Cal process. Previous studies on GABPA have hinted at a role in controlling cell migration. For example, it was shown that depletion ofGABPA reduced the migratory properties of vascular smooth muscle cells [14]. These effects on migration were attributed to its 
role in controlling the expression of the kinase KIS, and the subsequent effects on phosphorylation and activity of the cell cycle inhibitor p27. However, here we have shown a wider role of GABPA in controlling the expression of genes directly involved in controlling cell migration. In the same study, depletion of GABPAGABPA and Cell Migration ControlFigure 3. GABPA controls the expression of a network of cytoskeleton-related genes. (A) A STRING-derived network of proteins encoded by all genes that exhibit a statistically significant change of expression in MCF10A cells depleted of GABPA, that are associated with regions bound by GABPA, and that belong to GO terms associated with the cytoskeleton, 22948146 cell migration or adhesion as determined by DAVID analysis. Proteins are circled whose encoding genes were chosen for further analysis. (B) The effect of siGABPA transfection on the expression of genes encoding proteins highlighted in panel A (green) and two negative controls (not GABPA targets; grey). Bars show average values from three biological repeats with standard deviation. Statistical AN-3199 significance was determined in paired Student’s t-tests (*P,0.05, **P,0.01). (C) Charts show the binding levels of GABPA to DNA regions associated with genes encoding proteins highlighted in panel A, as determined in ChIP-qPCR ZK-36374 experiments in MCF10A cells transfected with the indicated siRNA species and starved for EGF for 48 hours. IgG immunoprecipitation indicates the level of non-specific binding. (D) ChIP-qPCR of ELK1 occupancy on regions tested in (C) and on two positive control regions (associated with CDKL3 and RFC4). doi:10.1371/journal.pone.0049892.gin MEFs reduced the numbers of cells entering the cell cycle [14], which is consistent with previous work that implicated GABPA as a key controller of cell cycle progression [9]. We also find that in MCF10A cells, GABPA plays an important role in controlling the activity of a programme of genes involved in cell cycle control (Fig. 2B; Figs. S3. S4) and it appears to do this by both indirect anddirect mechanisms. In keeping with this finding, depletion of GABPA in MCF10A cells leads to changes in their overall cell cycle distributions (data not shown). In another study, the analysis of the entire GABPA regulome led to the identification of many of the functional categories that also appear in our data as potentially directly regulated by GABPA such as “transcriptional regulators”GABPA and Cell Migration ControlFigure 4. Depletion of direct target genes of GABPA slows down MCF10A cell migration. (A) Graph shows the mRNA levels of four GABPA target genes in cells 
transfected with the respective siRNA species. Values were normalised to control (siGAPDH transfection) and are presented on one chart for clarity. Bars represent average values from three biological repeats with standard deviation. Statistical significance was determined in Student’s paired t-tests (*P,0.001). (B and C) MCF10A cells were transfected with the indicated siRNAs, starved for EGF for 48 hours, stimulated with media containing 20 ng/ml EGF and imaged for 24 hours. (B) Shown are trajectories travelled by cells in the first six hours of live imaging experiments in the presence.Cal process. Previous studies on GABPA have hinted at a role in controlling cell migration. For example, it was shown that depletion ofGABPA reduced the migratory properties of vascular smooth muscle cells [14]. These effects on migration were attributed to its role in controlling the expression of the kinase KIS, and the subsequent effects on phosphorylation and activity of the cell cycle inhibitor p27. However, here we have shown a wider role of GABPA in controlling the expression of genes directly involved in controlling cell migration. In the same study, depletion of GABPAGABPA and Cell Migration ControlFigure 3. GABPA controls the expression of a network of cytoskeleton-related genes. (A) A STRING-derived network of proteins encoded by all genes that exhibit a statistically significant change of expression in MCF10A cells depleted of GABPA, that are associated with regions bound by GABPA, and that belong to GO terms associated with the cytoskeleton, 22948146 cell migration or adhesion as determined by DAVID analysis. Proteins are circled whose encoding genes were chosen for further analysis. (B) The effect of siGABPA transfection on the expression of genes encoding proteins highlighted in panel A (green) and two negative controls (not GABPA targets; grey). Bars show average values from three biological repeats with standard deviation. Statistical significance was determined in paired Student’s t-tests (*P,0.05, **P,0.01). (C) Charts show the binding levels of GABPA to DNA regions associated with genes encoding proteins highlighted in panel A, as determined in ChIP-qPCR experiments in MCF10A cells transfected with the indicated siRNA species and starved for EGF for 48 hours. IgG immunoprecipitation indicates the level of non-specific binding. (D) ChIP-qPCR of ELK1 occupancy on regions tested in (C) and on two positive control regions (associated with CDKL3 and RFC4). doi:10.1371/journal.pone.0049892.gin MEFs reduced the numbers of cells entering the cell cycle [14], which is consistent with previous work that implicated GABPA as a key controller of cell cycle progression [9]. We also find that in MCF10A cells, GABPA plays an important role in controlling the activity of a programme of genes involved in cell cycle control (Fig. 2B; Figs. S3. S4) and it appears to do this by both indirect anddirect mechanisms. In keeping with this finding, depletion of GABPA in MCF10A cells leads to changes in their overall cell cycle distributions (data not shown). In another study, the analysis of the entire GABPA regulome led to the identification of many of the functional categories that also appear in our data as potentially directly regulated by GABPA such as “transcriptional regulators”GABPA and Cell Migration ControlFigure 4. Depletion of direct target genes of GABPA slows down MCF10A cell migration. (A) Graph shows the mRNA levels of four GABPA target genes in cells transfected with the respective siRNA species. Values were normalised to control (siGAPDH transfection) and are presented on one chart for clarity. Bars represent average values from three biological repeats with standard deviation. Statistical significance was determined in Student’s paired t-tests (*P,0.001). (B and C) MCF10A cells were transfected with the indicated siRNAs, starved for EGF for 48 hours, stimulated with media containing 20 ng/ml EGF and imaged for 24 hours. (B) Shown are trajectories travelled by cells in the first six hours of live imaging experiments in the presence.
