Ving peaks with unloading in an unbiased fashion. However, there are other genes with Bcl-3 peaks in the promoter region that are likely to be important to atrophy. For example, several proteolytic pathway genes not identified by iPAGE also show Bcl-3 peaks with unloading (Psmc1, Psmb7, Ube2b, Ubb, Cul4a, Rnf135, Rnf13, Atg3). For transcription factors, Foxo1, Foxo3, and Cebpa show peaks as well as several translation initiating genes including Eif4b and Eif3f. All of the genes with unloading-induced increased Bcl-3 binding in their promoters are listed in Table S1.promoters (Figure 3). We then focused on the peaks in the promoters of the genes found, from 24 to 12926553 +2 kb relative to the TSS (n = 845).Direct and Indirect Targets of Bcl-Since we were interested in further describing 
direct and indirect targets of the Bcl-3 transactivator at the genome-wide level, we used the algorithms of ChIPArray [25] to bring together our ChIPseq data on Bcl-3 binding to promoters with the genes whose mRNA was upregulated as determined by global gene expression array (28,853 transcripts) of control vs. unloaded muscle (Figure 6). ChIPArray found 241 direct targets, 5 direct targets with indirect targets (transcription factors) and 305 indirect target genes of Bcl-3. The indirect target genes, according to this analysis, are order Rubusoside controlled by the direct Bcl-3 targeted transcription factors Max, Zfp740, Nfic, Cux1 and Pou2f1. Max ITI-007 web appears to regulate the largest number of indirect target genes.Gene Ontology Terms Identified by Genome-wide Increased Bcl-3 Binding to Promoter Regions in Unloaded MuscleTo find the important functional groups of genes that show increased Bcl-3 binding with muscle unloading, we evaluated the peaks found in unloaded compared to control muscle for gene ontology terms/pathways. To do this we used the iPAGE algorithm, a module of the ChIPseeqer set of computational programs (Figure 4). iPAGE was set up to restrict its analysis to the 845 peaks (out of the 2,817 total) which were found in promoters (24 kb to +2 kb relative to TSS). As with any gene ontology (GO) mapping algorithm, iPAGE identifies GO terms in which the peaks found are statistically over-represented relative to calculations for random distribution. The 23 GO terms that were found for genes containing Bcl-3 peaks in unloaded muscle were from three biological processes: protein catabolism, development/ differentiation and sugar/glucose metabolism. There were 24 genes found in the 23 GO pathways and these are presented in Table 1. The most abundant group with 14 genes in 11 GO pathways was for protein catabolism. The genes are ones that function in several aspects of catabolism in muscle including several E3 ligases of the ubiquitin proteasome pathway, and importantly, two genes that contribute to the cell catabolism driven by the N-end rule. Those genes are Ubr1/E3a, the N-end recognin E3 ligase, and Ate1, the arginyltransferase responsible for modifying several amino acid amino termini for Ubr1 recognition. The sequence alignments and locations for the peaks for these two genes have been visualized by use of Integrative Genomics Viewer (IGV) [22], (http://www.broadinstitute.org/igv/) and are shown in Figure 5. For both genes, a Bcl-3 peak due to unloading was identified at an evolutionary conserved region close to the TSS and was in close proximity to a JASPAR matrices defined NF-kB site. In addition, data for ChIP-seq with p50 antibodies showed p50 binding at or very near.Ving peaks with unloading in an unbiased fashion. However, there are other genes with Bcl-3 peaks in the promoter region that are likely to be important to atrophy. For example, several proteolytic pathway genes not identified by iPAGE also show Bcl-3 peaks with unloading (Psmc1, Psmb7, Ube2b, Ubb, Cul4a, Rnf135, Rnf13, Atg3). For transcription factors, Foxo1, Foxo3, and Cebpa show peaks as well as several translation initiating genes including Eif4b and Eif3f. All of the genes with unloading-induced increased Bcl-3 binding in their promoters are listed in Table S1.promoters (Figure 3). We then focused on the peaks in the promoters of the genes found, from 24 to 12926553 +2 kb relative to the TSS (n = 845).Direct and Indirect Targets of Bcl-Since we were interested in further describing direct and indirect targets of the Bcl-3 transactivator at the genome-wide level, we used the algorithms of ChIPArray [25] to bring together our ChIPseq data on Bcl-3 binding to promoters with the genes whose mRNA was upregulated as determined by global gene expression array (28,853 transcripts) of control vs. unloaded muscle (Figure 6). ChIPArray found 241 direct targets, 5 direct targets with indirect targets (transcription factors) and 305 indirect target genes of Bcl-3. The indirect target genes, according to this 
analysis, are controlled by the direct Bcl-3 targeted transcription factors Max, Zfp740, Nfic, Cux1 and Pou2f1. Max appears to regulate the largest number of indirect target genes.Gene Ontology Terms Identified by Genome-wide Increased Bcl-3 Binding to Promoter Regions in Unloaded MuscleTo find the important functional groups of genes that show increased Bcl-3 binding with muscle unloading, we evaluated the peaks found in unloaded compared to control muscle for gene ontology terms/pathways. To do this we used the iPAGE algorithm, a module of the ChIPseeqer set of computational programs (Figure 4). iPAGE was set up to restrict its analysis to the 845 peaks (out of the 2,817 total) which were found in promoters (24 kb to +2 kb relative to TSS). As with any gene ontology (GO) mapping algorithm, iPAGE identifies GO terms in which the peaks found are statistically over-represented relative to calculations for random distribution. The 23 GO terms that were found for genes containing Bcl-3 peaks in unloaded muscle were from three biological processes: protein catabolism, development/ differentiation and sugar/glucose metabolism. There were 24 genes found in the 23 GO pathways and these are presented in Table 1. The most abundant group with 14 genes in 11 GO pathways was for protein catabolism. The genes are ones that function in several aspects of catabolism in muscle including several E3 ligases of the ubiquitin proteasome pathway, and importantly, two genes that contribute to the cell catabolism driven by the N-end rule. Those genes are Ubr1/E3a, the N-end recognin E3 ligase, and Ate1, the arginyltransferase responsible for modifying several amino acid amino termini for Ubr1 recognition. The sequence alignments and locations for the peaks for these two genes have been visualized by use of Integrative Genomics Viewer (IGV) [22], (http://www.broadinstitute.org/igv/) and are shown in Figure 5. For both genes, a Bcl-3 peak due to unloading was identified at an evolutionary conserved region close to the TSS and was in close proximity to a JASPAR matrices defined NF-kB site. In addition, data for ChIP-seq with p50 antibodies showed p50 binding at or very near.