Fig. 4: Matr3 interacts with architectural proteins including CTCF and cohesin, and Matr3 loss alters their chromatin occupancy.

a Parental and Matr3 KO MEL cells were engineered to express BirA and Flag-Biotin tagged Matr3. Western blot discriminated endogenous (green arrow) and/or biotinylated (yellow arrow) forms of Matr3 protein. Biotinylated form of Matr3 was recovered using streptavidin magnetic beads. BirA expressing cell was used as a control. From the result of mass-spectroscopy (MS) analysis (Fig. S3a), the number of unique and total peptides of the selected chromatin remodeling factors are shown in the table. Data were the result of 2 independent experiments. b Endogenous Matr3 protein was immunoprecipitated and its interaction with other proteins was examined by Western blot. Data were the result of 2–3 independent experiments. c The Smc1a subunit of the cohesin complex was pulled down in Stag2 wild type (WT) and KO U937 cells and subjected to mass-spectroscopy (MS)⁸⁰. (left) Matr3 interaction to the cohesin complex is revealed by log2FC of Smc1a and IgG immunoprecipitation (IP)-MS in Stag2 WT cells. (right) The disrupted Matr3 interaction on the cohesin complex in Stag2 KO is measured by log2FC of Smc1a IP-MS in Stag2 KO and WT cells. Error bars represent mean ± 1 s.d. across two independent experiments. d ChIP-seq datasets of CTCF and Rad21 in parental and Matr3 KO cells were quantitatively compared³⁸. The results of at least two independent experiments were combined to generate a more stringent peak list. The numbers of specific and shared peaks in each comparison are shown in the Venn diagram. e Differentially bound CTCF and Rad21 sites between parental and Matr3 KO cells were identified using³⁹. Sites with p-values from the Wald test less than or equal to 0.05 are shown in red on the plot. f Genome-wide contact probability calculated from Hi-C data (Fig. S2k). Derivative plot of the contact probability curve suggests low cohesin density in Matr3 KO compared to parental cells. The flatter minimum expected to be seen with a reduced level of cohesin occupancy is indicated by an arrow.