Generation and Interconversion of Multiple Distinct Nucleosomal States as a Mechanism for Catalyzing Chromatin Fluidity  Geeta J. Narlikar, Michael L. Phelan, Robert E. Kingston  Molecular Cell  Volume 8, Issue 6, Pages 1219-1230 (December 2001) DOI: 10.1016/S1097-2765(01)00412-9

Figure 1 Quantification of ATPase and Remodeling Activities of BRG1 and Substrate Binding (A) Top, TLC analysis of ATPase reactions (20 μM ATP/Mg, 1 nM BRG1, saturating nucleosomes, or TPT DNA). Bottom, quantification of the data in the top panel showing unstimulated (open squares), nucleosome-stimulated (closed circles), and DNA-stimulated (open circles) ATPase activity of BRG1. (B) A schematic of TPT, the 157-bp DNA fragment used to reconstitute mononucleosomes. (C) BRG1 increases restriction enzyme cleavage of nucleosomal DNA (15 nM BRG1 and <1 nM nucleosomes). Top, uncut and cut DNA resolved on a gel. Bottom, quantification of the data in the top panel. The rate constants are 4.4 × 10−5 min−1 (open circles, without ATP) and 9.7 × 10−2 min−1 (closed circles, with ATP). (D) An increasing fraction of DNA is retained on the top nitrocellulose membrane upon increasing [BRG1]. Unbound DNA is retained on the bottom, positively charged membrane. Fits to the data give a Kd for TPT DNA of 0.5 nM ([TPT] = 0.02 nM). (E) Nucleosomes displace TPT from BRG1. This is manifested as a decrease in the fraction of DNA retained on the top membrane. The average Kd for nucleosomes (19 nM) using data such as those supplied here is given in Table 1. Molecular Cell 2001 8, 1219-1230DOI: (10.1016/S1097-2765(01)00412-9)

Figure 2 The Individual Steps in Nucleosome Remodeling by BRG1 (A) A pulse-chase experiment. The addition of chase (2 mM ATP/Mg, excess cold nucleosomes [220 nM] and excess PstI) after allowing 32P-labeled nucleosomes (<1 nM) to bind BRG1 (40 nM) decreases the cleavage rate (closed diamonds) compared to reactions without chase (closed circles), suggesting that nucleosomes fall off faster than they are remodeled. The effectiveness of the chase is demonstrated by the simultaneous addition of chase and 32P-labeled nucleosomes (open squares). (B) Kinetic and thermodynamic scheme for nucleosome remodeling. The framework is drawn for Model 1 (see “BRG1 Continuously Generates Multiple Remodeled Products”). The kinetic and thermodynamic constants are the averages of numbers from Tables 1 and 2, except for kremodel, which is derived from the section mentioned above. The Kd values are assumed to equal the respective Km values (see the main text). The lower limit for koffN, the rate constant for the dissociation of nucleosomes from BRG1/ATP, is based on the result that nucleosomes equilibrate with BRG1/ATP faster than ATP hydrolysis, which is rate limiting. The lower limit for the value of koffATP is analogously obtained from the result that ATP binding is not rate limiting in the ATPase reaction. The lower limit for konN is obtained from koffN and KdN (Table 1), and that for konATP from koffATP and KdATP. Molecular Cell 2001 8, 1219-1230DOI: (10.1016/S1097-2765(01)00412-9)

Figure 3 Investigating the Formation of Multiple Remodeled Products Using DNase I (A) Two extreme models for BRG1 action. Also see the Supplementary Material. (B) The generation of the altered DNase I pattern is complete by 6.5 min. The rate constants from quantification of the given bands are shown. The “rungs” of the 10-bp ladder that are closest to the bands being quantified are marked with letters. (C) Quantification of band 6 (normalized signal, closed circles) in (B) is shown and is the average of two independent experiments. The REA reaction with PstI continuously present is also shown (fraction uncut nucleosomes, open circles). Both reactions have identical BRG1, nucleosome, and ATP concentrations. Molecular Cell 2001 8, 1219-1230DOI: (10.1016/S1097-2765(01)00412-9)

Figure 4 Investigating the Formation of Multiple Remodeled Products Using Different Restriction Enzymes (A) Remodeling at different DNA sites (2 mM ATP/Mg and 18 nM BRG1). The rate constants for BRG1-enhanced cleavage by XhoI (squares), PstI (circles), SpeI (triangles), and all three enzymes together (diamonds) are 0.015 min−1, 0.097 min−1, 0.028 min−1, and 0.2 min−1, respectively. (B) Remodeling of a PstI site in the same position as in the TPT fragment (Figure 1B) (circles, rate constant = 0.08 min−1) compared with remodeling of the PstI site moved to replace the original XhoI site (squares, rate constant = 0.01 min−1). Reactions contained 2 mM ATP/Mg and ∼34 nM BRG1. (C) Determination of the fraction of PstI- and XhoI-accessible products. After allowing BRG1 (13 nM) to remodel 32P-labeled nucleosomes (<1 nM) for 40 min with 2 mM ATP/Mg, PstI (circles), XhoI (squares), or PstI and XhoI together (diamonds) were added, giving rate constants of cleavage of ∼4–8 min−1 and endpoints of 26%, 15%, and 38% cut nucleosomes, respectively, after including the 5% background cleavage. With PstI continuously present in a parallel reaction, ∼80% of the nucleosomes are cleaved, as indicated by the dashed line. (D) Approximately 15 nM BRG1 was allowed to react with nucleosomes for varying times, t1, before the removal of aliquots and the addition of PstI to a final concentration of 1 U/μl for 30 s (closed circles). Approximately 20% of PstI-accessible states are generated with a rate constant of 0.32 min−1. In a parallel reaction performed under the same BRG1 and nucleosome conditions, except for the continuous presence of PstI, the rate constant for PstI cleavage was 0.048 min−1 (open circles). Molecular Cell 2001 8, 1219-1230DOI: (10.1016/S1097-2765(01)00412-9)

Figure 5 Human SWI/SNF Displays the Same Fundamental Mechanistic Features as BRG1 (A) Measuring the rate constant for remodeling as observed via DNase I. The experiment was performed as in Figure 3B, using ∼65 ng/μl hSWI/SNF. (B) Band 6 (normalized signal, closed circles) in (A) is generated with a rate constant of 1.6 min−1. The REA reaction with PstI continuously present (fraction uncut substrate, open circles) has a rate constant of 0.14 min−1. Both reactions have identical hSWI/SNF, nucleosome, and ATP concentrations. (C) Determination of the fraction of PstI-accessible states and the rate constant with which they are generated. The experiment was performed as in Figure 4D, using 60 ng/μL hSWI/SNF. Approximately 22% of PstI-accessible states are generated with a rate constant of 0.7 min−1 (closed circles). In a parallel reaction performed under the same hSWI/SNF and nucleosome conditions, except for the continuous presence of PstI, the rate constant for PstI cleavage was 0.12 min−1 (open circles). Molecular Cell 2001 8, 1219-1230DOI: (10.1016/S1097-2765(01)00412-9)

Figure 6 Model for How Remodeling by SWI/SNF Can Create DNA Access to Repressors and Activators Molecular Cell 2001 8, 1219-1230DOI: (10.1016/S1097-2765(01)00412-9)