DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC

Abstract

ATP-dependent chromatin-remodeling complexes (remodelers) modulate gene transcription by regulating the accessibility of highly packaged genomic DNA. However, the molecular mechanisms involved at the nucleosomal level in this process remain controversial. Here, we monitor the real-time activity of single ySWI/SNF or RSC complexes on single, stretched nucleosomal templates under tensions above 1 pN forces. We find that these remodelers can translocate along DNA at rates of approximately 13 bp/s and generate forces up to approximately 12 pN, producing DNA loops of a broad range of sizes (20-1200 bp, average approximately 100 bp) in a nucleosome-dependent manner. This nucleosome-specific activity differs significantly from that on bare DNA observed under low tensions and suggests a nucleosome-remodeling mechanism through intranucleosomal DNA loop formation. Such loop formation may provide a molecular basis for the biological functions of remodelers.

Figure 1

ATP- and Nucleosome-Dependent Translocation and Loop Formation by SWI/SNF at 3 pN Constant Tension (A) Illustration of the setup used for the remodeling assay (not in scale). DNA ends were attached to two polystyrene beads, one kept in a force-measuring optical trap and another fixed on the tip of a micropipette by suction. The pipette bead can move relative to the trap center, thus maintaining a constant stretching force through a feedback mechanism. (B) Time-dependent extension of either bare DNA in the presence of 4 nM SWI/SNF (SWI) and 1 mM ATP (purple trace) or nucleosomal template with no SWI/SNF (magenta) or with 4 nMSWI/SNF in the presence of 0mM(blue), 0.1mM(red), or 1mM(black) ATP. In comparison, the Michaelis constant (K_M) for ATP is ~0.1 mM (Cairns et al., 1996). Loop formation signals in the red trace are marked with triangles (see Figure S1 for their identification). An enlarged view of a small signal in the black trace is shown as an insert (cyan curve). The ATP- and remodeler-dependent DNA looping on the nucleosomal template was confirmed by more extensive observations. In a total of 8.6 hr accumulated observation time, 12 signals with an average size of 25 (±5) bp were found in the presence of 4 nMSWI/SNF but no ATP. This occurrence rate (0.023 min⁻¹) is close to that in the absence of remodeler (0.019 min⁻¹). In 0.1mMATP, SWI/SNF translocates at lower speed and shorter distance than in 1mMATP (compare red and black traces). An analysis of 92 looping events found in 0.1mM ATP yields 78 bp average loop size and average velocities of 6.2 bp/s for loop generation and of 6.6 bp/s for reverse translocation. (C and D) Enlarged views of the individual translocation signals from the black trace in (B). Several translocation regions are fitted with straight lines (red) to calculate translocation velocities (Experimental Procedures). The 3750 bp DNA molecule was used in these experiments.

Figure 2

Distributions of the Translocation Velocity and Loop Size for SWI/SNF Distributions of the translocation velocity (A) and loop size (B) for SWI/SNF. In (A), the histograms for positive and negative velocity values are separately fitted with Gaussian functions (red), yielding the indicated means and standard deviations of 5 bp/s for the positive translocation and of 6 bp/s for the reverse translocation. The accumulative translocation length at the specified velocity is shown. In (B), the loop size for each loop formation event is defined as the corresponding DNA contour-length change from the start point of the first translocation phase to the endpoint of the last translocation phase. The loop size for reverse translocation is the DNA length that is removed from the loop after its maximum size is attained. Note that velocity and loop size values outside the range drawn (±30 bp/s for velocity and −200/+500 bp for loop size) are binned to the corresponding endpoints. The distributions were calculated (Experimental Procedures) from 241 DNA-looping events measured on 67 different DNA molecules.

Figure 3

Effect of Constant Nucleosomal Template Tension upon SWI/SNF Translocation (A) SWI/SNF translocation velocity and loop size are not affected by tensions between 3 pN and 6 pN. The error bars shown are standard deviations of three independent calculations performed on the same set of extension-time data (Experimental Procedures). (B) The SWI/SNF-dependent DNA translocation and loop formation activity is inhibited at 7 pN tension. Instead, nucleosomal array length quickly increases due to DNA unwrapping from histones. This DNA-unwrapping process contains continuous and discontinuous DNA releases from histones under tension (Brower-Toland et al., 2002). Note that at least two nucleosomes still remain on the 5040 bp DNA molecule between 200 s and 500 s.

Figure 4

SWI/SNF-Dependent DNA Translocation and Loop Formation on DNA Templates Containing Single Nucleosomes (A) A DNA extension-time trace at 3 pN tension in the presence of 4 nM SWI/SNF and 1 mM ATP. A close-up view of an individual loop formation event is shown in insert. (B) The complete force-extension curve corresponding to the same DNA molecule as in (A). The nucleosomal template was pulled to (blue) and then held at (black) 3 pN, at which point the nucleosome-remodeling activity shown in (A) was detected. After this observation phase, the template was pulled to high forces to disrupt the nucleosome on the template (red) and to confirm the involvement of a single DNA molecule (Smith et al., 1996). Here, the single rip in the force-extension curve (insert) confirms the presence of a single nucleosome on this template (Brower-Toland et al., 2002). (C and D) Velocity and loop size distributions for SWI/SNF. They were calculated from a total 217 looping events. Here, the looping events on single-nucleosome templates obtained at 3 pN and 4 pN constant tensions were combined to achieve statistical significance, since such translocation and loop formation properties were not altered by the tension within this range (Figure 3A).

Figure 5

SWI/SNF and RSC Can Translocate against High Forces Force is monitored in passive mode by pulling the array template initially to <5 pN here, with the micropipette then retained in a fixed position relative to the trap center (insert). The engagement in translocation sometimes is not disrupted by abrupt loop relaxation (black), which can remain at high force and restart translocation after pauses (magenta) without initiation at low force. Due to the low processivity of remodeler translocase, a stiff trap (~20 bp/pN) is required to measure the stall force, which can be seen in comparison with a soft trap (~150 bp/pN). The remodeler-, nucleosome-, and ATP-dependent (1 mM) DNA translocation and loop formation activity was detected at any tension above 1 pN force (blue, magenta, and black). In contrast, DNA looping was not found on nucleosome templates with remodeler but without ATP (cyan) or on bare DNA at tensions ≥0.7 pN (red) in the presence of both remodeler and ATP under our experimental conditions.

Figure 6

Processive Nucleosome Remodeling Caused by a Single Remodeler Complex (A) SWI/SNF generates a burst of looping events on a single-nucleosome-containing DNA template under a constant tension of 3 pN. (B and C) (B) SWI/SNF or (C) RSC generates correlated looping events on nucleosomal array templates at 4 pN tension.

Figure 7

A Model for Nucleosome Remodeling (i) Unbound state. (ii) The remodeler (Rem) binds the nucleosome (Nuc) in a pocket. (iii) The ATPase/translocase subunit (Tr) engages nucleosomal DNA at a position flanking the dyad, forming a small bulge near the dyad. (iv) Subsequent processive translocation generates large intranucleosomal DNA loops that have three possible fates: forward propagation (resulting in nucleosome jumping [v]), active reverse translocation, or DNA sliding (which may reflect the disengagement of the translocase subunit). Alternatively, the translocation can lead to immediate nucleosome sliding, as indicated by the dashed line, without large loops having been accumulated (from state [iii] to state [v]). (v) Following a remodeling cycle, the remodeler may release the nucleosome (from state [v] to state [i]).