Investigation into SATB2 DNA-binding sites and the effect of SATB2 removal on the transcriptome of skeletal muscle satellite cells

Induction of lineage-specific gene programs are strongly influenced by alterations in local chromatin architecture. However, key players that impact this genome reorganization remain largely unknown. In our associated paper, we found that the removal of special AT-rich binding protein 2 (SATB2), a nuclear protein that binds matrix attachment regions, is a key event in initiating myogenic differentiation. This study included ChIP-seq analyses to assess the genetic binding sites of SATB2 prior to differentiation and categorize their respective roles within the cell. Furthermore, transcriptome analyses using RNA-seq was conducted on C2C12 cells treated with control siRNA and siRNA against SATB2 prior to differentiation. This was done to assess the changes in transcript expression following the loss of SATB2. For the ChIP-seq experiments, the cells that were used were C2C12 skeletal muscle myoblasts in the proliferation phase. The control for the ChIP experiments was a pulldown using a mouse IgG instead of the mouse SATB2 antibody. The ChIP-seq analysis was done on n = 2 independent samples. For the RNA-seq experiments, we used C2C12 skeletal muscle myoblasts in the growth stage. The control for this experiment was C2C12 cells that were treated with control siRNA, while the experimental condition was C2C12 cells that were treated with siRNA against SATB2. These experiments were done at an n=3 on independent samples.