S seen between the genes deregulated by GABPA loss and genes

S seen between the genes deregulated by GABPA loss and genes whose regulatory buy 4EGI-1 regions are bound by ELK1 (Fig. S2). Next, we used gene ontology (GO) analysis to assess the processes associated with the genes deregulated upon GABPA depletion. A number of functional categories were enriched, including several terms associated with the cell cycle, but also additional terms associated with the actin cytoskeleton (Fig. 2B). Further GO term analysis on the genes directly regulated by GABPA (i.e. both bound and deregulated) still returned terms associated with the cell cycle but those associated with the cytoskeleton were absent (Fig. 2C). This suggests that GABPA has a major direct role in cell cycle control as reported previously [9] but it mainly controls genes associated with the cytoskeleton in an indirect manner. Although, the majority of regulation of cytoskeletal genes by GABPA appears to be indirect, we sought evidence that GABPA might also influence the formation of the actin cytoskeleton and cell migration in a more direct manner by acting through a more limited number of genes that are not abundant enough to constitute an over-represented GO term category. To test this, we manually extracted all the genes coding for cytoskeletal-, migration-, and adhesion-related proteins from the dataset of genes bound and regulated by GABPA, and looked at their expression in more detail (Fig. 2D). Of the 34 genes that matched this description, 70 showed downregulation upon GABPA depletion, indicating that GABPA acts predominantly as an activator in this context (Fig. 2D, top). Importantly, only two of these directly regulated genes were shown by ChIP-seq to be occupied and regulated by ELK1 in MCF10A cells (Fig. 2D) [7]. However, despite the lack of apparent ELK1 occupancy, a number of the genes directly regulated by GABPA were also deregulated upon ELK1 depletion, suggesting that an indirect mechanism is involved. Nevertheless, a number of these direct GABPA target genes are downregulated upon GABPA depletion but not following ELK1 depletion (eg RAC2, RACGAP1, SEMA3A; Fig. 2D) demonstrating the unique activity of GABPA in this context. Conversely, there are also a large number of genes associated with cytoskeletal and migratory functions that are bound and regulated by ELK1 and again ELK1 acts predominantly as a transcriptional activator in this context (Fig. 2D, bottom). Only a small proportion (27 ) of these direct ELK1 target genes are also deregulated upon GABPA depletion, reinforcing the notion that ELK1 has a specific activity in directly regulating the expression of a large cohort of genes involved in these cellular functions. Together these results demonstrate that GABPA controls the expression of a large number of genes associated with the formation of the actin cytoskeleton and required for cell migration. Comparisons with ELK1 reveal that there are a number of shared target genes but GABPA and ELK1 each control 12926553 the expression of a group of specific target genes within these functional categories.GABPA controls an integrated network of cytoskeletonrelated genesGO term enrichment suggested that GABPA, either directly or indirectly, controls the expression of groups of genes associated with the actin cytoskeleton and cell migration. Many of the changes in gene expression that occur upon GABPA depletion are moderate, despite the strong phenotype we see, and part of the Indolactam V reason for this could be that the GABPA target genes might be function.S seen between the genes deregulated by GABPA loss and genes whose regulatory regions are bound by ELK1 (Fig. S2). Next, we used gene ontology (GO) analysis to assess the processes associated with the genes deregulated upon GABPA depletion. A number of functional categories were enriched, including several terms associated with the cell cycle, but also additional terms associated with the actin cytoskeleton (Fig. 2B). Further GO term analysis on the genes directly regulated by GABPA (i.e. both bound and deregulated) still returned terms associated with the cell cycle but those associated with the cytoskeleton were absent (Fig. 2C). This suggests that GABPA has a major direct role in cell cycle control as reported previously [9] but it mainly controls genes associated with the cytoskeleton in an indirect manner. Although, the majority of regulation of cytoskeletal genes by GABPA appears to be indirect, we sought evidence that GABPA might also influence the formation of the actin cytoskeleton and cell migration in a more direct manner by acting through a more limited number of genes that are not abundant enough to constitute an over-represented GO term category. To test this, we manually extracted all the genes coding for cytoskeletal-, migration-, and adhesion-related proteins from the dataset of genes bound and regulated by GABPA, and looked at their expression in more detail (Fig. 2D). Of the 34 genes that matched this description, 70 showed downregulation upon GABPA depletion, indicating that GABPA acts predominantly as an activator in this context (Fig. 2D, top). Importantly, only two of these directly regulated genes were shown by ChIP-seq to be occupied and regulated by ELK1 in MCF10A cells (Fig. 2D) [7]. However, despite the lack of apparent ELK1 occupancy, a number of the genes directly regulated by GABPA were also deregulated upon ELK1 depletion, suggesting that an indirect mechanism is involved. Nevertheless, a number of these direct GABPA target genes are downregulated upon GABPA depletion but not following ELK1 depletion (eg RAC2, RACGAP1, SEMA3A; Fig. 2D) demonstrating the unique activity of GABPA in this context. Conversely, there are also a large number of genes associated with cytoskeletal and migratory functions that are bound and regulated by ELK1 and again ELK1 acts predominantly as a transcriptional activator in this context (Fig. 2D, bottom). Only a small proportion (27 ) of these direct ELK1 target genes are also deregulated upon GABPA depletion, reinforcing the notion that ELK1 has a specific activity in directly regulating the expression of a large cohort of genes involved in these cellular functions. Together these results demonstrate that GABPA controls the expression of a large number of genes associated with the formation of the actin cytoskeleton and required for cell migration. Comparisons with ELK1 reveal that there are a number of shared target genes but GABPA and ELK1 each control 12926553 the expression of a group of specific target genes within these functional categories.GABPA controls an integrated network of cytoskeletonrelated genesGO term enrichment suggested that GABPA, either directly or indirectly, controls the expression of groups of genes associated with the actin cytoskeleton and cell migration. Many of the changes in gene expression that occur upon GABPA depletion are moderate, despite the strong phenotype we see, and part of the reason for this could be that the GABPA target genes might be function.