Genome-wide identification of Bcl-3 and P50 target genes in disuse muscle atrophy
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NF-κB plays a central role in regulating skeletal muscle atrophy. We previously showed that a NF-κB transcription factor p50 and its transcriptional coactivator Bcl-3 are both required for inducing muscular disuse atrophy due to hind limb unloading in a mouse model. However, less is known about the molecular mechanisms of the atrophy-resistant phenotype seen in nfkb1^-1- (lack of p50 protein) and bcl-3^-1- mice. The purpose of this study is to identify genes that are targets of p50 and Bcl-3 in unloading atrophy at a genome-wide level. Global gene expressions of plantar flexor muscles was first measured from wildtype, nfkb1^-1- and bcl-3^-1- mice with or without 6 days of hind limb unloading. Genes that were upregulated in wild-type mice due to unloading but not in the knockout mice were considered p50 or Bcl-3 direct or indirect target genes. 185 p50 and 240 Bcl-3 target genes were identified in disuse atrophy, and most of these genes encoded proteins involved in proteolysis and transcriptional regulation. All p50 target genes were also identified as Bcl-3 targets. Direct Bcl-3 binding targets in unloading atrophy were identified using ChIP-sequencing. In atrophied muscles there was an increase in Bcl-3 binding to the promoter regions of genes encoding E3 ligases, N-end rule proteins, kinase and glycolysis enzymes. By studying the expression changes of Bcl-3 binding targets, a Bcl-3 regulated gene network that is responsible for processes underlying unloading atrophy was mapped. One Bcl-3 direct target in unloading atrophy, Muscle specific Ring finger protein 1 (MuRF1), was studied in detail by qPCR, ChIP-seq, and MuRF1 promoter-reporter assays. These results provided the first direct evidence that the p50 and Bcl-3 bind to NF-κB binding sites to transactivate MuRF1 during muscle atrophy. Taken together, our data support Bcl-3 as a global regulator of genes involved in the proteolysis and the change in energy metabolism that are essential components of muscle atrophy due to disuse.
Thesis (Ph.D.)--Boston University