The findings were interpreted as indicating that reduced neuron-specific expression of the TAF1 gene is associated with XDP.
SVA retrotransposon insertions are thought to be active in the human genome and to alter the expression level of adjacent genes that cause diseases. The SVA retrotransposon has a high GC content (approximately 70%) and a large number of CpG sites (more than 150) in its nucleotide sequence, so that it is frequently hypermethylated in its insertion site. Makino et al. (2007) suggested that, in XDP, the decreased expression of the neuron-specific TA14-391 isoform, and probably other TAF1 isoforms, results in transcriptional dysregulation of many neuronal genes, including that which encodes dopamine receptor DR (DRD2; 126450). They suggested that the findings in XDP support the concept of 'transcription syndromes' involving TFIID (Vermeulen et al., 1994), which include congenital cataracts, facial dysmorphism, and neuropathy syndrome (CCFDN; 604168), caused by partial deficiency of RNA polymerase II (CTDP1; 604927); dentatorubral-pallidoluysian atrophy (DRPLA; 125370), caused by interference in the signals to TFIID; and spinocerebellar ataxia-17 (SCA17; 607136), caused by an expanded polyglutamine in the TATA-binding protein (TBP; 600075).
X-linked Syndromic Intellectual Developmental Disorder 33
In 12 boys from 9 unrelated families with X-linked syndromic intellectual developmental disorder-33 (MRXS33; 300966), O'Rawe et al. (2015) identified 9 different hemizygous mutations in the TAF1 gene (see, e.g., 313650.0002-313650.0006). Most of the mutations occurred de novo, although 3 were inherited from an unaffected mother, 1 of whom showed skewed X-inactivation. Functional studies were not performed, but many of the variants affected highly conserved residues in domains critical for interaction with TAF7 (600573), and were predicted to disrupt this interaction. Gene expression studies in 1 family with a missense mutation (I1337T; 313650.0002) suggested that the phenotype is associated with downregulation of a set of genes regulated by E-box proteins. The mutations were found by several strategies, including whole-genome sequencing, exome sequencing, targeted gene-panel sequencing, and microarray-based strategies, and all were confirmed by Sanger sequencing.
Maile et al. (2004) reported that serine-33 of histone H2B (see 609904) (H2B-S33) is a physiologic substrate for the TAF1 C-terminal kinase domain (CTK) and that H2B-S33 phosphorylation is essential for transcriptional activation events that promote cell cycle progression and development. Because of image manipulation that rendered the data, results, and conclusions not reliable, the journal Science retracted the paper of Maile et al. (2004) at the request of the University of California, Riverside and Dr. Frank Sauer.
O'Rawe et al. (2015) found that knockdown of the taf1 gene in zebrafish resulted in a 10% reduction in the relative area of the optic tectum, suggesting a neuronal defect.
Makino et al. (2007) demonstrated that the X-linked dystonia-parkinsonism that is very frequent in Filippinos living on Panay Island (DYT3; 314250) is caused by an SVA retrotransposon insertion in intron 32 of the TAF1 gene. The insertion is 2,627 bp in length.
In 2 teenaged brothers of European descent with X-linked syndromic intellectual developmental disorder-33 (MRXS33; 300966) O'Rawe et al. (2015) identified a hemizygous c.4010T-C transition (chrX.70,621,541T-C, GRCh37) in the TAF1 gene, resulting in an ile1337-to-thr (I1337T) substitution at a highly conserved residue. The mutation was inherited from the unaffected mother who showed highly skewed X-inactivation. The mutation was not found in the dbSNP (build 137), 1000 Genomes Project, Exome Variant Server, or ExAC databases. Functional studies of the variant were not performed, but gene expression analysis of blood showed differential expression of over 200 genes between the affected boys and noncarrier family members, with an association with downregulation of a set of genes regulated by E-box proteins.
In a 5-year-old boy of European descent with X-linked syndromic intellectual developmental disorder-33 (MRXS33; 300966), O'Rawe et al. (2015) identified a de novo hemizygous c.2419T-C transition (chrX.70,607,243T-C, GRCh37) in the TAF1 gene, resulting in a cys807-to-arg (C807R) substitution at a highly conserved residue in the central domain (DUF3591) that encompasses a HAT domain that interacts with TAF7 (600573). Although in vitro functional studies were not performed, the C807R mutation was predicted to destabilize this region and interfere with the interaction between TAF1 and TAF7. The mutation was not found in the dbSNP (build 137), 1000 Genomes Project, Exome Variant Server, or ExAC databases.
In a 6-year-old boy of European descent with X-linked syndromic intellectual developmental disorder-33 (MRXS33; 300966), O'Rawe et al. (2015) identified a de novo hemizygous c.3736C-T transition (chrX.70,618,477C-T, GRCh37) in the TAF1 gene, resulting in an arg1246-to-trp (R1246W) substitution at a highly conserved residue important for binding with TAF7 (600573). Although in vitro functional studies were not performed, the R1246W mutation was predicted to interfere with the interaction between TAF1 and TAF7. The mutation was not found in the dbSNP (build 137), 1000 Genomes Project, Exome Variant Server, or ExAC databases.
In 3 boys of Columbian descent with X-linked syndromic intellectual developmental disorder-33 (MRXS33; 300966), O'Rawe et al. (2015) identified a hemizygous c.1786C-T transition (chrX.70,602,671C-T, GRCh37) in the TAF1 gene, resulting in a pro596-to-ser (P596S) substitution at a highly conserved residue in the central domain (DUF3591) that encompasses a HAT domain that interacts with TAF7 (600573). Although in vitro functional studies were not performed, the P596S mutation was predicted to interfere with the interaction between TAF1 and TAF7. The mutation, which was inherited from the unaffected mother, was not found in the dbSNP (build 137), 1000 Genomes Project, Exome Variant Server, or ExAC databases.
In a 3-year-old boy of Spanish descent with X-linked syndromic intellectual developmental disorder-33 (MRXS33; 300966), O'Rawe et al. (2015) identified identified a de novo hemizygous c.2926G-C transversion (chrX.70,612,503G-C, GRCh37) in the TAF1 gene, resulting in an asp976-to-his (D976H) substitution at a highly conserved residue in the central domain (DUF3591) that encompasses a HAT domain that interacts with TAF7 (600573). Although in vitro functional studies were not performed, the D976H mutation was predicted to interfere with the interaction between TAF1 and TAF7. The mutation was not found in the dbSNP (build 137), 1000 Genomes Project, Exome Variant Server, or ExAC databases.
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