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Gene profiling of MTA1 identifies novel gene targets and functions.

Ghanta KS, Li DQ, Eswaran J, Kumar R - PLoS ONE (2011)

Bottom Line: Metastasis-associated protein 1 (MTA1), a master dual co-regulatory protein is found to be an integral part of NuRD (Nucleosome Remodeling and Histone Deacetylation) complex, which has indispensable transcriptional regulatory functions via histone deacetylation and chromatin remodeling.Emerging literature establishes MTA1 to be a valid DNA-damage responsive protein with a significant role in maintaining the optimum DNA-repair activity in mammalian cells exposed to genotoxic stress.Thus, the presented data emphasizes the known functions of Mta1 and serves as a rich resource which could help us identify novel Mta1 functions.

View Article: PubMed Central - PubMed

Affiliation: McCormick Genomic and Proteomic Center, The George Washington University Medical Center, Washington, D.C., United States of America.

ABSTRACT

Background: Metastasis-associated protein 1 (MTA1), a master dual co-regulatory protein is found to be an integral part of NuRD (Nucleosome Remodeling and Histone Deacetylation) complex, which has indispensable transcriptional regulatory functions via histone deacetylation and chromatin remodeling. Emerging literature establishes MTA1 to be a valid DNA-damage responsive protein with a significant role in maintaining the optimum DNA-repair activity in mammalian cells exposed to genotoxic stress. This DNA-damage responsive function of MTA1 was reported to be a P53-dependent and independent function. Here, we investigate the influence of P53 on gene regulation function of Mta1 to identify novel gene targets and functions of Mta1.

Methods: Gene expression analysis was performed on five different mouse embryonic fibroblasts (MEFs) samples (i) the Mta1 wild type, (ii) Mta1 knock out (iii) Mta1 knock out in which Mta1 was reintroduced (iv) P53 knock out (v) P53 knock out in which Mta1 was over expressed using Affymetrix Mouse Exon 1.0 ST arrays. Further Hierarchical Clustering, Gene Ontology analysis with GO terms satisfying corrected p-value<0.1, and the Ingenuity Pathway Analysis were performed. Finally, RT-qPCR was carried out on selective candidate genes.

Significance/conclusion: This study represents a complete genome wide screen for possible target genes of a coregulator, Mta1. The comparative gene profiling of Mta1 wild type, Mta1 knockout and Mta1 re-expression in the Mta1 knockout conditions define "bona fide" Mta1 target genes. Further extensive analyses of the data highlights the influence of P53 on Mta1 gene regulation. In the presence of P53 majority of the genes regulated by Mta1 are related to inflammatory and anti-microbial responses whereas in the absence of P53 the predominant target genes are involved in cancer signaling. Thus, the presented data emphasizes the known functions of Mta1 and serves as a rich resource which could help us identify novel Mta1 functions.

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Related in: MedlinePlus

Genes regulated by Mta1 in the presence and absence of P53.A: Venn diagrams showing the number of genes that are identified to be genuinely regulated by Mta1 in the presence and absence of P53. (i) The genes shown in WT vs. Mta1-KO (1124) are the genes affected by Mta1 knock out and the genes that are present in Mta1-KO vs. Mta1-KO/Mta1 (184) are affected due to re-expression of Mta1 in the knockout MEFs. The genes that are differentially regulated in both the sets with opposite trends in the regulation are considered as the ‘bona fide’ genes regulated by Mta1. ii) Similarly, the intersection of P53-KO and P53-KO/Mta1 represents the genes differentially regulated by Mta1 over expression in the P53-KO MEFs. i.e. the genes regulated by Mta1 in the absence of P53.This scenario of Mta1 over expression and P53 knock out/mutation mimics most of the cancers iii) The Venn diagram between genes regulated by Mta1 in the presence of P53, 126 and genes regulated by Mta1 in the absence of P53, 266 gives the genes that are regulated by Mta1 only in the presence of P53, irrespective of P53 status and only in the absence of P53 respectively. B: Heat maps representing hierarchical clustering of the differentially regulation, plotted using the log2 values of the genes with p-value≤0.05 (unpaired t-test) and with fold change of at least 2 between the comparisons Mta1 knock out vs. Mta1 knock out/Mta1 and P53 knock out vs. P53 knock out/Mta1. Each column represents a sample plotted in triplicates and each row in the heat map represents a gene that is differentially regulated in that particular comparison of samples. The color scale represents the degree of expression of the gene, green being the lowly expressed (below −3.0) and red being (above +3.0) the highly expressed genes in the sample sets with black as the center of the scale at ‘0’. C: Pie diagrams showing the percentage of up-regulated and the down-regulated genes in each sample comparison. The red segment of the pie represents the up-regulated genes whereas; the green segments represent the down regulated genes.
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pone-0017135-g003: Genes regulated by Mta1 in the presence and absence of P53.A: Venn diagrams showing the number of genes that are identified to be genuinely regulated by Mta1 in the presence and absence of P53. (i) The genes shown in WT vs. Mta1-KO (1124) are the genes affected by Mta1 knock out and the genes that are present in Mta1-KO vs. Mta1-KO/Mta1 (184) are affected due to re-expression of Mta1 in the knockout MEFs. The genes that are differentially regulated in both the sets with opposite trends in the regulation are considered as the ‘bona fide’ genes regulated by Mta1. ii) Similarly, the intersection of P53-KO and P53-KO/Mta1 represents the genes differentially regulated by Mta1 over expression in the P53-KO MEFs. i.e. the genes regulated by Mta1 in the absence of P53.This scenario of Mta1 over expression and P53 knock out/mutation mimics most of the cancers iii) The Venn diagram between genes regulated by Mta1 in the presence of P53, 126 and genes regulated by Mta1 in the absence of P53, 266 gives the genes that are regulated by Mta1 only in the presence of P53, irrespective of P53 status and only in the absence of P53 respectively. B: Heat maps representing hierarchical clustering of the differentially regulation, plotted using the log2 values of the genes with p-value≤0.05 (unpaired t-test) and with fold change of at least 2 between the comparisons Mta1 knock out vs. Mta1 knock out/Mta1 and P53 knock out vs. P53 knock out/Mta1. Each column represents a sample plotted in triplicates and each row in the heat map represents a gene that is differentially regulated in that particular comparison of samples. The color scale represents the degree of expression of the gene, green being the lowly expressed (below −3.0) and red being (above +3.0) the highly expressed genes in the sample sets with black as the center of the scale at ‘0’. C: Pie diagrams showing the percentage of up-regulated and the down-regulated genes in each sample comparison. The red segment of the pie represents the up-regulated genes whereas; the green segments represent the down regulated genes.

Mentions: When Mta1 was transfected into the Mta1 knock-out MEFs and compared against the Mta1-KO, 184 differentially regulated genes were identified. The top 25 differentially regulated genes based upon fold change are shown in Table 2 (the entire list is shown in Table S3 and statistical summary in Table S4). Out of these 184 genes, 126 genes were found to be present in WT Vs Mta1-KO as well (1124 genes, Figure 3A top panel). Majority of these 126 genes appear to restore their functioning when Mta1 is transfected back into the Mta1 knock out cells. Among these 126 genes except 6 genes, rest of them regained their expression levels similar to WT. Therefore these represent “bona fide” Mta1 target genes (Table 3 and Table S5). Since P53 is present in all the three samples they reflect the number of genes influenced by MTA1 in the presence of P53.


Gene profiling of MTA1 identifies novel gene targets and functions.

Ghanta KS, Li DQ, Eswaran J, Kumar R - PLoS ONE (2011)

Genes regulated by Mta1 in the presence and absence of P53.A: Venn diagrams showing the number of genes that are identified to be genuinely regulated by Mta1 in the presence and absence of P53. (i) The genes shown in WT vs. Mta1-KO (1124) are the genes affected by Mta1 knock out and the genes that are present in Mta1-KO vs. Mta1-KO/Mta1 (184) are affected due to re-expression of Mta1 in the knockout MEFs. The genes that are differentially regulated in both the sets with opposite trends in the regulation are considered as the ‘bona fide’ genes regulated by Mta1. ii) Similarly, the intersection of P53-KO and P53-KO/Mta1 represents the genes differentially regulated by Mta1 over expression in the P53-KO MEFs. i.e. the genes regulated by Mta1 in the absence of P53.This scenario of Mta1 over expression and P53 knock out/mutation mimics most of the cancers iii) The Venn diagram between genes regulated by Mta1 in the presence of P53, 126 and genes regulated by Mta1 in the absence of P53, 266 gives the genes that are regulated by Mta1 only in the presence of P53, irrespective of P53 status and only in the absence of P53 respectively. B: Heat maps representing hierarchical clustering of the differentially regulation, plotted using the log2 values of the genes with p-value≤0.05 (unpaired t-test) and with fold change of at least 2 between the comparisons Mta1 knock out vs. Mta1 knock out/Mta1 and P53 knock out vs. P53 knock out/Mta1. Each column represents a sample plotted in triplicates and each row in the heat map represents a gene that is differentially regulated in that particular comparison of samples. The color scale represents the degree of expression of the gene, green being the lowly expressed (below −3.0) and red being (above +3.0) the highly expressed genes in the sample sets with black as the center of the scale at ‘0’. C: Pie diagrams showing the percentage of up-regulated and the down-regulated genes in each sample comparison. The red segment of the pie represents the up-regulated genes whereas; the green segments represent the down regulated genes.
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3045407&req=5

pone-0017135-g003: Genes regulated by Mta1 in the presence and absence of P53.A: Venn diagrams showing the number of genes that are identified to be genuinely regulated by Mta1 in the presence and absence of P53. (i) The genes shown in WT vs. Mta1-KO (1124) are the genes affected by Mta1 knock out and the genes that are present in Mta1-KO vs. Mta1-KO/Mta1 (184) are affected due to re-expression of Mta1 in the knockout MEFs. The genes that are differentially regulated in both the sets with opposite trends in the regulation are considered as the ‘bona fide’ genes regulated by Mta1. ii) Similarly, the intersection of P53-KO and P53-KO/Mta1 represents the genes differentially regulated by Mta1 over expression in the P53-KO MEFs. i.e. the genes regulated by Mta1 in the absence of P53.This scenario of Mta1 over expression and P53 knock out/mutation mimics most of the cancers iii) The Venn diagram between genes regulated by Mta1 in the presence of P53, 126 and genes regulated by Mta1 in the absence of P53, 266 gives the genes that are regulated by Mta1 only in the presence of P53, irrespective of P53 status and only in the absence of P53 respectively. B: Heat maps representing hierarchical clustering of the differentially regulation, plotted using the log2 values of the genes with p-value≤0.05 (unpaired t-test) and with fold change of at least 2 between the comparisons Mta1 knock out vs. Mta1 knock out/Mta1 and P53 knock out vs. P53 knock out/Mta1. Each column represents a sample plotted in triplicates and each row in the heat map represents a gene that is differentially regulated in that particular comparison of samples. The color scale represents the degree of expression of the gene, green being the lowly expressed (below −3.0) and red being (above +3.0) the highly expressed genes in the sample sets with black as the center of the scale at ‘0’. C: Pie diagrams showing the percentage of up-regulated and the down-regulated genes in each sample comparison. The red segment of the pie represents the up-regulated genes whereas; the green segments represent the down regulated genes.
Mentions: When Mta1 was transfected into the Mta1 knock-out MEFs and compared against the Mta1-KO, 184 differentially regulated genes were identified. The top 25 differentially regulated genes based upon fold change are shown in Table 2 (the entire list is shown in Table S3 and statistical summary in Table S4). Out of these 184 genes, 126 genes were found to be present in WT Vs Mta1-KO as well (1124 genes, Figure 3A top panel). Majority of these 126 genes appear to restore their functioning when Mta1 is transfected back into the Mta1 knock out cells. Among these 126 genes except 6 genes, rest of them regained their expression levels similar to WT. Therefore these represent “bona fide” Mta1 target genes (Table 3 and Table S5). Since P53 is present in all the three samples they reflect the number of genes influenced by MTA1 in the presence of P53.

Bottom Line: Metastasis-associated protein 1 (MTA1), a master dual co-regulatory protein is found to be an integral part of NuRD (Nucleosome Remodeling and Histone Deacetylation) complex, which has indispensable transcriptional regulatory functions via histone deacetylation and chromatin remodeling.Emerging literature establishes MTA1 to be a valid DNA-damage responsive protein with a significant role in maintaining the optimum DNA-repair activity in mammalian cells exposed to genotoxic stress.Thus, the presented data emphasizes the known functions of Mta1 and serves as a rich resource which could help us identify novel Mta1 functions.

View Article: PubMed Central - PubMed

Affiliation: McCormick Genomic and Proteomic Center, The George Washington University Medical Center, Washington, D.C., United States of America.

ABSTRACT

Background: Metastasis-associated protein 1 (MTA1), a master dual co-regulatory protein is found to be an integral part of NuRD (Nucleosome Remodeling and Histone Deacetylation) complex, which has indispensable transcriptional regulatory functions via histone deacetylation and chromatin remodeling. Emerging literature establishes MTA1 to be a valid DNA-damage responsive protein with a significant role in maintaining the optimum DNA-repair activity in mammalian cells exposed to genotoxic stress. This DNA-damage responsive function of MTA1 was reported to be a P53-dependent and independent function. Here, we investigate the influence of P53 on gene regulation function of Mta1 to identify novel gene targets and functions of Mta1.

Methods: Gene expression analysis was performed on five different mouse embryonic fibroblasts (MEFs) samples (i) the Mta1 wild type, (ii) Mta1 knock out (iii) Mta1 knock out in which Mta1 was reintroduced (iv) P53 knock out (v) P53 knock out in which Mta1 was over expressed using Affymetrix Mouse Exon 1.0 ST arrays. Further Hierarchical Clustering, Gene Ontology analysis with GO terms satisfying corrected p-value<0.1, and the Ingenuity Pathway Analysis were performed. Finally, RT-qPCR was carried out on selective candidate genes.

Significance/conclusion: This study represents a complete genome wide screen for possible target genes of a coregulator, Mta1. The comparative gene profiling of Mta1 wild type, Mta1 knockout and Mta1 re-expression in the Mta1 knockout conditions define "bona fide" Mta1 target genes. Further extensive analyses of the data highlights the influence of P53 on Mta1 gene regulation. In the presence of P53 majority of the genes regulated by Mta1 are related to inflammatory and anti-microbial responses whereas in the absence of P53 the predominant target genes are involved in cancer signaling. Thus, the presented data emphasizes the known functions of Mta1 and serves as a rich resource which could help us identify novel Mta1 functions.

Show MeSH
Related in: MedlinePlus