Nup93 modulates spatiotemporal dynamics and function of the HOXA gene cluster during differentiation

The central role of nucleoporins is to transport RNA and proteins. In addtion, nucleoporins are also involved in gene regulation. Furthermore, nucleoporins - Nup93, Nup153, Nup98 and Nup210, directly associate with developmental genes and regulate developmental processes by direct association with developmental genes. Here, we identified genome wide binding profile of Nup93 - a core component of the nuclear pore complex in colorectal cancer cell line DLD-1 by ChIP-seq. Our ChIP-seq analysis revealed significant association of Nup93 with developmental genes and known enhancer marks such as H3K4me1 and H3K27Ac . We found that Nup93 shares binding sites with CTCF - the well known chromatin organizer, suggesting a functional overlap between Nup93 and CTCF in the organization and regulation of developmental gene expression such as the the HOXA gene cluster. ChIP-seq was performed to determine the chromatin occupancy of Nup93 in DLD-1 cells in two independent biological replicates. Sonicated chromatin from Input sample was used as a control.