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1 TFIID assists in nucleating PIC formation, completed by
2 TFIID binds promoter DNA to recruit RNA polymerase II an
3 TFIID comprises the TATA-binding protein (TBP) and 13 TB
4 TFIID depletion can be complemented in vitro by addition
5 TFIID is recruited to the promoter through DTIE but is d
6 TFIID, a megadalton-sized multiprotein complex comprisin
7 TFIID-a complex of TATA-binding protein (TBP) and TBP-as
10 at the SAGA Taf and Taf-like subunits form a TFIID-like core complex at the center of SAGA that makes
11 myotubes, the cells undergo a switch from a TFIID-based transcription system to a TRF3-TAF3-based sy
12 clude that TAF7, until now considered only a TFIID component and regulator of TAF1-dependent transcri
13 clearly define the human Pol II promoter: a TFIID binding site with built-in downstream information
14 yeast TFIIA in the integration of activator-TFIID contacts with promoter conformation and downstream
15 tep toward structurally dissecting activator/TFIID interactions, we determined the three-dimensional
16 in the presence of a taf1 mutation affecting TFIID activity that otherwise blocks HO transcription.
19 ed SAGA (Spt-Ada-Gcn5-acetyltransferase) and TFIID (Transcription factor-IID)-dependent mechanisms of
21 We show that promoters of SAGA-dominated and TFIID-dominated genes can be statistically distinguished
23 ochemical studies have shown that Pol II and TFIID (transcription factor IID) contact overlapping reg
25 tor required for Sp1 activation/Mediator and TFIID complexes at both the RNA and protein level, and t
26 re consistent with a model in which PRC1 and TFIID could co-occupy genes poised for activation during
29 st different implementations of the SAGA and TFIID assembly pathways that may depend upon whether a s
30 n and the relative contributions of SAGA and TFIID at genes regulated by both complexes have not been
38 nding of both TATA binding protein (TBP) and TFIID to the TATA box of core promoters and ICP4 has bee
41 onstrated that promoters of both classes are TFIID dependent, in agreement with recent in vivo findin
43 pon depletion of Kin28 is more pronounced at TFIID-dominated promoters compared to SAGA-dominated pro
44 ion with BTAF1, hence the formation of the B-TFIID complex, and its dynamic cycling on and off of DNA
46 est a mechanism for how interactions between TFIID, TFIIA, and Rap1 contribute to the high rate of tr
47 atistical PIC preferences of binding to both TFIID-dominated and SAGA-dominated genes correlate with
49 , we find that TFIID is associated with both TFIID- and SAGA-dependent genes and that TFIID and Media
50 g arrests an isomerization of promoter-bound TFIID that is required for the engagement of Pol II duri
51 cription factors rapidly bind promoter-bound TFIID-TFIIA, after which complexes undergo a slow isomer
57 ernative core factor TAF3, but not canonical TFIID subunits, away from the nuclear periphery, where t
59 complex is required to replace the canonical TFIID to recapitulate MyoD-dependent activation of Myoge
61 results thus have implications for cellular TFIID assembly and suggest a novel regulatory state for
62 of TFIID by rapid depletion of S. cerevisiae TFIID subunits and measurement of changes in nascent tra
66 ltisubunit core promoter recognition complex TFIID in vivo requires knowledge of how individual subun
67 ole in the core promoter recognition complex TFIID, genome-wide binding studies reveal that TAF3 loca
72 ed RNA polymerase II transcription factor D (TFIID) complex is composed of TATA box-binding protein (
76 ng purified PRC1, transcription factor II D (TFIID), and Mediator indicate that PRC1 blocks the recru
79 of the genome can be characterized as either TFIID- or SAGA-dominant, it is expected that many genes
82 Pol II initiation complex and then exchanges TFIID for complexes containing ELL/EAF and P-TEFb to fac
83 as well as a mechanism involving facilitated TFIID binding through direct interaction with an E-prote
93 d Taf1 for a subunit of transcription factor TFIID that serves as a multifunctional transcriptional r
94 pted the binding of the transcription factor TFIID, the major component of the pre-initiation complex
99 genes, such as RPS5, RPL2B, and RPS11B, for TFIID recruitment to initiate transcription, and the rec
100 sses and better defines the binding site for TFIID and is surprisingly invariant over a wide range of
105 well as general transcription factors (e.g., TFIID, TFIIB, and Mediator) for antisense transcription
106 factors that govern Pol II initiation (e.g., TFIID, TFIIH, and Mediator), pausing, and elongation (e.
107 that H3K4me3-TAF3 interactions direct global TFIID recruitment to active genes, some of which are p53
110 systematic characterization of the HNF4alpha-TFIID link revealed that the HNF4alpha DNA-binding domai
113 a stepwise assembly pathway of nuclear holo-TFIID, regulated by nuclear import of preformed cytoplas
120 xamined changes in transcription factor IID (TFIID) and cofactor required for Sp1 activation/Mediator
128 a gene-specific role for the TAFH domain in TFIID recruitment and activation of a large subset of ge
129 nd its TBP-interacting region are similar in TFIID, whereas Taf5 and the Taf6 HEAT domain adopt disti
132 hese general transcription factors including TFIID, BAF, and Mediator may facilitate global changes i
133 studies reveal that TAF4b incorporation into TFIID induces an open conformation at the lobe involved
137 bsence of NuA4, ribosomal protein genes lose TFIID dependency and become SAGA dependent for transcrip
138 e functions of the TAF subunits of mammalian TFIID in physiological processes remain poorly character
144 In addition, purified Taf2-DeltaC mutant TFIID is devoid of Taf14, making this variant a powerful
145 either Mediator, the activator Gal4-V16, nor TFIID specifically compensate for the low transcription
148 reviously proposed, with limiting amounts of TFIID-TBP being required to promote muscle-specific gene
151 gly, we found that while promoter binding of TFIID and TFIIA is stable, promoter binding by TFIIB is
158 required for interactions with components of TFIID and mediator and, as a consequence, are necessary
159 ggest that ICP4 interacts with components of TFIID and Mediator in the context of viral infection, an
160 as not found in complexes with components of TFIID and mediator, suggesting that the defect in RNA po
161 ors can interact with multiple components of TFIID, it is unknown whether common or distinct surfaces
163 e the effects of changing the composition of TFIID in a simple system, we depleted TATA box-binding p
164 on with extracts made from cells depleted of TFIID subunit Taf1 demonstrated that promoters of both c
165 -containing promoters, which are depleted of TFIID, a +1 nucleosome was positioned to be in competiti
166 have revealed significant downregulation of TFIID subunits in terminally differentiated myocytes, he
167 act may induce unique structural features of TFIID, thus providing nanoscale information on activator
168 ucturally and functionally distinct forms of TFIID suggests that the different conformers may serve a
171 f H4) promotes transcriptional initiation of TFIID (a complex of TBP and TBP-associated factors [TAFs
176 developmental stage-specific organization of TFIID or SAGA complexes, in unicellular genomes, however
177 Here we report that TAF7L, a paralogue of TFIID subunit TAF7, is enriched in adipocytes and white
178 moter recognition complex takes the place of TFIID in adult hepatocytes and to uncover the mechanisms
181 n a Deltaeaf1 strain depletes recruitment of TFIID (a TAF-dependent form of TBP) but not the TAF-inde
182 otein genes to facilitate the recruitment of TFIID for transcriptional stimulation, hence providing a
184 he conserved additional C-terminal region of TFIID subunit TAF6 can be divided into two domains: a sm
186 ides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcr
188 tates the formation of a rearranged state of TFIID that enables promoter recognition and binding.
190 termined the three-dimensional structures of TFIID bound to three distinct activators (i.e., the tumo
191 gh the TATA-binding protein (TBP) subunit of TFIID is necessary and sufficient for in vitro transcrip
192 on in mice, we show that the TAF4 subunit of TFIID is required for post-natal hepatocyte maturation.
194 nding protein-associated factor) subunits of TFIID alter the kinetic mechanism by which complexes ass
195 mains in histone fold-containing subunits of TFIID and of co-activator SAGA are important for the ass
197 tively the Taf4, Taf5, and Taf12 subunits of TFIID represent the physical and functional targets for
198 ors 1 and 7 (TAF1 and TAF7), two subunits of TFIID, are integral to the regulation of eukaryotic tran
200 omoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions w
201 ver, the understanding in molecular terms of TFIID assembly and function remains poorly understood.
205 AL10 antisense transcription is dependent on TFIID, its sense transcription does not require TFIID.
208 through this interaction, can target TBP or TFIID to promoters containing HNF4alpha-binding sites in
209 P4 to stabilize the binding of either TBP or TFIID to the TATA box of representative early, late, and
213 ng with Mediator, but leaves TBP and perhaps TFIID intact, highlighting a specific mechanism for PRC1
214 ure/function relationships of the prototypic TFIID versus 4b/4-IID, we have compared their 3D structu
215 hat the MTE promotes the binding of purified TFIID to the core promoter and that the TAF6 and TAF9 su
216 of assemblies generated with purified Rap1, TFIID, and TFIIA on RPG enhancer-promoter DNA indicate t
218 RPG enhancer-promoter DNA indicate that Rap1-TFIID interaction induces dramatic conformational rearra
219 IID-dependent' are highly sensitive to rapid TFIID depletion and insensitive to rapid SAGA depletion.
221 t by targeting the core promoter recognition TFIID complex and aiding in its recruitment to promoter
222 to uncover the mechanisms that down-regulate TFIID during this critical developmental transition.
226 t involving SAGA and then involving a slower TFIID recruitment, whereas heat shock genes utilize the
227 ith in vitro studies, we found that specific TFIID subunits, in addition to cross-linking at the core
228 ssed by overexpression of the yeast-specific TFIID subunit TAF14 but not by overexpression of any oth
229 functional INR, ICP4 can no longer stabilize TFIID binding to the TATA box of the late promoter and r
230 s TFIID's ability to bind DNA by stabilizing TFIID contacts with both the core promoter and a region
232 tion and transcription; and (3) H3K4me3-TAF3/TFIID interactions regulate gene-selective functions of
233 s, NuA4 plays an important role in targeting TFIID to the promoters of ribosomal protein genes for tr
234 SS selection, in contrast with canonical TBP/TFIID-driven TATA-less promoters that have broader TSS a
235 maining 87% of expressed genes that we term 'TFIID-dependent' are highly sensitive to rapid TFIID dep
237 d Hmo1), the transcription machinery (TFIIB, TFIID, and RNA polymerase II), and chromatin at near-bas
238 erase II and protein complexes TFIIA, TFIIB, TFIID (or TBP), TFIIE, TFIIF, TFIIH and TFIIK were posit
241 ingle-molecule imaging data demonstrate that TFIID alone binds poorly to native p53 target promoters.
242 the same approach to map TFIID, we find that TFIID is associated with both TFIID- and SAGA-dependent
246 -molecule dissociation kinetics reveals that TFIID interacts with promoters via transient and prolong
247 mportantly, our structural work reveals that TFIID's conversion to a rearranged DNA binding conformat
248 on, based on recent structural studies, that TFIID may not remain bound to gene promoters through the
250 lishing a specific regulatory network at the TFIID-dependent promoter for productive transcriptional
252 tational and transcriptional analyses at the TFIID-dependent ribosomal protein genes such as RPS5, RP
253 imentally validated binding site, called the TFIID localization sequence (DLS) and found three times
254 tions in developmental transcription for the TFIID basal transcription factors and for the DNA core p
255 dies have uncovered a novel function for the TFIID subunit TAF7 as a phosphorylation-dependent regula
262 nt, pausing was lost upon replacement of the TFIID complex with TATA-binding protein (TBP), and PRO-s
263 l to the core promoter and regulators of the TFIID pathway located proximally, and (5) distinct mobil
266 iously shown that Rap1 directly binds to the TFIID complex through interaction with its TATA-binding
267 e SAGA transcription pathway compared to the TFIID pathway, (2) new regulators enriched at tRNA genes
270 CREB showed facilitated interaction with the TFIID subunit coactivator TAF4 assessed by immunoprecipi
271 n (TBP)-associated factors (TAFs) within the TFIID complex and counteracts negative regulators of TBP
274 on how Taf2-Taf14 interaction contributes to TFIID complex organization and identifying a potential r
278 e formation of the complex between these two TFIID subunits do not only depend on their histone fold
285 d DNA sequence that probably associates with TFIID but detected no evidence of RNA secondary structur
286 a molecular switch that interacts first with TFIID in the Pol II initiation complex and then exchange
287 ers and ICP4 has been shown to interact with TFIID, we tested the ability of ICP4 to stabilize the bi
289 ated in the PIC through its interaction with TFIID but is released from TFIID upon transcription init
290 tivation domain, mediating interactions with TFIID, mediator, and perhaps other transcription factors
291 assays reveal that ERCC1-XPF interacts with TFIID and assembles with POL II and the basal transcript
293 eans by which p53 dynamically interacts with TFIID to facilitate assembly on target gene promoters re
294 TBP, Pol II, and other Mediator modules with TFIID-dependent genes is largely independent of the tail
295 e regulation, its structural similarity with TFIID, and functional interactions between the SAGA modu
296 sruption of the TAF1/TAF7 interaction within TFIID by protein phosphorylation leads to activation of
298 vide evidence that SAGA, not TAF(II)s within TFIID, are largely responsible for TBP recruitment.
299 n whether common or distinct surfaces within TFIID are targeted by activators and what changes if any