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The Mediator complex and transcription regulation.

Poss ZC, Ebmeier CC, Taatjes DJ - Crit. Rev. Biochem. Mol. Biol. (2013)

Bottom Line: Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression).We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing.We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of Colorado , Boulder, CO , USA.

ABSTRACT
The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.

Show MeSH
A working model for Mediator and CDK8-Mediator regulation of transcription initiation and elongation. This model depicts four functionally distinct structural states (I–IV) for Mediator. We hypothesize that different Mediator surfaces will be exposed in each state, which may help coordinate timing of factor recruitment to the promoter, in accordance with requirements for various stages of transcription. According to this model, state I and state II are compatible with pre-initiation events, state III represents transcription initiation (possibly including paused pol II), and state IV represents an elongation-competent structure. In state I, Mediator is not bound to a TF; Mediator is capable of binding pol II in this structural state, but pol II will be inactive or minimally active (i.e. basal transcription). TF binding (e.g. VP16) causes a structural shift to state II. Mediator is also capable of binding pol II in this conformational state, with the potential to direct high levels of “activated” transcription. This structural state might also coordinate timing of other Mediator-cofactor interactions at the promoter that could regulate subsequent stages of transcription (Ebmeier & Taatjes, 2010). If pol II binds the TF-Mediator complex, this leads to structural state III. This structural state may be compatible with activated transcription, perhaps by promoting synergy among PIC factors (e.g. TFIIH, TFIID and TFIIB) that assemble around the Mediator–pol II complex. Note that in this structural state, the CDK8 module is incapable of binding Mediator. Upon transcription initiation and pol II transition to productive elongation, pol II breaks contacts with Mediator; Mediator structure transitions back to state II (TF bound, but no pol II). The CDK8 module is able to bind Mediator in this structural state. If the CDK8 module binds Mediator, Mediator adopts structural state IV. This structural state (i.e. CDK8-Mediator) does not allow pol II binding. Thus, the CDK8-Mediator complex prevents a second pol II enzyme from immediately re-engaging the promoter, which might otherwise cause defects in mRNA processing or defects during initiation by this second pol II. Furthermore, the CDK8-Mediator complex could help assemble and/or regulate elongation factors, thereby influencing ongoing elongation events. The ability of CDK8-Mediator or core Mediator (i.e. Mediator containing MED26) to positively influence pol II elongation has been documented by several groups (Donner et al., 2010; Galbraith et al., 2013; Takahashi et al., 2011). Yet Mediator and other PIC components remain at the promoter following pol II promoter escape, leaving a “scaffold” complex (Yudkovsky et al., 2000). These apparently contradictory findings are reconciled by growing evidence that elongating pol II complexes are likely stationary, and that rather than moving directionally along DNA, pol II instead “reels in” the DNA template (Papantonis et al., 2010). This has already been demonstrated for bacterial polymerases (Kapanidis et al., 2006; Revyakin et al., 2006), and DNA polymerases work in much the same way (Anachkova et al., 2005). Stationary, elongating pol II complexes could be juxtaposed with promoter-bound factors, facilitating Mediator- or CDK8-Mediator-dependent regulation of pol II elongation. We emphasize that this is a model, and that many aspects remain to be rigorously tested. (see colour version of this figure online at www.informahealthcare.com/bmg).
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f9: A working model for Mediator and CDK8-Mediator regulation of transcription initiation and elongation. This model depicts four functionally distinct structural states (I–IV) for Mediator. We hypothesize that different Mediator surfaces will be exposed in each state, which may help coordinate timing of factor recruitment to the promoter, in accordance with requirements for various stages of transcription. According to this model, state I and state II are compatible with pre-initiation events, state III represents transcription initiation (possibly including paused pol II), and state IV represents an elongation-competent structure. In state I, Mediator is not bound to a TF; Mediator is capable of binding pol II in this structural state, but pol II will be inactive or minimally active (i.e. basal transcription). TF binding (e.g. VP16) causes a structural shift to state II. Mediator is also capable of binding pol II in this conformational state, with the potential to direct high levels of “activated” transcription. This structural state might also coordinate timing of other Mediator-cofactor interactions at the promoter that could regulate subsequent stages of transcription (Ebmeier & Taatjes, 2010). If pol II binds the TF-Mediator complex, this leads to structural state III. This structural state may be compatible with activated transcription, perhaps by promoting synergy among PIC factors (e.g. TFIIH, TFIID and TFIIB) that assemble around the Mediator–pol II complex. Note that in this structural state, the CDK8 module is incapable of binding Mediator. Upon transcription initiation and pol II transition to productive elongation, pol II breaks contacts with Mediator; Mediator structure transitions back to state II (TF bound, but no pol II). The CDK8 module is able to bind Mediator in this structural state. If the CDK8 module binds Mediator, Mediator adopts structural state IV. This structural state (i.e. CDK8-Mediator) does not allow pol II binding. Thus, the CDK8-Mediator complex prevents a second pol II enzyme from immediately re-engaging the promoter, which might otherwise cause defects in mRNA processing or defects during initiation by this second pol II. Furthermore, the CDK8-Mediator complex could help assemble and/or regulate elongation factors, thereby influencing ongoing elongation events. The ability of CDK8-Mediator or core Mediator (i.e. Mediator containing MED26) to positively influence pol II elongation has been documented by several groups (Donner et al., 2010; Galbraith et al., 2013; Takahashi et al., 2011). Yet Mediator and other PIC components remain at the promoter following pol II promoter escape, leaving a “scaffold” complex (Yudkovsky et al., 2000). These apparently contradictory findings are reconciled by growing evidence that elongating pol II complexes are likely stationary, and that rather than moving directionally along DNA, pol II instead “reels in” the DNA template (Papantonis et al., 2010). This has already been demonstrated for bacterial polymerases (Kapanidis et al., 2006; Revyakin et al., 2006), and DNA polymerases work in much the same way (Anachkova et al., 2005). Stationary, elongating pol II complexes could be juxtaposed with promoter-bound factors, facilitating Mediator- or CDK8-Mediator-dependent regulation of pol II elongation. We emphasize that this is a model, and that many aspects remain to be rigorously tested. (see colour version of this figure online at www.informahealthcare.com/bmg).

Mentions: The Mediator structural changes outlined above involve what appear to be coordinated and robust structural shifts throughout the complex. Moreover, the conformational shifts are distinct based upon whether pol II, CDK8 module, or TFs bind the Mediator complex. This suggests a straightforward mechanism to regulate Mediator activity, summarized schematically in Figure 9. Note that in some circumstances, Mediator is rendered incapable of specific interactions (e.g. the CDK8 module does not interact with Mediator in its pol II-bound structural state). This could be important to ensure appropriate timing of events during various stages of transcription.Figure 9.


The Mediator complex and transcription regulation.

Poss ZC, Ebmeier CC, Taatjes DJ - Crit. Rev. Biochem. Mol. Biol. (2013)

A working model for Mediator and CDK8-Mediator regulation of transcription initiation and elongation. This model depicts four functionally distinct structural states (I–IV) for Mediator. We hypothesize that different Mediator surfaces will be exposed in each state, which may help coordinate timing of factor recruitment to the promoter, in accordance with requirements for various stages of transcription. According to this model, state I and state II are compatible with pre-initiation events, state III represents transcription initiation (possibly including paused pol II), and state IV represents an elongation-competent structure. In state I, Mediator is not bound to a TF; Mediator is capable of binding pol II in this structural state, but pol II will be inactive or minimally active (i.e. basal transcription). TF binding (e.g. VP16) causes a structural shift to state II. Mediator is also capable of binding pol II in this conformational state, with the potential to direct high levels of “activated” transcription. This structural state might also coordinate timing of other Mediator-cofactor interactions at the promoter that could regulate subsequent stages of transcription (Ebmeier & Taatjes, 2010). If pol II binds the TF-Mediator complex, this leads to structural state III. This structural state may be compatible with activated transcription, perhaps by promoting synergy among PIC factors (e.g. TFIIH, TFIID and TFIIB) that assemble around the Mediator–pol II complex. Note that in this structural state, the CDK8 module is incapable of binding Mediator. Upon transcription initiation and pol II transition to productive elongation, pol II breaks contacts with Mediator; Mediator structure transitions back to state II (TF bound, but no pol II). The CDK8 module is able to bind Mediator in this structural state. If the CDK8 module binds Mediator, Mediator adopts structural state IV. This structural state (i.e. CDK8-Mediator) does not allow pol II binding. Thus, the CDK8-Mediator complex prevents a second pol II enzyme from immediately re-engaging the promoter, which might otherwise cause defects in mRNA processing or defects during initiation by this second pol II. Furthermore, the CDK8-Mediator complex could help assemble and/or regulate elongation factors, thereby influencing ongoing elongation events. The ability of CDK8-Mediator or core Mediator (i.e. Mediator containing MED26) to positively influence pol II elongation has been documented by several groups (Donner et al., 2010; Galbraith et al., 2013; Takahashi et al., 2011). Yet Mediator and other PIC components remain at the promoter following pol II promoter escape, leaving a “scaffold” complex (Yudkovsky et al., 2000). These apparently contradictory findings are reconciled by growing evidence that elongating pol II complexes are likely stationary, and that rather than moving directionally along DNA, pol II instead “reels in” the DNA template (Papantonis et al., 2010). This has already been demonstrated for bacterial polymerases (Kapanidis et al., 2006; Revyakin et al., 2006), and DNA polymerases work in much the same way (Anachkova et al., 2005). Stationary, elongating pol II complexes could be juxtaposed with promoter-bound factors, facilitating Mediator- or CDK8-Mediator-dependent regulation of pol II elongation. We emphasize that this is a model, and that many aspects remain to be rigorously tested. (see colour version of this figure online at www.informahealthcare.com/bmg).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852498&req=5

f9: A working model for Mediator and CDK8-Mediator regulation of transcription initiation and elongation. This model depicts four functionally distinct structural states (I–IV) for Mediator. We hypothesize that different Mediator surfaces will be exposed in each state, which may help coordinate timing of factor recruitment to the promoter, in accordance with requirements for various stages of transcription. According to this model, state I and state II are compatible with pre-initiation events, state III represents transcription initiation (possibly including paused pol II), and state IV represents an elongation-competent structure. In state I, Mediator is not bound to a TF; Mediator is capable of binding pol II in this structural state, but pol II will be inactive or minimally active (i.e. basal transcription). TF binding (e.g. VP16) causes a structural shift to state II. Mediator is also capable of binding pol II in this conformational state, with the potential to direct high levels of “activated” transcription. This structural state might also coordinate timing of other Mediator-cofactor interactions at the promoter that could regulate subsequent stages of transcription (Ebmeier & Taatjes, 2010). If pol II binds the TF-Mediator complex, this leads to structural state III. This structural state may be compatible with activated transcription, perhaps by promoting synergy among PIC factors (e.g. TFIIH, TFIID and TFIIB) that assemble around the Mediator–pol II complex. Note that in this structural state, the CDK8 module is incapable of binding Mediator. Upon transcription initiation and pol II transition to productive elongation, pol II breaks contacts with Mediator; Mediator structure transitions back to state II (TF bound, but no pol II). The CDK8 module is able to bind Mediator in this structural state. If the CDK8 module binds Mediator, Mediator adopts structural state IV. This structural state (i.e. CDK8-Mediator) does not allow pol II binding. Thus, the CDK8-Mediator complex prevents a second pol II enzyme from immediately re-engaging the promoter, which might otherwise cause defects in mRNA processing or defects during initiation by this second pol II. Furthermore, the CDK8-Mediator complex could help assemble and/or regulate elongation factors, thereby influencing ongoing elongation events. The ability of CDK8-Mediator or core Mediator (i.e. Mediator containing MED26) to positively influence pol II elongation has been documented by several groups (Donner et al., 2010; Galbraith et al., 2013; Takahashi et al., 2011). Yet Mediator and other PIC components remain at the promoter following pol II promoter escape, leaving a “scaffold” complex (Yudkovsky et al., 2000). These apparently contradictory findings are reconciled by growing evidence that elongating pol II complexes are likely stationary, and that rather than moving directionally along DNA, pol II instead “reels in” the DNA template (Papantonis et al., 2010). This has already been demonstrated for bacterial polymerases (Kapanidis et al., 2006; Revyakin et al., 2006), and DNA polymerases work in much the same way (Anachkova et al., 2005). Stationary, elongating pol II complexes could be juxtaposed with promoter-bound factors, facilitating Mediator- or CDK8-Mediator-dependent regulation of pol II elongation. We emphasize that this is a model, and that many aspects remain to be rigorously tested. (see colour version of this figure online at www.informahealthcare.com/bmg).
Mentions: The Mediator structural changes outlined above involve what appear to be coordinated and robust structural shifts throughout the complex. Moreover, the conformational shifts are distinct based upon whether pol II, CDK8 module, or TFs bind the Mediator complex. This suggests a straightforward mechanism to regulate Mediator activity, summarized schematically in Figure 9. Note that in some circumstances, Mediator is rendered incapable of specific interactions (e.g. the CDK8 module does not interact with Mediator in its pol II-bound structural state). This could be important to ensure appropriate timing of events during various stages of transcription.Figure 9.

Bottom Line: Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression).We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing.We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of Colorado , Boulder, CO , USA.

ABSTRACT
The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.

Show MeSH