The Dynamics of Chromatin Remodeling at Promoters Jane Mellor  Molecular Cell  Volume 19, Issue 2, Pages 147-157 (July 2005) DOI: 10.1016/j.molcel.2005.06.023 Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 1 The Dynamic Nucleosome—A Substrate for Chromatin Remodeling ATPases Nucleosomes (shaded circles) are shown by looking down the axis of the 10 nm fiber. The 10 bp intervals at which DNA (blue line) contacts the nucleosome are indicated by small red ovals. At the top is a schematic representing the propensity of the nucleosome to spontaneously unwrap and rewrap, starting at the entry and exit points (red arrow) for the nucleosomal DNA. The bottom portion is a schematic showing how capture of the intermediate unwrapped state by an ATPase such as SWI/SNF may lead, by the loop-recapture model, to a 10 bp change in the translational rotation of the nucleosome relative to the starting position on the DNA (yellow circles). For clarity, only one strand of DNA is shown. Molecular Cell 2005 19, 147-157DOI: (10.1016/j.molcel.2005.06.023) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 2 Dynamic Remodeling of a Nucleosome by an ATPase and a Transcription Factor (A) Periodicity and residence time of glucocorticoid receptor (GR)-ligand (Dexamethasone [Dex]) interaction with promoter nucleosomes are determined by the amount of SWI/SNF (Brg) in the reaction. (B) Model summarizing the nucleosome dynamics during one cycle of GR-Dex/SWI/SNF (Brg) interactions with promoter nucleosomes. Changes shown include changes to DNA-histone interactions (wavy lines) and the transient and sequential modifications to H2B (purple) and H2A (red) in the nucleosomes mobilized by SWI/SNF (Brg), followed by the cyclical collapse of the remodeled state into the ground state that correlates with displacement of GR/Dex and SWI/SNF. Taken from (Nagaich et al., 2004). Molecular Cell 2005 19, 147-157DOI: (10.1016/j.molcel.2005.06.023) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 3 Dynamic Remodeling of Nucleosomes Leading to TBP-Dependent Nucleosome Sliding Accurate positioning of promoter nucleosomes is essential for gene repression and efficient activation. Barriers play a key role in determining nucleosome positioning. Upstream of the promoter, the barrier (diamonds) is mediated by a DNA sequence that excludes nucleosomes. (i) The nucleosomes that can act as a substrate for remodeling or modification are shaded cyan and red. (ii) Acetylation (“ac”) of the nucleosomes by a HAT recruited by sequence-specific transcription factor (TF) is essential for SWI/SNF-dependent ([iii], “A,” cyan circle) remodeling of nucleosomes (wavy lines on nucleosomes). This potentiates SWI/SNF-independent repositioning of nucleosomes downstream from the TATA box by TBP, which binds to the TATA region and bends DNA (iv), perhaps in association with a second ATPase (“A,” yellow oval). Other factors that bend DNA also facilitate sliding, suggesting that sliding is solely a function of the DNA conformation. Nucleosomes that slide into their new positions are shaded red (heavy arrows), revealing the transcription initiation site (arrow). Sliding stops at the barrier, represented here by a highly positioned nucleosome (dark blue). This may be close to the promoter, as shown, or alternatively may reside toward the 3′ region of the gene, as sliding of up to 14 nucleosomes has been observed at some genes in yeast. The histone tails are omitted from the final two steps for clarity. Molecular Cell 2005 19, 147-157DOI: (10.1016/j.molcel.2005.06.023) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 4 Nucleosome Dynamics Mediated by the Estrogen Receptor at the pS2 Promoter in the Presence or Absence of Estrogen (± Ligand) (A) Receptor (blue circles) and nucleosome dynamics in untreated cells (−ligand; unproductive cycles). The transient and periodic association of the ER with nucleosome E (NucE) is shown graphically (top) and in a model of nucleosome dynamics (bottom) and is compared to the association of TBP (red arc) with Nuc T, nucleosome modifications (such as H3K14ac or H4R3me2, red shaded nucleosomes), recruitment of modifying enzymes such as the p300 HAT and PRMT1 methyltransferase, and the association of a complex containing HDACs and the Mi2 ATPase that correlates with TBP displacement and the return of chromatin to the ground state. No SWI/SNF activity can be detected with the nucleosomes in these cells, suggesting that some nucleosome dynamics may be mediated by histone tail modifications and transcription factors. (B) Receptor-ligand (blue arcs) and nucleosome dynamics in estrogen-treated cells (+ligand; leading to productive cycles). The periodic association of histone acetyl transferases, histone deacetylases, and SWI/SNF (Brg/Brm) that may control ER dynamics and promoter clearance is shown with arrows on the graph. Mi2 (NuRD) remodeling and displacement of TBP and turnover of H4R3me2 marks on NucE and NucT occurs every second cycle, leading to the ground state. Taken from (Metivier et al., 2004,2003). Molecular Cell 2005 19, 147-157DOI: (10.1016/j.molcel.2005.06.023) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 5 Dynamic Linker Histones May Be Stabilized by Modifications or Association with Specific Transcription Factors (A) Role for dynamic histone H1 in localized gene repression. (i) H1b may be recruited by a transcription factor (TF, e.g., Mxl1) that reduces the propensity of H1 to dissociate from the linker DNA. (ii) Alternatively, histone H1 can be recruited by the SirT1 component of the PCR, which deacetylates and potentiates subsequent methylation of lysine 26 of H1b by Ezh2. (B) Transcription factors, such as the GATA factor or FOXA, a Fkh transcription factor, may antagonize H1-mediated repression by their ability to “open up” chromatin arrays repressed with histone H1. The winged helix domain of a Fkh factor is shown associated with the DNA helix on the edge of a nucleosome (Clark et al., 1993). Repressed nucleosomes are shaded gray, and nucleosomes that can act as a substrate for remodeling are cyan. Molecular Cell 2005 19, 147-157DOI: (10.1016/j.molcel.2005.06.023) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 6 Stable but TBP-Independent Remodeling Leading to Displacement of the TATA Nucleosome by SAGA (Spt3) and Mot1 In this schematic, remodeling of the TATA nucleosomes depends on transcription factor binding (TF) to a remodeled nucleosome (circular “A” is a SWI/SNF-like ATPase) and recruitment of SAGA. The Gcn5 HAT in SAGA antagonizes repression by acetylating histone tails. The TATA nucleosome is mobilized by the Spt3 component of SAGA together with the Mot1 ATPases (yellow oval) (i). The interaction with the remodeled DNA is proposed to be stabilized by interactions with components of SAGA containing a histone fold motif. SAGA in turn stabilizes the interaction of Mot1 with the region. (ii and iii) Stable remodeling may lead to transcription by binding of TBP and recruitment of the initiation complex including RNAPII. It is not known whether displacement is by disassembly or by sliding of the TATA nucleosome. Molecular Cell 2005 19, 147-157DOI: (10.1016/j.molcel.2005.06.023) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 7 Nucleosome Disassembly at PHO5 A sequential series of modifications to nucleosomes containing the variant histone (Htz1) on the repressed promoter is initiated by (i) TF1 (Pho2) recruitment of a HAT complex (NuA4) leading to (ii) acetylation (tails, “ac”). On activation of the promoter (iii), these modifications facilitate recruitment of a second factor (TF2, Pho4), a fresh wave of acetylation (SAGA, Gcn5), and a putative SWI/SNF-like ATPase (“A,” cyan circle) that remodels the nucleosomes (wavy lines on nucleosome). A second putative ATPase (“A,” yellow ovals) may initiate nucleosome disassembly of the H2A:H2B and H3:H4 dimers in association with the histone chaperone Asf1 (iv). TF2 binding spreads across the promoter to stabilize the structure. TBP binding initiates transcription. The remodeling of the promoter and TATA nucleosomes may be through distinct mechanisms. The histone tails are omitted from the final steps for clarity. Molecular Cell 2005 19, 147-157DOI: (10.1016/j.molcel.2005.06.023) Copyright © 2005 Elsevier Inc. Terms and Conditions