Dynamic Association of NUP98 with the Human Genome

Abstract

Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.

Author Summary

Development of multicellular organisms such as humans requires appropriate activation of gene expression programs according to stages of differentiation. Many proteins that directly regulate this process have been identified, including histone-modifying enzymes and transcription factors. It is not clear whether nuclear pore proteins, proteins that form the only channels in the nuclear envelope that mediate nuclear transport, regulate developmental gene regulation in higher organisms such as humans. Here we show that one nuclear pore protein has a role in gene regulation during human cell differentiation, providing insight into the development-related and transport-independent function of nuclear pore proteins. We have found that the nuclear pore protein interacts with the human genome in a dynamic manner that is tightly linked to the developmental stage. In addition, manipulating the functional levels of the nuclear pore protein can disrupt expression of the developmental genes it associates with. Our results suggest that the nuclear pore protein functionally interacts with the genome during cell differentiation, uncovering an additional layer of developmental gene regulation in humans.