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J Cell Sci. Feb 1, 2009; 122(3): 345–356.
Published online Jan 6, 2009. doi:  10.1242/jcs.035865
PMCID: PMC2724732

Combinatorial probabilistic chromatin interactions produce transcriptional heterogeneity

Summary

Gene regulation often appears deterministic in the average cell population, but transcription is a probabilistic process at the single-cell level. Although many mechanisms are invoked to account for this behavior, it is difficult to determine how cell-to-cell variation in the interactions of transcription factors with target chromatin impact transcriptional output. Here, we use cells that contain a 200-copy tandem array of promoter or reporter gene units to simultaneously visualize transient interaction, equilibrium or steady-state binding of fluorescent-protein-labeled glucocorticoid receptor with its DNA response elements, the recruitment of diverse coregulators, and transcriptional output at the single-cell level. These regulatory proteins associate with target chromatin via a probabilistic mechanism that produces cell-to-cell variability in binding. The multiple steps of this process are partially independent and differ between individual regulators. The association level of each regulator influences the transcriptional output in individual cells, but this does not account for all transcriptional heterogeneity. Additionally, specific combinatorial interactions of the glucocorticoid receptor and coregulators with response elements regulate transcription at the single-cell level. Like many endogenous genes, the average array transcriptional activity evolves over time. This apparently deterministic average temporal promoter progression involves changes in the probability that specific combinatorial glucocorticoid receptor and coregulator interactions will occur on the response elements in single cells. These data support the emerging `return-to-template' transcription model, which mechanistically unifies the observed extremely transient interactions between the transcription factor and response elements, cell-to-cell variability in steady-state association of factors with chromatin, and the resulting heterogeneous gene expression between individual cells.

Keywords: Chromatin, Steroid receptor, Stochastics, Transcription

Introduction

In response to a specific developmental or homeostatic signal, the average transcriptional output from a cell population is typically regulated in a reproducible manner, giving rise to deterministic models of gene expression. Deterministic models predict that increasing concentrations of activated nuclear transcription factor complexes will uniformly interact with the target gene promoters and cause homogenous transcription in all of the individual cells within the population. By contrast, numerous studies reveal that expression of a given gene is highly variable between individual isogenic cells in the population. This heterogeneous gene expression exists in systems ranging from bacteria and yeast to mammalian cells derived from normal tissue, suggesting that cell-to-cell variation is fundamental to the process of gene activation (Bahar et al., 2006; Blake et al., 2003; Elowitz et al., 2002). These results have led to the development of stochastic gene expression models (reviewed by Kaern et al., 2005; Kaufmann and van Oudenaarden, 2007), where each allele is activated by multiple regulatory events that occur with some controlled probability. However, the mechanistic details of how the probabilistic transcription factor interactions with chromatin give rise to the deterministic transcriptional response observed in the averaged cell population require further clarification.

Transcriptional heterogeneity can be caused by regulatory events that occur independently at each allele. This variability, termed gene intrinsic noise, is predicted to be caused by the inherently random association of low concentrations of transcription factors with the limiting number of regulatory elements in the target gene promoters (Elowitz et al., 2002; Raser and O'Shea, 2004; Swain et al., 2002). Additionally, random transitions in the surrounding chromatin environment also affect the heterogeneous transcription of individual homologous alleles. Studies in yeast reveal that the state of the surrounding chromatin regulates all the promoters at a single genomic locus in a coordinated manner, but individual homologous loci have variable regulation (Becskei et al., 2005). Mammalian cells exhibit similar behavior (Raj et al., 2006), suggesting a strong evolutionary conservation of the mechanisms that link the local chromatin environment to the probabilistic regulation of gene expression.

The mouse mammary tumor virus long terminal repeat (MMTV-LTR) promoter provides a well-characterized system to define the probabilistic transcriptional mechanisms that underlie the apparent deterministic behavior of the averaged mammalian cell population. When bound by the synthetic steroid dexamethasone (Dex), glucocorticoid receptor (GR) protein associates with six DNA response elements located in the MMTV-LTR to strongly activate transcription (Huang et al., 1981; Payvar et al., 1983; Scheidereit et al., 1983). When the GR binds to the response elements, there is an extensive reorganization of the chromatin, which allows additional DNA-binding transcription factors and coregulators to access the site (Richard-Foy and Hager, 1987). This change in the chromatin conformation involves the action of the Brg1 containing ATP-dependent nucleosome-remodeling complex (Fryer and Archer, 1998). GRs also recruit many other coregulator protein complexes to activate the promoter, including complexes that contain the p160 coactivator GRIP, additional histone acetyltransferases (HATs), and histone deacetylases (HDACs) (Li et al., 2003; Qiu et al., 2006). The GR-dependent activation of MMTV transcription is temporally complex, reaching a maximal level within 30 minutes then rapidly evolving to an attenuated state within 2 hours (Archer et al., 1994; Becker et al., 2002). This reproducible, time-dependent progression of the averaged cell population appears to be strongly deterministic.

We have previously studied how GR association with response elements and the surrounding chromatin environment interact to control transcription using a cell line that contains a 200-copy MMTV-LTR reporter gene tandem array integrated at a single genomic locus (referred to as the MMTV array) (McNally et al., 2000; Walker et al., 1999). Importantly, photobleaching experiments on living cells demonstrate that the GR and coregulators concentrated at the MMTV array are not stably bound, but are dynamically exchanging with the surrounding nucleoplasm over a time scale of seconds (Becker et al., 2002; McNally et al., 2000). The `return-to-template' model proposes that the transient recruitment of multiple transcription factor-coregulator complexes over time causes multiple stochastic regulatory events at each promoter during transcriptional activation (Hager et al., 2004; Hager et al., 2006). In the current report, we reveal how the probabilistic formation of many different transcription-factor–chromatin states at the MMTV promoter can give rise to both heterogeneous transcriptional behavior within single cells, and also produce an apparent deterministic response in the averaged cell population.

Results

Steady-state binding of GR and associated coregulators with chromatin and resulting transcription in the averaged cell population

We generated two stable inducible cell lines to explore the actions of the GR and interacting coregulator proteins at the single-cell level. The 3617 cell line, which contains the integrated MMTV promoter-reporter gene array and expresses GFP-labeled GR (GFP-GR), was the founder cell line for the two additional lines. The resulting 6643 cell line and 6790 cell line express exogenous Brg1 or GRIP, respectively, as a fusion protein labeled with the monomeric Cherry red fluorescent protein (Ch-Brg1 or Ch-GRIP). High-resolution fluorescence micrographs show the subnuclear localization of each separate fluorophore signal (Fig. 1, left three panels). The overlay images demonstrate that in response to Dex treatment Ch-Brg1 and Ch-GRIP concentrate with GFP-GR at the site of MMTV array transcription (Fig. 1, right panel). This increased steady-state concentration of transcription factors in a distinct subnuclear region results from the balance of highly transient interactions with the MMTV promoter chromatin (Hager et al., 2006).

Fig. 1.
Transcriptional coregulators concentrate at the MMTV gene array when expressed in stable inducible cell lines. (A,B) Fluorescence microscopy images are shown for (A) the 6643 cell line expressing Ch-Brg1 or (B) the 6790 cell line expressing Ch-GRIP. ...

We have previously developed an unbiased high-resolution microscopy method and an automated image analysis algorithm that together systematically measure the factors associated with the MMTV array and the resulting transcriptional output in large numbers of cells (Voss et al., 2006). Averaging the measurements from more than 500 individual 3617 cells reveals a ~tenfold increase of MMTV-dependent transcription following 30 minutes of Dex treatment (Fig. 2A). After 4 hours of continuous Dex treatment, the RNA FISH signal decreases ~40% compared with maximal levels. The intensity of fluorescent protein at the MMTV array relative to the surrounding nucleoplasm intensity, referred to as the array loading ratio, approximates the amount of steady-state association with the promoters in each cell (Voss et al., 2006). An example of the automated image analysis algorithm measurement of cell line 3617 with different levels of GFP-GR array loading is shown in supplementary material Fig. S1. Although this assay of GR-MMTV array interaction utilizes measurement of a single pixel, the method is not dominated by random noise in the images (supplementary material Fig. S2). In the averaged cell line 3617 populations, the average GFP-GR array loading ratio significantly increases threefold after 30 minutes, then decreases slightly but significantly from the maximal level after 4 hours of continuous Dex treatment (Fig. 2B). The details of all statistical pairwise comparisons of the mean values in Fig. 2 are shown in supplementary material Table S1.

Fig. 2.
Temporal progression of MMTV promoter activity in the averaged cell populations. The parental 3617 cell line, the Ch-Brg1-expressing 6643 cell line, and the Ch-GRIP expressing 6790 cell line were treated with 100 nM Dex for the indicated lengths of ...

The ATP-dependent Brg1-containing chromatin-remodeling complexes, have an important role in the regulation of GR-mediated transcription. Exogenous expression of Ch-Brg1 in cell line 6643 causes a modest increase in the average MMTV transcriptional activity compared with cell line 3617 (Fig. 2A). This slight difference becomes statistically significant when comparing the 6643 cell line with the 3617 cell line after 4 hours of Dex treatment (Fig. 2A; supplementary material Table S1). Ch-Brg1 expression also leads to a modest but significant decrease in the mean steady-state association of GR with the MMTV array (Fig. 2B; supplementary material Table S1). In response to hormone, there is a slight but significant increase in the average steady-state association of Ch-Brg1 with the MMTV array (Fig. 2C; supplementary material Table S1). Although it is clear that exogenous Ch-Brg1 regulates MMTV promoter activity, the general behavior observed in cell line 6643 is probably similar to that of cells expressing only endogenous Brg1. Western blots reveal that there is relatively little overexpression of Ch-Brg1 compared with endogenous protein (supplementary material Fig. S3B), consistent with the minor effects observed in the Ch-Brg1 cells.

The p160 coactivator GRIP directly interacts with GR (Hong et al., 1996; Hong et al., 1999). In turn, GRIP facilitates the recruitment of additional coregulator proteins, which possess enzymatic functions required for gene activation (Li et al., 2003; Ma et al., 2001). Unlike Ch-Brg1, exogenous Ch-GRIP has statistically significant effects on transcription only after long-term hormone treatment compared with short-term treatment, preventing the time-dependent decrease seen in cell line 3617 (Fig. 2A; supplementary material Table S1). Ch-GRIP expression also causes significantly increased steady-state association of GR with the MMTV array compared with cell line 3617 (Fig. 2B; supplementary material Table S1), suggesting that additional GRIP modifies the balance of dynamic GR association-dissociation rates with the MMTV-LTR. In response to hormone, there is also a large increase in the amount of Ch-GRIP associated with the MMTV array (Fig. 2C; supplementary material Table S1). Unlike the response in cell line 3617, the steady-state levels of GR and GRIP at the array do not decrease significantly at the later time point in cell line 6790 (supplementary material Table S1). Ch-GRIP is expressed approximately twofold over endogenous protein levels in these cells (supplementary material Fig. S3C). Although it is clear that this Ch-GRIP expression level alters normal MMTV promoter progression in the 6790 cell line, the cell line provides insight into how this important coregulator influences probabilistic transcriptional regulation.

Heterogeneity within the cell population of GR-coregulator-chromatin association and transcriptional output

At the averaged cell population level, the time-dependent hormone response is very reproducible and appears deterministic. However, we questioned whether the system behaves probabilistically at the single-cell level. Indeed, there is a large degree of heterogeneity between individual cells within each population, suggesting probabilistic mechanisms drive the process. This heterogeneity is illustrated by histogram stair-step plots showing the fraction of the cell population at each measured level of the response (Fig. 3). In the absence of hormone, the majority of cells from the 3617 cell line have low levels of RNA FISH signal (Fig. 3A). Treatment with Dex for 30 minutes produces a broad shift in population where many more cells have higher levels of RNA FISH signal. Strikingly, the plot shows that the RNA FISH signal after 30 minutes of Dex treatment varies by as much as 25-fold between individual cells.

Fig. 3.
Cell-to-cell variability during MMTV promoter progression. The single-cell microscopy measurements, which were averaged in Fig. 1, were sorted into histogram bins according to levels of the measured parameters: (A,C,F) RNA FISH signal, (B,D,G) GFP-GR ...

Gene expression variability within a cell population can be quantified using the noise strength term (calculated as the square of s.d. divided by the mean) (reviewed by Kaern et al., 2005). The statistically larger value of the FISH noise strength in 3617 cells after 30 minutes compared with values before hormone treatment indicates an increase in variability (Fig. 4A; supplementary material Table S2). After 4 hours of hormone treatment, there is a broad shift in the population to lower RNA FISH values, accompanied by a further significant increase in the noise strength. Thus, transcriptional output becomes more heterogeneous over time in cell line 3617 populations. Similar transcriptional noise strength trends are found for cells expressing Ch-Brg1 or Ch-GRIP, although the values are not significantly different at 0.5 hours compared with 4 hours of Dex treatment (Fig. 4A; supplementary material Table S2). This time-dependent trend of RNA FISH noise strength in the Ch-GRIP cell line (Fig. 4A) suggests that the relative degree of heterogeneity is independent of the average level of transcription, but additional studies are required for confirmation.

Fig. 4.
Mean noise strength for the cell populations. For each biological condition, a noise-strength value was calculated for individual cells in each replicate culture that was assayed. These noise-strength values from replicate cultures were averaged to ...

Time-dependent changes in GR and MMTV array loading ratio noise-strength values show similar trends to those measured for the RNA FISH signal in all three cell lines (compare Fig. 4A with Fig. 4B). Similarly to the difference in RNA FISH noise-strength values, the difference between 0.5 and 4 hour GR array loading ratio noise-strength values is only statistically significant in the 3617 cell line (supplementary material Table S2). These trends provide further evidence that probabilistic GR and MMTV association, and transcriptional output might be linked at the single-cell level. Interestingly, the loading ratios for the coregulators do not show a strong time-dependent increase in noise strength (Fig. 4; supplementary material Table S2). Therefore, the probabilistic association of these coregulators with the promoter appear to be partially independent from the GR, and less tightly correlated with transcriptional output.

Some general mechanistic information can be derived from measurements of heterogeneity within the cell populations. Completely independent events occurring in a given time span generate a Poisson distribution when sampled, and the Poisson distribution, by definition, produces a noise-strength value equal to 1. Noise-strength values that differ from 1 indicate that the measured events are not fully independent. The FISH signal noise strength for each hormone treated condition is greater than 1 (Fig. 4). Also, the array association noise strength values are greater than 1 for GRIP. Single-cell gene expression analysis has previously revealed noise-strength values greater than 1 (Becskei et al., 2005; Raj et al., 2006). This has been interpreted as strong evidence for transcriptional bursting, resulting from a temporary chromatin state that allows rapid transcriptional reinitiation at a given promoter (Kaufmann and van Oudenaarden, 2007). In contrast to the analysis of transcriptional output and GRIP-MMTV association, GR and Brg1 association with MMTV measurement produce noise-strength values that are less than 1. Similar decreases in variability are possible when negative-feedback loops regulate gene expression (Becskei and Serrano, 2000). These data suggest that the two coregulators associate with the MMTV array under control of different probabilistic rules, which might involve multiple interrelated steps. Interestingly, recent quantitative models suggest that single-molecule experiments are necessary to dissect the specific source of gene expression variability involving multiple connected regulatory steps (Pedraza and Paulsson, 2008). Therefore, additional experiments are required to expand these novel findings.

Connections between transcription factor and chromatin association, and transcriptional output at the single-cell level

Locally weighted scatter-plot smoothing (Loess) analysis was used to calculate the average level of RNA FISH signal for the entire range of GR array loading ratios measured in individual cells. Analyzing cell line 6643 cells that express Ch-Brg1, the Loess average line confirms that there is a non-linear relationship between the GR-MMTV association, and transcriptional output (Fig. 5A). Low level increases in GR-MMTV association stimulate transcription, illustrating that GR interactions with chromatin at the single-cell level influence transcriptional output. The transcriptional response plateaus at higher levels of GR-MMTV association, suggesting that other factors become limiting under these conditions. The measurements from individual cells are widely scattered around the average line, and additional probabilistic factors must be responsible for the remaining transcriptional heterogeneity. Best-fit Loess lines from cell line 6643 show a decrease in the transcriptional efficiency at any given level of GR-MMTV association at the 4 hour time point compared with that at the 0.5 hour time point (Fig. 5A). This difference is statistically significant over the GR array loading ratio range of 1.8 to 4.3 (supplementary material Fig. S4F), suggesting that the activation is mediated by factors other than GR changes during promoter progression. These non-linear relationships are qualitatively similar to those observed in cell line 3617. However, at either time point, expression of Ch-Brg1 significantly increases the transcriptional output over a broad range of GR-MMTV association values, as determined by comparison with Loess lines calculated from cell line 3617 data (Fig. 5A; supplementary material Fig. S4B,E). These single-cell data demonstrate how the loss of GR-MMTV association can coincide with increased transcription in the cell population. The relationships between Ch-Brg1–MMTV association and transcriptional output are qualitatively similar to those observed for GR-MMTV association and transcription (compare Loess lines for cell line 6643 in Fig. 5A,C). At the 4 hour time point compared with the 0.5 hour time point, the relationships between Ch-Brg1–MMTV association and transcriptional output also show a significant decrease in the transcriptional efficiency over a broad range of GR-MMTV association levels (Fig. 5C; supplementary material Fig. S6A). Together, these results suggest that GR and Brg1 association with the array are partially correlated at the single-cell level.

Fig. 5.
Pairwise statistical modeling of GR-chromatin association, coregulator-chromatin association and transcriptional output in single cells during MMTV promoter progression. (A) The GFP-GR array loading ratio and RNA FISH signal or (C) Ch-Brg1 array loading ...

Qualitatively similar non-linear relationships between the GR-MMTV association and transcriptional output are also present in the Ch-GRIP-expressing cells from the 6790 cell line (Fig. 5B), again indicating that other factors contribute to the variable transcription within this cell line. The Loess average lines show that the non-linear relationship between GR-MMTV association and transcription only changes slightly over time in these cells. However, the slight differences between these relationships are statistically significant, except near the GR-MMTV association value range where the lines cross each other (supplementary material Fig. S5F). Furthermore, the non-linear relationship between GR-MMTV association and transcription in Ch-GRIP-expressing cells is quantitatively similar to the relationship in cell line 3617 after 30 minutes of hormone treatment (supplementary material Fig. S5B). However, comparing cell line 6790 and cell line 3617 after 4 hours of hormone treatment, the transcriptional efficiency increases dramatically in individual cells from the 6790 cell line at any level of GR-MMTV association (Fig. 5B), and this difference is statistically significant (supplementary material Fig. S5E). This indicates that exogenous GRIP expression alters the balance of complexes at the promoter to increase the efficiency of GR-dependent transcription at later time points. Consistent with this finding, the non-linear relationship between Ch-GRIP–MMTV association and transcription also remains relatively constant over time (Fig. 5D; supplementary material Fig. S6B). These results reveal how the Ch-GRIP-induced changes at the single-cell level alter promoter progression in the averaged cell population.

Association of GR with chromatin influences the recruitment of coregulators at the single-cell level

Analysis of single-cell data also delineates the quantitative relationships between the steady-state association of GR with the MMTV array and the association of the coregulators with the MMTV array. The Loess line shows that the average amount on Ch-Brg1 associated with the array plateaus in cells with increasing GR-MMTV association (Fig. 6A). Other factors that are required for GR to interact with Brg1, such as BAF60a (Hsiao et al., 2003), might become limiting and cause this non-linear relationship. By contrast, the association of Ch-GRIP with the MMTV array linearly correlates with the increases in GFP-GR-MMTV association (Fig. 5B). This is consistent with the direct physical interaction between the GR and GRIP (Hong et al., 1996; Hong et al., 1999), and further highlights the differences between the two coregulators at the single-cell level. For both coregulators, the Loess lines only slightly change from 0.5 to 4 hours of hormone treatment (Fig. 6). These relationships are statistically different only over relatively limited ranges of GR array loading values (supplementary material Fig. S7), indicating that on average, a given level of GR at the MMTV array has a relatively constant probabilistic efficiency for recruiting these coregulators during temporal promoter progression. Importantly, the data from individual cells is widely scattered around the average Loess lines (Fig. 6), suggesting that the level of associated coregulator is not strictly determined by the level of GR-MMTV association.

Fig. 6.
Relationships between GR-chromatin association and coregulator-chromatin association in single cells during MMTV promoter progression. (A) The GFP-GR array loading ratio and Ch-Brg1 array loading ratio were plotted for cell line 6643 populations. Each ...

GR and coregulators combinatorially interact with chromatin to influence probabilistic transcription

The wide distributions of array loading values for the individual transcription factors demonstrate the probabilistic nature of GR and coregulator interactions with chromatin targets (Fig. 3). The probabilities of these individual interactions change over time, and contribute to time-dependent regulation of transcription. Since there are detectable relationships between GR-MMTV association and the recruitment of the coregulators (Fig. 6), we must understand how the probability of combinatorial GR-coregulator-MMTV interactions change during promoter progression. The distribution of individual cells exhibiting different combinations of GR loading ratios and coregulator loading ratios can be analyzed using local-likelihood statistical methods. The fraction of cells with any given GR and cofactor loading-ratio combination is related to the probability that this specific combination of interactions will occur in an individual cell. The resulting probability plots are similar to the results from multi-factor FACS analysis, and represent the relative number individual cells with each combination of GR and coregulator interaction in a color-coded format (Fig. 7).

Fig. 7.
Distribution of combinatorial GR-array association and cofactor-array association in the cell populations. Local-likelihood statistical methods calculate the probability that an individual cell will concentrate any given level of GFP-GR and coregulator ...

After 30 minutes of hormone treatment, the highest probability combination in an individual cell for GFP-GR and Ch-Brg1 array loading ratio is approximately 3.7 and 1.9, respectively (Fig. 7A). Therefore, the highest probability combination of GR-MMTV and Brg1-MMTV association in single cells closely agrees with the single-parameter measurements averaged for the cell population (compare with Fig. 2B,C). There is a continuous decrease in probability that radiates from the maximal point in an ellipsoid fashion (Fig. 7A), with more variability in the GR parameter relative (range laterally) to the Brg1 parameter (range vertically). After 4 hours of hormone treatment, the highest probability combination moves to lower values of GR and Brg1 loading ratios (Fig. 7B), again in agreement with the averaged measurements (compare with Fig. 2B,C). The more widely spread probability combinations (the decrease in the area of the red region indicating high probability combinations) show the effect of additional variability in GR-MMTV association after 4 hours of hormone treatment (Fig. 7B). By subtracting the earlier time point distribution from the later one, the array association combinations with higher probability and lower probability at the later time point become more easily detected (Fig. 7C, note the green color indicates no time-dependent change). The most probable combination of loading-ratio values in an individual cell is approximately 4.5 for both GFP-GR and Ch-GRIP after 30 minutes of hormone treatment (Fig. 7D). The distribution of probabilities shifts at the later time points, with a single cell having a higher probability of associating combinations of more GR and more GRIP with the array (Fig. 7E). The red areas in the difference plot highlight this time-dependent increase in probability (Fig. 7F). These data demonstrate that the probability of specific combinatorial protein and chromatin interactions changes during promoter progression.

The large amount of transcriptional scatter surrounding the best-fit relationship with single factor and array association indicated that additional factors must be also be variable at the single-cell level to produce the transcriptional heterogeneity within the cell populations (Fig. 5). Multivariate local regression methods were used to test this prediction further. Local regression calculated the average transcriptional output for each measured combination of GR and coregulator-array association. The calculated transcriptional output relative to the mean transcription in cells without hormone is presented for each level of GR array loading ratio and coregulator array loading ratio (Fig. 8). After 30 minutes of hormone treatment, the transcription levels from combinations of GFP-GR array loading and Ch-GRIP array loading show a complex pattern. The pattern demonstrates that for a given level of steady-state GR-MMTV association (all the cells on a given vertical column on the graph, Fig. 8B) a critical level of Brg1-MMTV association is also required to efficiently activate transcription at the single-cell level (increase in transcription along the same vertical column on the graph). Although the transcriptional output pattern is different for combinations of GR and GRIP-array association, again the amount of both GR and coregulator associated with the array at the single-cell level control the level of transcription (Fig. 8D). For both coregulators, the transcriptional output from GR and array binding combinations changes over time (Fig. 8B,E). There is a general trend for lower levels of GR-coregulator-MMTV association to become less transcriptionally active whereas higher-level factor combinations become more transcriptionally active over time. This trend is illustrated in the time difference plots, with red values showing the combinations of array association that increase transcriptional output at the later time points (Fig. 8C,F). Taken together, these results strongly support a general mechanism in which probabilistic combinatorial interactions of regulatory proteins with target chromatin contribute to the heterogeneous transcriptional output observed at the single-cell level.

Fig. 8.
Multivariate statistical modeling of GR-coregulator-chromatin association and transcriptional output in single cells during MMTV promoter progression. Multivariate local regression was used to calculate the average FISH signal in individual cells that ...

Discussion

Although much progress has been made in understanding the probabilistic nature of gene expression, very little was previously known about the connections between steady-state binding of transcription factors with integrated DNA response elements and transcriptional output at the single-cell level. Our analysis indicates that the GR and interacting transcriptional coregulators associate with the MMTV array to widely different degrees in individual cells within the population. The quantitative microscopy methods used in this study accurately measure the steady-state binding of array-associated proteins as previously shown by comparison to chromatin immunoprecipitation assays (Voss et al., 2006). The imaging assay is further validated by the biologically induced statistical differences that we observe in parameters (mean values, noise-strength values, non-linear Loess relationships) that are derived from measurements of many single cells. If the imaging assay results were dominated by random methodological variation, then statistically significant differences could not be detected between different biological conditions. Our statistically validated results indicate that the probabilistic interactions of multiple factors with promoter chromatin produce the deterministic temporal progression of transcriptional activity, which is observed in the averaged cell population.

Probabilistic transcription factor association with target promoters

Variable transcription factor binding to target promoters between individual cells might be caused by many possible mechanisms. However, the potential mechanisms probably exhibit a small set of general underlying properties. In some systems, cell-to-cell variation is due to finite number effects, in which limited numbers of molecules cause random and infrequent productive biochemical interactions with target promoters (Elowitz et al., 2002; Raser and O'Shea, 2004; Swain et al., 2002). These inherently random biochemical interactions make each promoter's activity independent of another homologous promoter. However, this type of gene intrinsic noise is unlikely to be a major cause of the MMTV array heterogeneity because the averaging of random independent events at the 200 constituent promoters in the array would cause a homogenous response in each cell.

Probabilistic mechanisms can coordinately regulate multiple promoters when they are integrated at a single site in the genome. When multiple copies of a promoter-reporter construct are tandemly inserted into a single yeast genomic locus and compared with an integrated single-copy promoter-reporter, the expression level increases to the expected level, but the relative cell-to-cell variability does not decrease (Becskei et al., 2005). As explained above, a decrease in cell-to-cell transcriptional variability is expected when multiple independently regulated promoters are in the same cell. However, when a single promoter-reporter construct is integrated in each homologous allele (two copies per cell), the expression level increases and the relative level of cell-to-cell variation decreases as expected (Becskei et al., 2005). Global extrinsic cell-to-cell differences would affect homologous alleles identically and cause relative variation levels to remain constant. Therefore, the decease in variation indicates that extrinsic variability is not the major determinant of heterogeneity in this system.

Transitions in the surrounding chromatin state also appear to coordinately regulate promoters that are tandemly integrated in mammalian cell (Raj et al., 2006). Diverse experimental evidence suggests this property regulates many different promoters, including the MMTV-LTR. For example, there is direct biochemical evidence that the MMTV-LTR in the averaged hormone-treated cell population exists in multiple native chromatin states (Georgel et al., 2003). In addition to the MMTV gene array, another tandemly integrated promoter-gene array model system is also heterogeneously bound by the estrogen receptor (Sharp et al., 2006), again suggesting that probabilistic association mechanisms might be widely utilized in transcriptional regulation. Similarly to the MMTV array, other tandem gene array systems are transiently associated with their activating transcription factor proteins (Bosisio et al., 2006; Sharp et al., 2006). Recent studies also demonstrate that transient protein interactions are involved in changing steady-state transcription-factor-chromatin interaction levels (Karpova et al., 2008). Considering these results, cell-to-cell variability in steady-state chromatin interactions probably involves changes in the balance of the dynamic association and disassociation rates for the interacting proteins.

Additional mechanisms might also regulate promoters that are integrated at a single genomic locus. The controlled movement of multiple promoters into specific subnuclear regions, which facilitate efficient transcription, is proposed to coordinately regulate promoters in a probabilistic manner (Faro-Trindade and Cook, 2006; Osborne et al., 2004). Other dynamic mechanisms such as the self-reinforcing linear spread of regulatory proteins along the chromatin fiber, also coordinately regulate adjacent genes (Grewal and Jia, 2007). Although further experiments are required to delineate which of these additional mechanisms are functioning at specific promoters, it is clear that cell-to-cell variability of transcription-factor-chromatin steady-state association contributes to probabilistic gene expression in the cell population. Importantly, the presented data indicate that probabilistic interactions of multiple factors with chromatin combine to produce transcriptional heterogeneity within the cell population.

Multiple dynamic and probabilistic interactions account for both single-cell and whole population behavior

The combinatorial probabilistic interaction hypothesis is consistent with the `return-to-template' model of transcription (Hager et al., 2004; Hager et al., 2006; Voss and Hager, 2008), where the rapid and transient interactions of GR and multiple coregulator complexes with the promoter chromatin produce many different regulatory events that together activate transcription (Fig. 9A). At the time of maximal activation, illustrated by the peak in the line plot of transcription level averaged for the cell population (Fig. 9C), there is the highest average steady-state level of GR and coregulators associated with the promoters (Fig. 9C). However, at the same time, the promoters in individual cells are associated with heterogeneous steady-state levels of GR and coregulators (Fig. 9B). According to the combinatorial probabilistic interaction hypothesis, probabilistic transitions in the chromatin environment occur at each promoter, and the likelihood of these chromatin transitions is also influenced by the steady-state combination of transcription factors at the promoter. As discussed in the preceding section, transitions probably coordinate large regions of chromatin. Different chromatin states at the genomic loci of promoters alter the probability that a given factor will associate and/or dissociate over a short time period, thus modulating both rapid exchange and steady-state levels of transcription factors at the promoter (Fig. 9B). This connection between transient chromatin states and multiple transcription factor interactions could account for noise-strength values (Fig. 4) that indicate the multiple regulatory events are not completely independent. In this way, the proposed model unifies the dynamic interactions of transcription factors with target promoters, the cell-to-cell variability in steady-state association of transcription factors with target promoters, and the resulting heterogeneous gene expression between individual cells.

Fig. 9.
Multiple probabilistic interactions regulate transcription. (A) Many different proteins rapidly exchange over the time scale of seconds with any given target promoter. These proteins include sequence-specific DNA-binding transcription factors such ...

Unlike the variable transcriptional activity measured at the single-cell level, the intricate time-dependent transcriptional response of the MMTV-LTR in the averaged cell population is highly reproducible. The consistent peak activation at 0.5-1 hour after hormone treatment followed by rapid attenuation of transcription at later time points appears to be deterministic in nature (Archer et al., 1994; Becker et al., 2002). In this study, we have examined this apparent contradiction in detail. At least two probabilistic mechanisms contribute to the temporal progression of promoter activity. The first mechanism involves a time-dependent decrease in probability of high-level GR and cofactor association with the MMTV LTR (Fig. 5). This property of promoter progression is illustrated at the level of the averaged population and the individual cell several times during hormone treatment (Fig. 9B,C). However, in cell subpopulations with equal levels of GR-MMTV association at early and late time points, the transcriptional activity still decreases at later time points (Fig. 5). Therefore, the loss of GR-MMTV association at later time points does not fully account for the decrease in transcription during promoter progression. These results are consistent with our previous single-cell analysis of GR-dependent transcription following both short-term and long-term glucocorticoid treatment (Voss et al., 2006). The second mechanism drives promoter progression independently of the time-dependent decrease in GR-MMTV association and the correlated decreases in Brg1 and GRIP recruitment. The multivariate analysis of the GR-coregulator-MMTV association and transcriptional output reveals that the same combinations of GR-coregulator binding are more transcriptionally active at the 0.5 hour time point relative to the 4 hour time point (Fig. 7). Therefore, some other modification of the proteins associated with the MMTV promoter must change during temporal promoter progression. The timing of maximal transcription at the average cell level is proposed to be caused by an increase in this activating event, which occurs probabilistically at the single-cell level (Fig. 9B,C).

Several previously identified events might drive temporal promoter progression independently of the decrease in steady-state GR-MMTV association. One likely candidate is the time-dependent control of HDAC1 deacetylase activity, which is required for high-level MMTV transcription (Qiu et al., 2006). Before hormone treatment, HDAC1 is unacetylated and enzymatically active, but between 15 minutes and 1 hour of hormone treatment there is a significant acetylation of HDAC1 and a dramatic loss of its deacetylase activity (Qiu et al., 2006). The acetylation of MMTV core histones is also transiently modified during promoter progression (Aoyagi and Archer, 2007), indicating that this might be a downstream effect of the changes in acetylase and deacetylase activities. The enzymatic activity of HDAC1 is regulated over time even when the steady-state association with the GR does not change. Although this independence from the GR is a predicted property of the hypothetical second mechanism, additional experiments are required to define how HDAC1 regulates MMTV transcription at the single-cell level. The dephosphorylation and loss of H1 linker histone from MMTV has also been proposed to have a role in the time-dependent suppression of transcription. However, significant decreases in H1 phosphorylation are first detected after 7 hours of hormone treatment (Lee and Archer, 1998), suggesting that this mechanism does not significantly attenuate earlier MMTV transcription. Additional experimental approaches are required to confirm how the covalent modification of protein complexes contributes to probabilistic behavior of promoters at the single-cell level.

Along with previous studies, the presented data reveal how multiple dynamic and probabilistic protein-chromatin interactions act in combination to generate a controlled transcriptional response in a eukaryotic cell population. Many endogenous genes exhibit a high degree of transcriptional variability between individual mammalian cells (Levsky et al., 2002), and it is likely that similar probabilistic mechanisms regulate endogenous promoters. Several lines of evidence suggest that probabilistic gene expression has many crucial roles in higher eukaryotes. Increases in cell-to-cell transcriptional heterogeneity correlate with aging in normal tissue and are hypothesized to be involved in oncogenesis (Bahar et al., 2006; Capp, 2005). These examples support the concept that probabilistic gene expression decreases viability in higher eukaryotes, but there are also cases where these mechanisms are essential for normal physiology. For instance, stochastic gene expression is thought to be critical for functional photoreactive cells in the retina and for functional odorant-receptor-expressing cells in the olfactory bulb (Shykind, 2005; Wernet et al., 2006). Considering these important aspects of single-cell behavior, we propose that probabilistic and dynamic interactions of multiple regulatory proteins with chromatin control the physiological expression of many genes.

Materials and Methods

Plasmids and generation of inducible cell lines

The coding sequence (CDS) for the monomeric Cherry red fluorescent protein (Ch) was amplified from the pRSET bacterial expression vector (Shaner et al., 2004) using primers with unique restriction enzyme sites. The Ch CDS was then cloned in-frame upstream of Brg1 or GRIP (Baumann et al., 2001) using standard recombinant methods. The fusion protein coding sequences were then subcloned into pRev-TRE retroviral Tet-inducible expression vector (Clontech).

Retroviral particles were produced in Phoenix cells (Swift et al., 2001) by standard methods. Mouse mammary carcinoma 3617 cells, which contain the integrated MMTV reporter gene array and a Tet-inducible GFP-GR expression vector (Walker et al., 1999) were infected with retroviral particles encoding Tet-regulated Ch-Brg1 or Ch-GRIP to produce the 6643 cell line or 6790 cell line, respectively. Cells with integrated retrovirus were selected with Hygromycin for at least 14 days prior to the start cell line characterization. For maintenance, cell line 3617, cell line 6643 and cell line 6790 cells were cultured with DMEM supplemented with 10% fetal calf serum and 5 μg/ml tetracycline to repress expression of the Tet-regulated fusion proteins (Walker et al., 1999).

RNA FISH, microscopy and automated image analysis

18 hours before RNA FISH experiments, cell lines 3617, 6643 and 6790 were plated on number 1 German 22×22 mm square coverslips in DMEM supplemented with 10% charcoal-stripped calf serum. Tetracycline was omitted from the medium to induce expression of the fluorescent fusion proteins. Cells on coverslips were treated with 100 nM dexamethasone for 0, 0.5 or 4 hours then immediately processed for RNA FISH to detect the MMTV-controlled reporter gene, as previously described (Voss et al., 2006).

Following the RNA FISH detection, images of several randomly selected fields of cells were digitally captured using a computer-controlled epifluorescence microscope fitted with a ×60/1.4 numerical aperture, oil-immersion objective (DeltaVision RT, Applied Precision, Issaquah, WA). Movement of a high-precision stage in the optical axis (9.3 μm range at 0.3 μm spacing between images) allowed digital imaging of the full volume of each nucleus. Automated filter wheels and a polychroic light splitter were used to capture images of each fluorophore. Images were batch processed with a commercially available constrained iterative digital deconvolution algorithm (Softworx Explorer Suite; Applied Precision) to quantitatively reassign out-of-focus light and restore signal contrast in the epifluorescence images.

The deconvolved images were processed and analyzed using a custom automated algorithm that was implemented in the Matlab scientific computing software, as previously described (Voss et al., 2006). Briefly, the nucleus of each cell is automatically identified. The algorithm then defines the discreet region in each nucleus containing the RNA FISH signal. The fluorescence intensity and size of the FISH signal are measured as an indicator of MMTV promoter activity in each cell. The positional information defining the FISH signal is then used to measure the degree of FP-fusion protein enrichment at the MMTV array. For each fluorescent protein image, the algorithm calculates the relative transcription factor concentration on the array as the maximal fluorescent protein pixel intensity value in the defined FISH signal region divided by the mean intensity of the fluorescent protein in the nucleus. Measurement from the individual nuclei were exported to spreadsheet software (Excel, Microsoft) for further analysis.

The images of three cells from the 3617 cell line illustrate the biological heterogeneity that exists between the individual clonal cells (supplementary material Fig. S1). The size and fluorescence intensity of the RNA fish signal varies between the cells, but because this area is much brighter than the surrounding nucleoplasm, the automated analysis algorithm uses this local intensity difference to reliably identify the region of interest (ROI) that contains the MMTV array (supplementary material Fig. S1B). In some cells the XFP-protein associated with the MMTV array is highly concentrated (supplementary material Fig. S1C,D, Cell 1), whereas in other cells, the local concentration increase is very low (supplementary material Fig. S1C,D, Cell 3).

Because the boundaries of the protein associated with the array are not robust, it is difficult for an expert user or an automated algorithm to accurately identify the area in the nucleus where the XFP-fusion proteins specifically associate with the MMTV array. To overcome this challenge, the algorithm uses the FISH ROI as a guide to find the maximal concentration of the XFP-fusion proteins at the array (supplementary material Fig. S1C). The single maximal pixel intensity value in the XFP image area that is identified using the FISH ROI is divided by mean nuclear XFP-fusion protein intensity to calculate the loading ratio, which approximates the relative degree of binding (supplementary material Fig. S1C).

The 3D fluorescence-intensity projections demonstrate that the GFP-GR forms `peaks' of intensity with a central maximal point (supplementary material Fig. S1E). We observe similar behavior for the other XFP-fusion proteins (data not shown). This suggests that the maximal single pixel intensity represents the intensity values of the immediately surrounding pixels. We tested this by calculating the loading ratio based on the mean of a 3×3 pixel area (9 pixels total) centered on the maximal intensity pixel. The 3×3 pixel loading ratios calculated for the example images show the same trend as the single maximal pixel loading ratios (supplementary material Fig. S1C). To systematically quantify this trend, the single pixel loading ratio and the 3×3 pixel loading ratio were calculated for many individual cells, and this analysis was performed for XFP-fusion proteins in all cell lines. Linear regression revealed that results from the two measurement methods were correlated with an R2 value of approximately 0.9 (supplementary material Fig. S2). Therefore, the loading ratio based on the maximal single pixel value is not dominated by methodological pixel-to-pixel variation and represents the relative local concentration of the immediately surrounding protein. Since the minimum size of the region where XFP-fusion proteins interact with the array is unknown, the single maximal pixel is used by the algorithm to calculate the loading ratio in the remaining analysis presented in this report.

Statistical analysis

Data were acquired from a minimum of three independent cultures with assays performed on multiple days. The combined morphometric data were imported from the spreadsheet into Matlab for statistical analysis and generation of all graphs. The functions in the Matlab statistics toolbox were used to calculate the mean value and s.e. for each experimental group. Noise strength was calculated as the s.d. squared divided by the mean value for each group (Kaern et al., 2005).

Multiple statistical comparisons are made between the mean parameter data in Fig. 2. When making comparisons between multiple conditions in a given data set using parametric statistical methods, ANOVA was used to first used to determine whether any significant differences existed between all conditions. If significant differences were identified by ANOVA, then a post-hoc test (also known as multiple comparison test) was used to detect differences between specific pairs of values. These parametric statistical methods assume that the measurements in each condition follow a normal distribution. Because the number of measurements for each condition in Fig. 2 is very large, it is possible to determine whether they are normally distributed using a Lilliefors statistical test. Documentation for Lillifors test and other statistical methods used is available at http://www.mathworks.com/access/helpdesk/help/toolbox/stats/. The results of Lilliefors test (data not shown) indicate that these data do not meet the criteria for a normal distribution (P>0.05). Because of this, we used the Kruskal-Wallis and Dunn's test, which are non-parametric equivalents of ANOVA and post-hoc test, to confirm the statistical differences. These non-parametric tests produce only slight changes in the statistical differences identified by the ANOVA and Tukey's HSD post hoc comparisons (Tukey's HSD is based on Student's t-test, http://www.mathworks.com/access/helpdesk/help/toolbox/stats/). We highlight the slight differences between the non-parametric and parametric statistical methods in supplementary material Table S1. Importantly, the two methods yield very similar biological conclusions, which are discussed in the Results section.

We also calculated the noise strength values in replicate cultures, allowing the statistical comparison of the resulting mean noise strength values (Fig. 4). Because there are relatively few calculated values from the individual cultures, parametric tests are more appropriate than non-parametric tests for identifying differences between the means. Therefore, we use ANOVA and Tukey's HSD post-hoc test to detect significant differences in mean noise-strength values between conditions. As detailed in the Results section, this analysis clearly demonstrates that specific biological conditions cause significant reproducible changes in mean noise strength values (supplementary material Table S2).

The best-fit lines for the two-factor analysis were calculated by locally weighted scatter-plot smoothing (Loess) technique implemented in the Matlab statistical toolbox software. A Loess curve from a locally weighted regression is a type of moving average representing the (linear or non-linear) relationship between two parameters (for example, FISH signal versus XFP-array loading ratio). We wished to determine whether two Loess curves are statistically different and also understand where along the x range the two Loess curves are different. We tested these differences between pairs of Loess curves by implementing a permutation test. This is a robust non-parametric statistical test that is valid even when data distributions are unknown.

The permutation test was implemented using the Matlab statistics toolbox software. For each pair of Loess curves, the distance between the curves was defined by the sum of absolute differences between y, using a (dx=0.1) grid over a fixed interval on the x axis. Randomized data sets were generated by combining all data from both groups and randomly reassigning the group labels. Each of the two randomized data sets was used to compute a new Loess curve and the distance between the two randomized Loess curves was calculated the same way as for the original data set. The randomization was repeated 1000 times and we obtained the number of cases where the distance between the two Loess curves was greater than that of the two original Loess curves. This number divided by 1000 is our permutation P value, which approximates the probability of obtaining the observed difference by random chance. We plotted these P values in parallel with the Loess lines for each pairwise comparison, setting the significance difference cut off at P<0.05 (supplementary material Figs S4-7).

The best-fit surfaces for the three-factor analysis (Figs (Figs77 and and8)8) were calculated using locally weighted regression and local-likelihood techniques implemented in the Locfit function package, which was written for Matlab by Catherine Loader (University of Aukland, Aukland, New Zealand). Full documentation for Locfit functions, including source code, is publicly available (http://locfit.herine.net/), and Locfit functions and documentation are also included in the widely used R statistical software package (http://www.r-project.org/).

Western blot analysis

Cell lysates were compared before and after 18 hours of induction of XFP-fusion protein expression, which was initiated by removal of tetracycline from the growth medium. Cells were lysed in RIPA buffer and protein concentration was measured using Bradford assay (Bio-Rad, Hercules CA). Lysates were loaded at 40 μg per well on 3-8% gradient acrylamide Tris-acetate gel (Invitrogen, Carlsbad, CA). Commercial antibodies were used in western blots as follows: anti-GR (PA1-511A, Affinity BioReagents, Golden, CO); anti-Brg1 (07-478 Millipore, Billerica, MA); anti-GRIP (610984, BD Biosciences, San Jose, CA).

Supplementary Material

[Supplementary Material]

Notes

Supplementary material available online at http://jcs.biologists.org/cgi/content/full/122/3/345/DC1

The authors thank Richard N. Day, Catherine L. Smith, and Tom Misteli for helpful discussion during preparation of the manuscript. The mCherry FP cDNA was a generous gift from Roger Tsien. Anindya Hendarwanto provided expert technical support. Tatiana Karpova assisted with experiments performed in the NCI Core Fluorescence Imaging Facility. This research was supported (in part) by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research. Deposited in PMC for release after 12 months.

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