The Experts below are selected from a list of 1953 Experts worldwide ranked by ideXlab platform
Roger Bradley - One of the best experts on this subject based on the ideXlab platform.
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a requirement for nf protocadherin and TAF1 set in cell adhesion and neural tube formation
Developmental Biology, 2006Co-Authors: Dana J. Rashid, Katie Newell, Leah Shama, Roger BradleyAbstract:Neurulation in vertebrates is an intricate process requiring extensive alterations in cell contacts and cellular morphologies as the cells in the neural ectoderm shape and form the neural folds and neural tube. Despite these complex interactions, little is known concerning the molecules that mediate cell adhesion within the embryonic neural plate and neural folds. Here, we demonstrate the requirement for NF-protocadherin (NFPC) and its cytosolic partner TAF1/Set for proper neurulation in Xenopus. Both NFPC and TAF1 function in cell-cell adhesion in the neural ectoderm, and disruptions in either NFPC or TAF1 result in a failure of the neural tube to close. This neural tube defect can be attributed to a lack of proper organization of the cells in the dorsal neural folds, manifested by a loss in the columnar epithelial morphology and apical localization of F-actin. However, the epidermal ectoderm is still able to migrate and cover the open neural tube, indicating that the fusions of the neural tube and epidermis are separate events. These studies demonstrate that NFPC and TAF1 function to maintain proper cell-cell interactions within the neural folds and suggest that NFPC and TAF1 participate in novel adhesive mechanisms that contribute to the final events of vertebrate neurulation.
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A requirement for NF-protocadherin and TAF1/Set in cell adhesion and neural tube formation
Developmental Biology, 2006Co-Authors: Dana J. Rashid, Katie Newell, Leah Shama, Roger BradleyAbstract:Neurulation in vertebrates is an intricate process requiring extensive alterations in cell contacts and cellular morphologies as the cells in the neural ectoderm shape and form the neural folds and neural tube. Despite these complex interactions, little is known concerning the molecules that mediate cell adhesion within the embryonic neural plate and neural folds. Here, we demonstrate the requirement for NF-protocadherin (NFPC) and its cytosolic partner TAF1/Set for proper neurulation in Xenopus. Both NFPC and TAF1 function in cell-cell adhesion in the neural ectoderm, and disruptions in either NFPC or TAF1 result in a failure of the neural tube to close. This neural tube defect can be attributed to a lack of proper organization of the cells in the dorsal neural folds, manifested by a loss in the columnar epithelial morphology and apical localization of F-actin. However, the epidermal ectoderm is still able to migrate and cover the open neural tube, indicating that the fusions of the neural tube and epidermis are separate events. These studies demonstrate that NFPC and TAF1 function to maintain proper cell-cell interactions within the neural folds and suggest that NFPC and TAF1 participate in novel adhesive mechanisms that contribute to the final events of vertebrate neurulation.
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the cytoplasmic domain of xenopus nf protocadherin interacts with TAF1 set
Developmental Cell, 2003Co-Authors: Mike A Heggem, Roger BradleyAbstract:Protocadherins are members of the cadherin superfamily of cell adhesion molecules proposed to play important roles in early development, but whose mechanisms of action are largely unknown. We examined the function of NF-protocadherin (NFPC), a novel cell adhesion molecule essential for the histogenesis of the embryonic ectoderm in Xenopus, and demonstrate that the cellular protein TAF1, previously identified as a histone-associated protein, binds the NFPC cytoplasmic domain. NFPC and TAF1 coprecipitate from embryo extracts when ectopically expressed, and TAF1 can rescue the ectodermal disruptions caused by a dominant-negative NFPC construct lacking the extracellular domain. Furthermore, disruptions in either NFPC or TAF1 expression, using NFPC- or TAF1-specific antisense morpholinos, result in essentially identical ectodermal defects. These results indicate a role for TAF1 in the differentiation of the embryonic ectoderm, as a cytosolic cofactor of NFPC.
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The Cytoplasmic Domain of Xenopus NF-Protocadherin Interacts with TAF1/Set
Developmental Cell, 2003Co-Authors: Mike A Heggem, Roger BradleyAbstract:Protocadherins are members of the cadherin superfamily of cell adhesion molecules proposed to play important roles in early development, but whose mechanisms of action are largely unknown. We examined the function of NF-protocadherin (NFPC), a novel cell adhesion molecule essential for the histogenesis of the embryonic ectoderm in Xenopus, and demonstrate that the cellular protein TAF1, previously identified as a histone-associated protein, binds the NFPC cytoplasmic domain. NFPC and TAF1 coprecipitate from embryo extracts when ectopically expressed, and TAF1 can rescue the ectodermal disruptions caused by a dominant-negative NFPC construct lacking the extracellular domain. Furthermore, disruptions in either NFPC or TAF1 expression, using NFPC- or TAF1-specific antisense morpholinos, result in essentially identical ectodermal defects. These results indicate a role for TAF1 in the differentiation of the embryonic ectoderm, as a cytosolic cofactor of NFPC.
Mark A. Nelson - One of the best experts on this subject based on the ideXlab platform.
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Evaluation of the effects of the T-type calcium channel enhancer SAK3 in a rat model of TAF1 deficiency.
Neurobiology of disease, 2020Co-Authors: Chinnasamy Dhanalakshmi, Aubin Moutal, Rajesh Khanna, Udaiyappan Janakiraman, Kohji Fukunaga, Mark A. NelsonAbstract:Abstract The TATA-box binding protein associated factor 1 (TAF1) is part of the TFIID complex that plays a key role during the initiation of transcription. Variants of TAF1 are associated with neurodevelopmental disorders. Previously, we found that CRISPR/Cas9 based editing of the TAF1 gene disrupts the morphology of the cerebral cortex and blunts the expression as well as the function of the CaV3.1 (T-type) voltage gated calcium channel. Here, we tested the efficacy of SAK3 (ethyl 8′-methyl-2′, 4-dioxo-2-(piperidin-1-yl)-2′H-spiro [cyclopentane-1, 3′-imidazo [1, 2-a] pyridine]-2-ene-3-carboxylate), a T-type calcium channel enhancer, in an animal model of TAF1 intellectual disability (ID) syndrome. At post-natal day 3, rat pups were subjected to intracerebroventricular (ICV) injection of either gRNA-control or gRNA-TAF1 CRISPR/Cas9 viruses. At post-natal day 21, the rat pups were given SAK3 (0.25 mg/kg, p.o.) or vehicle for 14 days (i.e. till post-natal day 35) and then subjected to behavioral, morphological, and molecular studies. Oral administration of SAK3 (0.25 mg/kg, p.o.) significantly rescued locomotion abnormalities associated with TAF1 gene editing. SAK3 treatment prevented the loss of cortical neurons and GFAP-positive astrocytes observed after TAF1 gene editing. In addition, SAK3 protected cells from apoptosis. SAK3 also restored the Brain-derived neurotrophic factor/protein kinase B/Glycogen Synthase Kinase 3 Beta (BDNF/AKT/GSK3β) signaling axis in TAF1 edited animals. Finally, SAK3 normalized the levels of three GSK3β substrates - CaV3.1, FOXP2, and CRMP2. We conclude that the T-type calcium channel enhancer SAK3 is beneficial against the deleterious effects of TAF1 gene-editing, in part, by stimulating the BDNF/AKT/GSK3β signaling pathway.
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The investigation of the T-type calcium channel enhancer SAK3 in an animal model of TAF1 intellectual disability syndrome.
Neurobiology of Disease, 2020Co-Authors: Udaiyappan Janakiraman, Aubin Moutal, Rajesh Khanna, Lisa Boinon, Chinnasamy Dhanalakshmi, Kohji Fukunaga, Mark A. NelsonAbstract:Abstract T-type calcium channels, in the central nervous system, are involved in the pathogenesis of many neurodegenerative diseases, including TAF1 intellectual disability syndrome (TAF1 ID syndrome). Here, we evaluated the efficacy of a novel T-type Ca2+ channel enhancer, SAK3 (ethyl 8′-methyl-2′, 4-dioxo-2-(piperidin-1-yl)-2′H-spiro [cyclopentane-1, 3′-imidazo [1, 2-a] pyridine]-2-ene-3-carboxylate) in an animal model of TAF1 ID syndrome. At post-natal day 3, rat pups were subjected to intracerebroventricular (ICV) injection of either gRNA-control or gRNA-TAF1 CRISPR/Cas9 viruses. At post-natal day 21 animals were given SAK3 (0.25 mg/kg, p.o.) or vehicle up to post-natal day 35 (i.e. 14 days). Rats were subjected to behavioral, morphological, electrophysiological, and molecular studies. Oral administration of SAK3 (0.25 mg/kg, p.o.) significantly rescued the behavior abnormalities in beam walking test and open field test caused by TAF1 gene editing. We observed an increase in calbindin-positive Purkinje cells and GFAP-positive astrocytes as well as a decrease in IBA1-positive microglia cells in SAK3-treated animals. In addition, SAK3 protected the Purkinje and granule cells from apoptosis induced by TAF-1 gene editing. SAK3 also restored the excitatory post synaptic current (sEPSCs) in TAF1 edited Purkinje cells. Finally, SAK3 normalized the BDNF/AKT signaling axis in TAF1 edited animals. Altogether, these observations suggest that SAK3 could be a novel therapeutic agent for TAF1 ID syndrome.
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TAF1-gene editing impairs Purkinje cell morphology and function
2019Co-Authors: Janakiraman Udaiyappan, Aubin Moutal, Shelby N. Batchelor, Annadurai Anandhan, Rajesh Khanna, Mark A. NelsonAbstract:TAF1 intellectual disability syndrome is an X-linked disorder caused by loss-of-function mutations in the TAF1 gene. How these mutations cause dysmorphology, hypotonia, intellectual and motor defects is unknown. Mouse models which have embryonically targeted TAF1 have failed, possibly due to TAF1 being essential for viability, preferentially expressed in early brain development, and intolerant of mutation. Novel animal models are valuable tools for understanding neuronal pathology. Here, we report the development and characterization of a novel animal model for TAF1 ID syndrome in which the TAF1 gene is deleted in embryonic rats using clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (Cas9) technology and somatic brain transgenesis mediated by lentiviral transduction. Rat pups, post-natal day 3, were subjected to intracerebroventricular (ICV) injection of either gRNA-control or gRNA-TAF1 vectors. Rats were subjected to a battery of behavioral tests followed by histopathological analyses of brains at post-natal day 14 and day 35. TAF1-edited rats exhibited behavioral deficits at both the neonatal and juvenile stages of development. Deletion of TAF1 lead to a hypoplasia and loss of the Purkinje cells. Abnormal motor symptoms in TAF1-edited rats were associated with irregular cerebellar output caused by changes in the intrinsic activity of the Purkinje cells. Immunostaining revealed a reduction in the expression of the CaV3.1 T-type calcium channel. This animal model provides a powerful new tool for studies of neuronal dysfunction in conditions associated with TAF1 abnormalities and should prove useful for developing therapeutic strategies to treat TAF1 ID syndrome.
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TAF1-gene editing alters the morphology and function of the cerebellum and cerebral cortex.
Neurobiology of Disease, 2019Co-Authors: Udaiyappan Janakiraman, Aubin Moutal, Shelby N. Batchelor, Annadurai Anandhan, Rajesh Khanna, Dhanalakshmi Chinnasamy, Lisa Boinon, Mark A. NelsonAbstract:Abstract TAF1/MRSX33 intellectual disability syndrome is an X-linked disorder caused by loss-of-function mutations in the TAF1 gene. How these mutations cause dysmorphology, hypotonia, intellectual and motor defects is unknown. Mouse models which have embryonically targeted TAF1 have failed, possibly due to TAF1 being essential for viability, preferentially expressed in early brain development, and intolerant of mutation. Novel animal models are valuable tools for understanding neuronal pathology. Here, we report the development and characterization of a novel animal model for TAF1 ID syndrome in which the TAF1 gene is deleted in embryonic rats using clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (Cas9) technology and somatic brain transgenesis mediated by lentiviral transduction. Rat pups, post-natal day 3, were subjected to intracerebroventricular (ICV) injection of either gRNA-control or gRNA-TAF1 vectors. Rats were subjected to a battery of behavioral tests followed by histopathological analyses of brains at post-natal day 14 and day 35. TAF1-edited rats exhibited behavioral deficits at both the neonatal and juvenile stages of development. Deletion of TAF1 lead to a hypoplasia and loss of the Purkinje cells. We also observed a decreased in GFAP positive astrocytes and an increase in Iba1 positive microglia within the granular layer of the cerebellum in TAF1-edited animals. Immunostaining revealed a reduction in the expression of the CaV3.1 T-type calcium channel. Abnormal motor symptoms in TAF1-edited rats were associated with irregular cerebellar output caused by changes in the intrinsic activity of the Purkinje cells due to loss of pre-synaptic CaV3.1. This animal model provides a powerful new tool for studies of neuronal dysfunction in conditions associated with TAF1 abnormalities and should prove useful for developing therapeutic strategies to treat TAF1 ID syndrome.
Tetsuro Kokubo - One of the best experts on this subject based on the ideXlab platform.
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The function of Spt3, a subunit of the SAGA complex, in PGK1 transcription is restored only partially when reintroduced by plasmid into TAF1 spt3 double mutant yeast strains.
Genes & Genetic Systems, 2020Co-Authors: Ryo Iwami, Naoki Takai, Tetsuro KokuboAbstract:In Saccharomyces cerevisiae, class II gene promoters contain two classes of TATA elements: the TATA box and the TATA-like element. Functional loss of TFIID and SAGA transcription complexes selectively impacts steady-state mRNA levels expressed from TATA-like element-containing (i.e., TATA-less) and TATA box-containing promoters, respectively. While nascent RNA analysis has revealed that TFIID and SAGA are required for both types of promoters, the division of their roles remains unclear. We show here that transcription from the PGK1 promoter decreased in some cases by more than half after disruption of the TATA box or SPT3 (spt3Δ), whereas spt3Δ did not affect transcription from the TATA-less promoter, consistent with the prevailing view that Spt3 functions specifically in a TATA box-dependent manner. Transcription from this promoter was abolished in the spt3Δ TAF1-N568Δ strain but unaffected in the TAF1-N568Δ strain, regardless of TATA box presence, suggesting that TFIID was functionally dispensable for PGK1 transcription at least in the SPT3 strain. Furthermore, transcription from the TATA box-containing PGK1 promoter was slightly reduced in the TAF1 strain lacking TAND (TAF1-ΔTAND) upon temperature shift from 25 to 37 °C, with restoration to normal levels within 2 h, in an Spt3-dependent manner. Interestingly, when SPT3 was reintroduced into the spt3Δ TAF1, spt3Δ TAF1-N568Δ or spt3Δ TAF1-ΔTAND strain, TATA box-dependent transcription from this promoter was largely restored, but TFIID independence in transcription was not restored, especially from the TATA-less promoter, and transient TAND/Spt3-dependent fluctuations of transcription after the temperature shift were also not recapitulated. Collectively, these observations suggest that Spt3 has multiple functions in PGK1 transcription, some of which may be intimately connected to TAF1 function and may therefore become unrestorable when the TFIID and SAGA functions are simultaneously compromised.
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High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation
Nature Structural & Molecular Biology, 2013Co-Authors: Madhanagopal Anandapadamanaban, Tetsuro Kokubo, Yoshifumi Ohyama, Cecilia Andresen, Sara Helander, Marina I Siponen, Patrik Lundström, Mitsuhiko Ikura, Martin Moche, Maria SunnerhagenAbstract:The general transcription factor TFIID comprises TATA-binding protein (TBP) and TBP-associated factors (TAFs). The high-resolution structure of yeast TBP in complex with yeast TAF1 containing both transcriptionally activating and repressing regions reveals detailed and specific molecular patterns of interactions with TBP and their significance for transcriptional regulation. The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 Å) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 bound to yeast TBP, together with mutational data. We find that yeast TAF1-TAND1, which in itself acts as a transcriptional activator, binds TBP's concave DNA-binding surface by presenting similar anchor residues to TBP as does Mot1 but from a distinct structural scaffold. Furthermore, we show how TAF1-TAND2 uses an aromatic and acidic anchoring pattern to bind a conserved TBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides insight into the competitive multiprotein TBP interplay critical to transcriptional regulation.
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Saccharomyces cerevisiae Ssd1p promotes CLN2 expression by binding to the 5′‐untranslated region of CLN2 mRNA
Genes to Cells, 2010Co-Authors: Yoshifumi Ohyama, Koji Kasahara, Tetsuro KokuboAbstract:In Saccharomyces cerevisiae, TFIID, which is composed of TATA-binding protein (TBP) and a set of TBP-associated factors (TAFs), mediates the transcription of most class II genes. Previous studies have shown that CLN2 expression was significantly reduced by TAF1–ts2, but not by TAF1-N568Δ, although both mutations display similar temperature-sensitive growth phenotypes and transcriptional defects in other genes. Here, we show that the reduced expression of CLN2 is not because of differences in TAF1 alleles in the previous experiments but because of allelic differences at the SSD1 locus in the host strains. Specifically, ssd1-d reduces CLN2 expression when combined with TAF1. Ssd1p expressed from SSD1-V, but not from ssd1-d, stabilizes a subpopulation of CLN2 mRNA in wild-type and TAF1-N568Δ strains and facilitates the continuous transcription of CLN2 after heat shock in the TAF1-N568Δ strain. Reporter assays show that both activities appear to depend on the 5′-untranslated region of CLN2 mRNA and that Ssd1p binds to this region via its amino- and carboxy-terminal domains. Based on these observations, we propose a model for the action of Ssd1p and discuss its biologic role.
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In vivo synthesis of TAF1p lacking the TAF N‐terminal domain using alternative transcription or translation initiation sites
Genes to Cells, 2004Co-Authors: Koji Kasahara, Masashi Kawaichi, Tetsuro KokuboAbstract:The TAF N-terminal domain (TAND) of TAF1 includes two subdomains, TAND1 and TAND2, which bind to the concave and convex surfaces of TBP, respectively. Previous studies showed that the substitution of yeast TAND1 or TAND2 with the equivalent domain from a Drosophila homologue leads to accumulation of truncated TAF1p in yeast. This study demonstrates that these truncated TAF1p derivatives lack TAND. However, full-length TAF1p and untruncated derivatives are produced in yeast when several Met-to-Ala mutations are introduced in the carboxy-terminus of TAND. In contrast, mutations that reduce expression of full-length TAF1 do not reduce the amount of truncated TAF1p derivatives that are produced. These data suggest that TAND-deficient TAF1 derivatives are produced by initiating translation at alternative initiation sites. In addition, the TAF1 mRNA structure suggests that the TAND-deficient TAF1 derivatives may also be formed in yeast by use of (cryptic) alternative transcription initiation sites. Importantly, TAND-deficient truncated TAF1p appears to be produced at a low level in wild-type yeast as well. Finally, this study also demonstrates that Drosophila TAND2 substitutes functionally for yeast TAND2, but Drosophila TAND1 does not substitute for yeast TAND1.
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mutations in the histone fold domain of the TAF12 gene show synthetic lethality with the TAF1 gene lacking the taf n terminal domain tand by different mechanisms from those in the spt15 gene encoding the tata box binding protein tbp
Nucleic Acids Research, 2003Co-Authors: Akiko Kobayashi, Tsuyoshi Miyake, Masashi Kawaichi, Tetsuro KokuboAbstract:The general transcription factor TFIID, composed of the TATA box-binding protein (TBP) and 14 TBP-associated factors (TAFs), is important for both basal and regulated transcription by RNA polymerase II. Although it is well known that the TAF N-terminal domain (TAND) at the amino-terminus of the TAF1 protein binds to TBP and thereby inhibits TBP function in vitro, the physiological role of this domain remains obscure. In our previous study, we screened for mutations that cause lethality when co-expressed with the TAF1 gene lacking TAND (TAF1-ΔTAND) and identified two ΔTAND synthetic lethal (nsl) mutations as those in the SPT15 gene encoding TBP. In this study we isolated another nsl mutation in the same screen and identified it to be a mutation in the histone fold domain (HFD) of the TAF12 gene. Several other HFD mutations of this gene also exhibit nsl phenotypes, and all of them are more or less impaired in transcriptional activation in vivo. Interestingly, a set of genes affected in the TAF1-ΔTAND mutant is similarly affected in the TAF12 HFD mutants but not in the nsl mutants of TBP. Therefore, we discovered that the nsl mutations of these two genes cause lethality in the TAF1-ΔTAND mutant by different mechanisms.
Elisabeth Scheer - One of the best experts on this subject based on the ideXlab platform.
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Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID
eLife, 2017Co-Authors: Kapil Gupta, Elisabeth Scheer, Aleksandra A Watson, Tiago Baptista, Anna L Chambers, Christine Koehler, Juan Zou, Ima Obong-ebong, Eaazhisai Kandiah, Arturo TembladorAbstract:General transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. We identified a ternary complex formed by TBP and the histone fold (HF) domain-containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1 previously implicated in TATA-box mimicry. In an integrative approach combining crystal coordinates, biochemical analyses and data from cross-linking mass-spectrometry (CLMS), we determine the architecture of the TAF11/TAF13/TBP complex, revealing TAF11/TAF13 interaction with the DNA binding surface of TBP. We identify a highly conserved C-terminal TBP-interaction domain (CTID) in TAF13, which is essential for supporting cell growth. Our results thus have implications for cellular TFIID assembly and suggest a novel regulatory state for TFIID function.
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Cytoplasmic TAF2–TAF8–TAF10 complex provides evidence for nuclear holo–TFIID assembly from preformed submodules
Nature Communications, 2015Co-Authors: Simon Trowitzsch, Gabor Papai, Christiane Schaffitzel, Elisabeth Scheer, Cristina Viola, Sascha Conic, Virginie Chavant, Marjorie Fournier, Ima-obong Ebong, Matthias HaffkeAbstract:General transcription factor TFIID is a cornerstone of RNA polymerase II transcription initiation in eukaryotic cells. How human TFIID—a megadalton-sized multiprotein complex composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs)—assembles into a functional transcription factor is poorly understood. Here we describe a heterotrimeric TFIID subcomplex consisting of the TAF2, TAF8 and TAF10 proteins, which assembles in the cytoplasm. Using native mass spectrometry, we define the interactions between the TAFs and uncover a central role for TAF8 in nucleating the complex. X-ray crystallography reveals a non-canonical arrangement of the TAF8–TAF10 histone fold domains. TAF2 binds to multiple motifs within the TAF8 C-terminal region, and these interactions dictate TAF2 incorporation into a core–TFIID complex that exists in the nucleus. Our results provide evidence for a stepwise assembly pathway of nuclear holo–TFIID, regulated by nuclear import of preformed cytoplasmic submodules. TFIID is an essential transcription factor complex that controls the expression of most protein-coding genes in eukaryotes. Here the authors identify and characterize a complex containing TAF2, TAF8 and TAF10, which assembles in the cytoplasm before integration into the nuclear holo–TFIID complex.
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tfiid taf6 taf9 complex formation involves the heat repeat containing c terminal domain of taf6 and is modulated by taf5 protein
Journal of Biological Chemistry, 2012Co-Authors: Elisabeth Scheer, Laszlo Tora, Frédéric Delbac, Dino Moras, Christophe RomierAbstract:The general transcription factor TFIID recognizes specifically the core promoter of genes transcribed by eukaryotic RNA polymerase II, nucleating the assembly of the preinitiation complex at the transcription start site. However, the understanding in molecular terms of TFIID assembly and function remains poorly understood. Histone fold motifs have been shown to be extremely important for the heterodimerization of many TFIID subunits. However, these subunits display several evolutionary conserved noncanonical features when compared with histones, including additional regions whose role is unknown. Here we show that the conserved additional C-terminal region of TFIID subunit TAF6 can be divided into two domains: a small middle domain (TAF6M) and a large C-terminal domain (TAF6C). Our crystal structure of the TAF6C domain from Antonospora locustae at 1.9 Å resolution reveals the presence of five conserved HEAT repeats. Based on these data, we designed several mutants that were introduced into full-length human TAF6. Surprisingly, the mutants affect the interaction between TAF6 and TAF9, suggesting that the formation of the complex between these two TFIID subunits do not only depend on their histone fold motifs. In addition, the same mutants affect even more strongly the interaction between TAF6 and TAF9 in the context of a TAF5-TAF6-TAF9 complex. Expression of these mutants in HeLa cells reveals that most of them are unstable, suggesting their poor incorporation within endogenous TFIID. Taken together, our results suggest that the conserved additional domains in histone fold-containing subunits of TFIID and of co-activator SAGA are important for the assembly of these complexes.
Edith H Wang - One of the best experts on this subject based on the ideXlab platform.
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Zinc knuckle of TAF1 is a DNA binding module critical for TFIID promoter occupancy
Nature Publishing Group, 2018Co-Authors: Elizabeth C Curran, Hui Wang, Thomas R Hinds, Ning Zheng, Edith H WangAbstract:Abstract The general transcription factor IID (TFIID) is the first component of the preinitiation complex (PIC) to bind the core promoter of RNA polymerase II transcribed genes. Despite its critical role in protein-encoded gene expression, how TFIID engages promoter DNA remains elusive. We have previously revealed a winged-helix DNA-binding domain in the N-terminal region of the largest TFIID subunit, TAF1. Here, we report the identification of a second DNA-binding module in the C-terminal half of human TAF1, which is encoded by a previously uncharacterized conserved zinc knuckle domain. We show that the TAF1 zinc knuckle aids in the recruit of TFIID to endogenous promoters vital for cellular proliferation. Mutation of the TAF1 zinc knuckle with defects in DNA binding compromises promoter occupancy of TFIID, which leads to a decrease in transcription and cell viability. Together, our studies provide a foundation to understand how TAF1 plays a central role in TFIID promoter binding and regulation of transcription initiation
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Crystal structure of a TAF1-TAF7 complex in human transcription factor IID reveals a promoter binding module
Cell Research, 2014Co-Authors: Hui Wang, Elizabeth C Curran, Thomas R Hinds, Edith H Wang, Ning ZhengAbstract:The general transcription factor IID (TFIID) initiates RNA polymerase II-mediated eukaryotic transcription by nucleating pre-initiation complex formation at the core promoter of protein-encoding genes. TAF1, the largest integral subunit of TFIID, contains an evolutionarily conserved yet poorly characterized central core domain, whose specific mutation disrupts cell proliferation in the temperature-sensitive mutant hamster cell line ts 13. Although the impaired TAF1 function in the ts 13 mutant has been associated with defective transcriptional regulation of cell cycle genes, the mechanism by which TAF1 mediates transcription as part of TFIID remains unclear. Here, we present the crystal structure of the human TAF1 central core domain in complex with another conserved TFIID subunit, TAF7, which biochemically solubilizes TAF1. The TAF1-TAF7 complex displays an inter-digitated compact architecture, featuring an unexpected TAF1 winged helix (WH) domain mounted on top of a heterodimeric triple barrel. The single TAF1 residue altered in the ts 13 mutant is buried at the junction of these two structural domains. We show that the TAF1 WH domain has intrinsic DNA-binding activity, which depends on characteristic residues that are commonly used by WH fold proteins for interacting with DNA. Importantly, mutations of these residues not only compromise DNA binding by TAF1, but also abrogate its ability to rescue the ts 13 mutant phenotype. Together, our results resolve the structural organization of the TAF1-TAF7 module in TFIID and unveil a critical promoter-binding function of TAF1 in transcription regulation.
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Phosphorylation-dependent regulation of cyclin D1 and cyclin A gene transcription by TFIID subunits TAF1 and TAF7.
Molecular and Cellular Biology, 2012Co-Authors: Susan L. Kloet, Jennifer L. Whiting, Phil Gafken, Jeff Ranish, Edith H WangAbstract:The largest transcription factor IID (TFIID) subunit, TBP-associated factor 1 (TAF1), possesses protein kinase and histone acetyltransferase (HAT) activities. Both enzymatic activities are essential for transcription from a subset of genes and G1 progression in mammalian cells. TAF7, another TFIID subunit, binds TAF1 and inhibits TAF1 HAT activity. Here we present data demonstrating that disruption of the TAF1/TAF7 interaction within TFIID by protein phosphorylation leads to activation of TAF1 HAT activity and stimulation of cyclin D1 and cyclin A gene transcription. Overexpression and small interfering RNA knockdown experiments confirmed that TAF7 functions as a transcriptional repressor at these promoters. Release of TAF7 from TFIID by TAF1 phosphorylation of TAF7 increased TAF1 HAT activity and elevated histone H3 acetylation levels at the cyclin D1 and cyclin A promoters. Serine-264 of TAF7 was identified as a substrate for TAF1 kinase activity. Using TAF7 S264A and S264D phosphomutants, we determined that the phosphorylation state of TAF7 at S264 influences the levels of cyclin D1 and cyclin A gene transcription and promoter histone H3 acetylation. Our studies have uncovered a novel function for the TFIID subunit TAF7 as a phosphorylation-dependent regulator of TAF1-catalyzed histone H3 acetylation at the cyclin D1 and cyclin A promoters.
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TAF1 histone acetyltransferase activity in Sp1 activation of the cyclin D1 promoter.
Molecular and Cellular Biology, 2005Co-Authors: Traci L. Hilton, Elizabeth L. Dunphy, Edith H WangAbstract:A missense mutation within the histone acetyltransferase (HAT) domain of the TATA binding protein-associated factor TAF1 induces ts13 cells to undergo a late G1 arrest and decreases cyclin D1 transcription. We have found that TAF1 mutants (Δ844-850 and Δ848-850, from which amino acids 844 through 850 and 848 through 850 have been deleted, respectively) deficient in HAT activity are unable to complement the ts13 defect in cell proliferation and cyclin D1 transcription. Chromatin immunoprecipitation assays revealed that histone H3 acetylation was reduced at the cyclin D1 promoter but not the c-fos promoter upon inactivation of TAF1 in ts13 cells. The hypoacetylation of H3 at the cyclin D1 promoter was reversed by treatment with trichostatin A (TSA), a histone deacetylase inhibitor, or by expression of TAF1 proteins that retain HAT activity. Transcription of a chimeric promoter containing the Sp1 sites of cyclin D1 and c-fos core remained TAF1 dependent in ts13 cells. Treatment with TSA restored full activity to the cyclin D1-c-fos chimera at 39.5°C. In vivo genomic footprinting experiments indicate that protein-DNA interactions at the Sp1 sites of the cyclin D1 promoter were compromised at 39.5°C in ts13 cells. These data have led us to hypothesize that TAF1-dependent histone acetylation facilitates transcription factor binding to the Sp1 sites, thereby activating cyclin D1 transcription and ultimately G1-to-S-phase progression.
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Transcription Factor IID Recruitment and Sp1 Activation DUAL FUNCTION OF TAF1 IN CYCLIN D1 TRANSCRIPTION
Journal of Biological Chemistry, 2003Co-Authors: Traci L. Hilton, Edith H WangAbstract:Cyclin D1 is an oncogene that regulates progression through the G(1) phase of the cell cycle. A temperature-sensitive missense mutation in the transcription factor TAF1/TAF(II)250 induces the mutant ts13 cells to arrest in late G(1) by decreasing transcription of cell cycle regulators, including cyclin D1. Here we provide evidence that TAF1 serves two independent functions, one at the core promoter and one at the upstream activating Sp1 sites of the cyclin D1 gene. Using in vivo genomic footprinting, we have identified protein-DNA interactions within the cyclin D1 core promoter that are disrupted upon inactivation of TAF1 in ts13 cells. This 33-bp segment, which we termed the TAF1-dependent element 1 (TDE1), contains an initiation site that displays homology to the consensus motif and is sufficient to confer a requirement for TAF1 function. Electrophoretic mobility shift assays reveal that binding of ts13-TAF1-containing TFIID complexes to the cyclin D1 TDE1 occurs at 25 degrees C but not at 37 degrees C in vitro and involves the initiator element. Temperature-dependent DNA binding activity is also observed for TAF1-TAF2 heterodimers assembled with the ts13 mutant but not the wild-type TAF1 protein. These data suggest that a function of TAF is required for the interaction of TFIID with the cyclin D1 initiator. Our finding that recruitment of TFIID, by insertion of a TBP binding site upstream of the TDE1, restores basal but not activated transcription supports the model that TAF1 carries out two independent functions at the cyclin D1 promoter.
