RNA Polymerase II and TAFs Undergo a Slow Isomerization after the Polymerase Is Recruited to Promoter-Bound TFIID

Yakovchuk, Petro; Gilman, Benjamin; Goodrich, James A.; Kugel, Jennifer F.

doi:10.1016/j.jmb.2010.01.025

Cited by 25 publications

(24 citation statements)

References 56 publications

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“…The apparent minor clash between the RBP5 Pol II subunit and the promoter-bound TAF1 suggest that a structural reorganization must occur prior to promoter engagement by Pol II. This proposal agrees with time-course DNA footprinting analysis showing a structural isomerization following the addition of Pol II-TFIIB-TFIIF to the promoter-bound TFIID-TFIIA complex [37]. …”

Section: Proposed Model For Tfiid Interaction With the Rest Of The Picsupporting

confidence: 88%

Towards a mechanistic understanding of core promoter recognition from cryo-EM studies of human TFIID

Nogales

Patel

Louder

2017

Current Opinion in Structural Biology

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TFIID is a critical component of the eukaryotic transcription pre-initiation complex (PIC) required for the recruitment of RNA Pol II to the start site of protein-coding genes. Within the PIC, TFIID’s role is to recognize and bind core promoter sequences and recruit the rest of the PIC components. Due to its size and its conformational complexity, TFIID poses a serious challenge for structural characterization. The limited amounts of purified TFIID that can be obtained by present methods of purification from endogenous sources has limited structural studies to cryo-EM visualization, which requires very small amounts of sample. Previous cryo-EM studies have shed light on how the extreme conformational flexibility of TFIID is involved in core promoter DNA binding. Recent progress in cryo-EM methodology has facilitated a parallel progress in the study of human TFIID, leading to an improvement in resolution and the identification of the structural elements in the complex directly involved in DNA interaction. While many questions remain unanswered, the present structural knowledge of human TFIID suggests a mechanism for the sequential engagement with different core promoter sequences and how it could be influenced by regulatory factors.

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Section: Proposed Model For Tfiid Interaction With the Rest Of The Picsupporting

confidence: 88%

Towards a mechanistic understanding of core promoter recognition from cryo-EM studies of human TFIID

Nogales

Patel

Louder

2017

Current Opinion in Structural Biology

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“…Indeed, it has been found that upon recruitment of Pol II, promoter-bound TFIID undergoes an isomerization in which the TFIID contacts with promoter DNA downstream of the +10 position are released concomitantly with the engagement of the promoter DNA with Pol II upstream of this position 43 . Those findings can be mapped onto our model (Fig.…”

Section: Taf-less Pic Structure and Full Pic Modelmentioning

confidence: 99%

Structure of promoter-bound TFIID and model of human pre-initiation complex assembly

Louder

López‐Blanco

et al. 2016

Nature

212

266

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The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the core promoter. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAF1-13), which specifically interact with a variety of core promoter DNA sequences. Here we present the structure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-electron microscopy (cryo-EM) at sub-nanometer resolution. All core promoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions with the downstream promoter. TFIIA bridges the TBP-TATA complex with lobe B of TFIID. We also present the cryo-EM reconstruction of a fully-assembled human TAF-less PIC. Superposition of common elements between the two structures provides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcription initiation.

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“…Given that TFIID has been known to exist in multiple conformers that footprint across the TSS (reviewed in ref. 35) and that a slow isomerization of TFIID has been shown to be rate-limiting for pol II transcription in vitro (36), it seems reasonable that this step may be rate-limiting at a subset of promoters in vivo. Therefore, eliminating this rate-limiting step by depleting TAFs from the cell may facilitate a higher transcription-initiation rate.…”

Section: Discussionmentioning

confidence: 99%

Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription

Pennington

Marr

Chirn

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Transcription factor (TF)IID is a central player in activated transcription initiation. Recent evidence suggests that the role and composition of TFIID are more diverse than previously understood. To investigate the effects of changing the composition of TFIID in a simple system, we depleted TATA box-binding protein-associated factor (TAF)1 from Drosophila cells and determined the consequences on metal-induced transcription at an inducible gene, metallothionein B. We observe a marked increase in the levels of both the mature message and pre-mRNA in TAF1-depleted cells. Under conditions of continued metal exposure, we show that TAF1 depletion increases the magnitude of the initial transcription burst but has no effect on the timing of that burst. We also show that TAF1 depletion causes delay in the shutoff of transcription upon removal of the stimulus. Thus, TAFs are involved in both establishing an upper limit of transcription during induction and efficiently turning the gene off once the inducer is removed. Using genome-wide nascent sequencing, we identify hundreds of genes that are controlled in a similar manner, indicating that the findings at this inducible gene are likely generalizable to a large set of promoters. There is a long-standing appreciation for the importance of the spatial and temporal control of transcription. Here we uncover an important third dimension of control: the magnitude of the response. Our results show that the magnitude of the transcriptional response to the same signaling event, even at the same promoter, can vary greatly depending on the composition of the TFIID complex in the cell.heavy metal | MtnA | coactivator | RNA polymerase

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RNA Polymerase II and TAFs Undergo a Slow Isomerization after the Polymerase Is Recruited to Promoter-Bound TFIID

Cited by 25 publications

References 56 publications

Towards a mechanistic understanding of core promoter recognition from cryo-EM studies of human TFIID

Towards a mechanistic understanding of core promoter recognition from cryo-EM studies of human TFIID

Structure of promoter-bound TFIID and model of human pre-initiation complex assembly

Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription

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