Fig. 7

HOXA is upregulated upon Nup93 depletion independent of CTCF. a Co-immunoprecipitation was performed using anti-Nup93 antibody and negative control IgG followed by Western blotting for CTCF, Nup205, Nup188 and Nup93 (data from two independent biological replicates, N = 2), b Co-IP for Nup93 and Western blot for Nup93, Nup188, Nup205 (data from three independent biological replicates, N = 3), PRC2 complex proteins EED and Suz12 (data from a single experiment). c Representative Western blot showing the levels of Nup93, Nup188, Nup205, Nup98, EZH2, Suz12, CTCF, EED upon Nup93, Nup188 and Nup205 Kd (data from a single experiment). d Representative Western blot showing siRNA-mediated knockdown of CTCF in DLD1 cells. e Epigenome Browser view of CTCF (GSM749729) (arrow indicates potential binding sites of Nup93) on HOXA gene cluster. f qRT-PCR analysis was used to determine mRNA levels of all HOXA genes (HOXA1 to HOXA13) upon CTCF and combined Nup93 + CTCF knockdowns in DLD1 cells. Graph represents fold change (\(2^{{ - {\Delta \Delta }C_{\text{t}} }}\)) in levels of mRNA normalized to untreated cells. Error bars SEM, data from two independent biological replicates (N = 2) that includes total of 6 technical replicates, GLCCI, served as control. Nup93 Kd data (green bars) is from Fig. 3a, plotted here for comparison between Nup93 Kd with Nup93 + CTCF Kd (orange bars). Nup93 does not interact with CTCF or PRC2 complex proteins. Nup93 Kd upregulates HOXA gene expression independent of CTCF. CTCF depletion alone upregulates GLCCI1, which is unaffected upon Nup93 knockdown