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Regulatory interplay between TFIID's conformational transitions and its modular interaction with core promoter DNA.

Cianfrocco MA, Nogales E - Transcription (2013)

Bottom Line: Recent structural and biochemical studies of human TFIID have significantly increased our understanding of the mechanisms underlying the recruitment of TFIID to promoter DNA and its role in transcription initiation.Here we propose a general model of promoter binding by TFIID, where co-activators, activators, and histone modifications promote and/or stabilize a conformational state of TFIID that results in core promoter engagement.Within this high affinity conformation, we propose that TFIID's extensive interaction with promoter DNA leads to topological changes in the DNA that facilitate the eventual loading of RNAP II.

View Article: PubMed Central - PubMed

Affiliation: Biophysics Graduate Group; University of California; Berkeley, CA USA.

ABSTRACT
Recent structural and biochemical studies of human TFIID have significantly increased our understanding of the mechanisms underlying the recruitment of TFIID to promoter DNA and its role in transcription initiation. Structural studies using cryo-EM revealed that modular interactions underlie TFIID's ability to bind simultaneously multiple promoter motifs and to define a DNA state that will facilitate transcription initiation. Here we propose a general model of promoter binding by TFIID, where co-activators, activators, and histone modifications promote and/or stabilize a conformational state of TFIID that results in core promoter engagement. Within this high affinity conformation, we propose that TFIID's extensive interaction with promoter DNA leads to topological changes in the DNA that facilitate the eventual loading of RNAP II. While more work is required to dissect the individual contributions of activators and repressors to TFIID's DNA binding, the recent cryo-EM studies provide a physical framework to guide future structural, biophysical, and biochemical experiments.

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Figure 1. TFIID introduces topological changes in promoter DNA upon formation of the rearranged, DNA-bound conformation. Cryo-EM structures of the canonical conformation of TFIID (A) and the rearranged conformation of TFIID-TFIIA-SCP (B). The BC core is shown in blue, the flexible lobe A in orange (A) and yellow (B), and the SCP DNA in green (B). Promoter DNA positions +1 and +45 are indicated (B). (C) Mesh: Cryo-EM structure of TFIID-TFIIA-SCP(-66) rotated by 90 degrees relative to (B). The structure shows the location of DNA position -66 exiting lobe A. Positions -66, +1, and +45 are indicated and colored according to promoter motifs in (G). (D) DNase I footprint modeled onto the DNA path through TFIID-TFIIA-SCP. Red surfaces: full cleavage; blue surfaces: partial cleavage; (E) MPE-Fe footprinting modeled onto the DNA path through TFIID-TFIIA-SCP. Pink surface: cleavage; MPE-Fe protection by TFIID-IIA indicated by black lines. (F) DNA model from the open complex of TBP/PIC.34 (G) Promoter DNA model from TFIID-TFIIA-SCP colored by promoter motifs and TFIID subunits that make sequence-specific contacts.
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Figure 1: Figure 1. TFIID introduces topological changes in promoter DNA upon formation of the rearranged, DNA-bound conformation. Cryo-EM structures of the canonical conformation of TFIID (A) and the rearranged conformation of TFIID-TFIIA-SCP (B). The BC core is shown in blue, the flexible lobe A in orange (A) and yellow (B), and the SCP DNA in green (B). Promoter DNA positions +1 and +45 are indicated (B). (C) Mesh: Cryo-EM structure of TFIID-TFIIA-SCP(-66) rotated by 90 degrees relative to (B). The structure shows the location of DNA position -66 exiting lobe A. Positions -66, +1, and +45 are indicated and colored according to promoter motifs in (G). (D) DNase I footprint modeled onto the DNA path through TFIID-TFIIA-SCP. Red surfaces: full cleavage; blue surfaces: partial cleavage; (E) MPE-Fe footprinting modeled onto the DNA path through TFIID-TFIIA-SCP. Pink surface: cleavage; MPE-Fe protection by TFIID-IIA indicated by black lines. (F) DNA model from the open complex of TBP/PIC.34 (G) Promoter DNA model from TFIID-TFIIA-SCP colored by promoter motifs and TFIID subunits that make sequence-specific contacts.

Mentions: The potential of EM as a structural tool to analyze heterogeneous samples is exemplified by our recent cryo-EM study of human TFIID bound to super core promoter (SCP) DNA.10 In order to determine the 3D structure of promoter-bound human TFIID, it was necessary to overcome a surprising discovery: that lobe A, the major lobe within the horseshoe-shaped human TFIID structure, moves by over 100 Å from a previously characterized “canonical” state into a newly discovered “rearranged” state (Fig. 1A and B). Past TFIID structural studies focused only on a single conformation of the complex, the canonical state,11-14 overlooking the dramatic structural transitions of lobe A as it changes connectivity from lobe C (canonical state) to lobe B (rearranged state) (Fig. 1A and B).


Regulatory interplay between TFIID's conformational transitions and its modular interaction with core promoter DNA.

Cianfrocco MA, Nogales E - Transcription (2013)

Figure 1. TFIID introduces topological changes in promoter DNA upon formation of the rearranged, DNA-bound conformation. Cryo-EM structures of the canonical conformation of TFIID (A) and the rearranged conformation of TFIID-TFIIA-SCP (B). The BC core is shown in blue, the flexible lobe A in orange (A) and yellow (B), and the SCP DNA in green (B). Promoter DNA positions +1 and +45 are indicated (B). (C) Mesh: Cryo-EM structure of TFIID-TFIIA-SCP(-66) rotated by 90 degrees relative to (B). The structure shows the location of DNA position -66 exiting lobe A. Positions -66, +1, and +45 are indicated and colored according to promoter motifs in (G). (D) DNase I footprint modeled onto the DNA path through TFIID-TFIIA-SCP. Red surfaces: full cleavage; blue surfaces: partial cleavage; (E) MPE-Fe footprinting modeled onto the DNA path through TFIID-TFIIA-SCP. Pink surface: cleavage; MPE-Fe protection by TFIID-IIA indicated by black lines. (F) DNA model from the open complex of TBP/PIC.34 (G) Promoter DNA model from TFIID-TFIIA-SCP colored by promoter motifs and TFIID subunits that make sequence-specific contacts.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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Figure 1: Figure 1. TFIID introduces topological changes in promoter DNA upon formation of the rearranged, DNA-bound conformation. Cryo-EM structures of the canonical conformation of TFIID (A) and the rearranged conformation of TFIID-TFIIA-SCP (B). The BC core is shown in blue, the flexible lobe A in orange (A) and yellow (B), and the SCP DNA in green (B). Promoter DNA positions +1 and +45 are indicated (B). (C) Mesh: Cryo-EM structure of TFIID-TFIIA-SCP(-66) rotated by 90 degrees relative to (B). The structure shows the location of DNA position -66 exiting lobe A. Positions -66, +1, and +45 are indicated and colored according to promoter motifs in (G). (D) DNase I footprint modeled onto the DNA path through TFIID-TFIIA-SCP. Red surfaces: full cleavage; blue surfaces: partial cleavage; (E) MPE-Fe footprinting modeled onto the DNA path through TFIID-TFIIA-SCP. Pink surface: cleavage; MPE-Fe protection by TFIID-IIA indicated by black lines. (F) DNA model from the open complex of TBP/PIC.34 (G) Promoter DNA model from TFIID-TFIIA-SCP colored by promoter motifs and TFIID subunits that make sequence-specific contacts.
Mentions: The potential of EM as a structural tool to analyze heterogeneous samples is exemplified by our recent cryo-EM study of human TFIID bound to super core promoter (SCP) DNA.10 In order to determine the 3D structure of promoter-bound human TFIID, it was necessary to overcome a surprising discovery: that lobe A, the major lobe within the horseshoe-shaped human TFIID structure, moves by over 100 Å from a previously characterized “canonical” state into a newly discovered “rearranged” state (Fig. 1A and B). Past TFIID structural studies focused only on a single conformation of the complex, the canonical state,11-14 overlooking the dramatic structural transitions of lobe A as it changes connectivity from lobe C (canonical state) to lobe B (rearranged state) (Fig. 1A and B).

Bottom Line: Recent structural and biochemical studies of human TFIID have significantly increased our understanding of the mechanisms underlying the recruitment of TFIID to promoter DNA and its role in transcription initiation.Here we propose a general model of promoter binding by TFIID, where co-activators, activators, and histone modifications promote and/or stabilize a conformational state of TFIID that results in core promoter engagement.Within this high affinity conformation, we propose that TFIID's extensive interaction with promoter DNA leads to topological changes in the DNA that facilitate the eventual loading of RNAP II.

View Article: PubMed Central - PubMed

Affiliation: Biophysics Graduate Group; University of California; Berkeley, CA USA.

ABSTRACT
Recent structural and biochemical studies of human TFIID have significantly increased our understanding of the mechanisms underlying the recruitment of TFIID to promoter DNA and its role in transcription initiation. Structural studies using cryo-EM revealed that modular interactions underlie TFIID's ability to bind simultaneously multiple promoter motifs and to define a DNA state that will facilitate transcription initiation. Here we propose a general model of promoter binding by TFIID, where co-activators, activators, and histone modifications promote and/or stabilize a conformational state of TFIID that results in core promoter engagement. Within this high affinity conformation, we propose that TFIID's extensive interaction with promoter DNA leads to topological changes in the DNA that facilitate the eventual loading of RNAP II. While more work is required to dissect the individual contributions of activators and repressors to TFIID's DNA binding, the recent cryo-EM studies provide a physical framework to guide future structural, biophysical, and biochemical experiments.

Show MeSH