Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching

Abstract

How site-specific transcription factors scan the genome to locate their target sites is a fundamental question in gene regulation. The in vivo binding interactions of several different transcription factors with chromatin have been investigated recently using quantitative fluorescence recovery after photobleaching (FRAP). These analyses have yielded significantly different estimates of both the binding rates and the number of predicted binding states of the respective transcription factors. We show here that these discrepancies are not due to fundamental differences among the site-specific transcription factors, but rather arise from errors in FRAP modeling. The two principal errors are a neglect of diffusion's role and an oversimplified approximation of the photobleach profile. Accounting for these errors by developing a revised FRAP protocol eliminates most of the previous discrepancies in the binding estimates for the three different transcription factors analyzed here. The new estimates predict that for each of the three transcription factors, approximately 75% of the molecules are freely diffusing within the nucleus, whereas the remainder is bound with an average residence time of approximately 2.5 s to a single type of chromatin binding site. Such consistent predictions for three different molecules suggest that many site-specific transcription factors may exhibit similar in vivo interactions with native chromatin.

FIGURE 1

FRAP with GR using the original circle, strip, and half-nuclear procedures. (A) Experimental data (gray circles) collected according to the original procedures are well fit (solid line) by the original FRAP models. Insets show a schematic illustrating the FRAP procedures. (B) The estimated values for k*_on and k_off are, however, radically different for each procedure (note the log scale). (C) Published estimates for each procedure (Circle FRAP for GR, strip FRAP for p53, half-nuclear FRAP for Max) are in the same range as the parameters estimated by each of the procedures for GR. This suggests that the FRAP procedure itself could significantly influence the binding estimates.

FIGURE 2

Test for diffusion-dependence of the FRAP. Schematic of the measurement for half-nuclear FRAP (A) and strip FRAP (B). The photobleach was performed in the dotted region. Intensity profiles were measured in the solid rectangle by starting at the base of the arrows (distance, 0 μm) and averaging pixels along lines perpendicular to the direction of the arrows. All postbleach profiles were normalized by the prebleach profile. Correction for observational photobleaching was performed as described in Methods. Scale bars, 5 μm. (C–H) Plots display averaged fluorescence intensity versus distance for Max, GR, and p53. The insets show the same profiles normalized between 0 and 1. Normalized profiles change in all cases indicating that diffusion should be incorporated into the FRAP model for Max, GR, and p53.

FIGURE 3

FRAP with GR, p53, and Max using the new circle and strip procedures. (A) Experimental single-cell data (shaded circles) collected according to the two new procedures are well fit (solid line) by the new FRAP models. (B) The estimated values for D_f, k*_on, and k_off from such fits show good agreement between circle and strip procedures for the same proteins, and also among different proteins. Average values from 10 to 15 cells are shown with standard deviations.

FIGURE 4

Reaction-diffusion FRAPs with one binding state are well described by a reaction-dominant model with two binding states, explaining the major difference in the old and new estimates for Max (A). A pure diffusion curve ((B) D_f = 10 μm²/s, shaded circles) or a full model curve ((C) D_f = 10 μm²/s, k*_on = 0.5 s⁻¹, k_off = 0.5 s⁻¹, shaded circles) are not well fit by a reaction-dominant model with one binding state (dashed line). However, both curves are well fit with a two binding state reaction-dominant model (solid line). Data from the original Max study (shaded circles) are also well fit by a two-binding state reaction-dominant model (D). The fit in D yields estimated off rates (k_off,1, k_off,2) and estimated bound fractions (C_eq,1, C_eq,2) for the two predicted binding states that are in good agreement with the published values (compare to A).

FIGURE 5

Differences in the old and new circle FRAP estimates for GR (A) are primarily due to changes in the initial conditions. To test the contribution of the initial conditions and the photobleaching correction (the other major difference between the old and new circle FRAP procedure), we collected FRAP data with the new acquisition procedure and fit the same data with different variants of the new circle FRAP model. First we processed the data with the original photobleaching correction procedure and fit these data with a form of the new circle FRAP model designed to mimic the old model: the nuclear radius was set to 50 μm to approximate an infinite nucleus, and the initial conditions were set to a uniform circular bleach to match the old initial conditions. (Each fitted data set is shown by an “×” and the mean of these fits by a dot). By themselves, these changes in analysis of the new circle FRAP data yielded estimates for k*_on and k_off (rows labeled Original Original) that were close to the original estimates. Then we used the new initial conditions (Gaussian edges in the photobleach) instead of the old uniform initial conditions but still corrected the data with the old photobleaching correction procedure. This converted the k*_on and k_off estimates from the same data set to values (rows labeled New Original) much closer to those from the new procedure (rows labeled New New). The “New New” estimates were obtained from the same data by applying the new photobleaching correction procedure and using a model with a finite nucleus with the same Gaussian initial conditions. This yielded some change in the average value of the estimates and a tightening in the spread of the estimated values. The sum of squared residual plots for these fits reveals how the initial conditions corrupted the original estimates (C). Shown for each of the conditions in B are corresponding one-dimensional profiles through the residuals plot along a path in (k*_on, k_off) space (corresponding to the gray line in the colored plot) that yielded the minimum sum of residuals for each k*_on. The old initial conditions created a global minimum (Original Original) that disappeared with the new initial conditions (New Original). The new photobleaching correction and finite nucleus yielded a more pronounced version of the new global minimum.

FIGURE 6

Influence of presuming uniform initial conditions for strip FRAP of p53. The original and new estimates were reasonably close (A), yet the original strip FRAP for p53, like the original circle FRAP for GR, presumed uniform initial conditions for the photobleach. The much smaller impact of this incorrect presumption on the p53 estimates was due to the presumed size of the uniformly bleached region for p53 versus GR. A simulated strip FRAP curve was generated with the estimated binding rates for p53 (k*_on = 0.15 s⁻¹, k_off = 0.4 s⁻¹) and Gaussian initial conditions (length of nucleus = 20 μm, σ = 1 μm, bleach depth θ = 0.2). Then this curve was fit with a strip FRAP model using a uniform photobleach profile of two different sizes. When the size (3 μm) was chosen to match the amount of fluorescence destroyed by the simulated Gaussian photobleach, then the residuals plot yielded a global minimum close to the global minimum produced with the Gaussian initial conditions (C, middle versus bottom, analog of p53 scenario). When the presumed size of the uniformly bleached area was too small (2.25 μm) to account for the fluorescence destroyed by the Gaussian photobleach, then a new global minimum appeared at much larger binding rates that yielded a slightly better fit than the original minimum (C, top, analog of GR scenario—compare to Fig. 5 C).

FIGURE 7

Observational photobleaching. (A) Fluorescence decay curves of GFP-GR in live cells consistently show a faster decay followed by a slower decay. The slower decay can be described by a single exponential (time constant shown in the box). When the decay is measured after a FRAP experiment has been performed, the slower fraction of the decay curve yields the same decay rate, indicating that this rate is not affected by the intervening FRAP experiment. (B) The fitted exponential function exhibits similar decay behavior as the equilibrated FRAP curve (both curves are shown 10 s after the start of image acquisition). (C) The FRAP curve is divided by the fitted exponential decay curve to correct for observational photobleaching. This yields a corrected curve that plateaus at a constant level, which is <1 due to the fluorescence destroyed by the intentional photobleach.

FIGURE 8

Determination of the initial condition. (A) Schematic illustrating the measurement procedure. The rectangle delineates the imaged area. Intensities were averaged along the directions indicated by the arrows. (B) Averaged radial intensity profile of a circle FRAP experiment (circles) was fitted (shaded line) with a central constant function with a Gaussian distribution at the edge. (C) Averaged linear intensity profile of a strip FRAP experiment (circles) was fit (shaded line) with a Gaussian distribution. The dashed lines mark the bleached regions, solid lines the measured regions. Both measured intensity profiles have been normalized by the prebleach intensity profile.

FIGURE 9

Correction for detector blinding in strip FRAP. (A) Integrating the intensity profile at a series of time points after the intentional photobleach yields changing values (open circles) instead of a constant over time. This contradicts conservation of total fluorescence. Correction for detector blinding (see below) yields the expected response (solid circles). (B) FRAP on a fluorescent plastic slide reveals that detector sensitivity transiently decreases immediately after the intentional photobleach. Intensity was averaged in the right quarter of the slide, whereas increasing portions on the left side of the slide were photobleached (over the full height of the image). The loss of sensitivity increases with increasing bleached areas, but still occurs even when the photobleached area is completely separate from the measured area, thus ruling out reversible photobleaching. (solid curve, full width bleached; shaded curve, half width bleached; dotted curve, quarter width bleached). (C) A comparable effect is seen with typical cellular intensities under our new strip FRAP conditions, as revealed by FRAP performed on fixed cells containing GFP-GR. A detector response curve (inset) was obtained by dividing the data by its final postbleach intensity. This response curve was used to correct strip FRAP data. (D) Early time points for uncorrected and corrected strip FRAP curves are shown, along with the parameter estimates obtained. For this p53 recovery, the principal error arising from neglecting detector blinding is in the estimated diffusion constant.