Proteins in Cell Nuclear Membrane Actively Influence Gene Expression

The nucleoporins are a family of proteins in the membrane of the cell nucleus, which are the constituent building blocks of the nuclear pore complex (NPC). The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the cell nucleus and the cytoplasm. Nuclear pores in turn allow the transport of water-soluble molecules across the nuclear envelope. Nucleoporins, a family of around 30 proteins, are the main components of the nuclear pore complex in eukaryotic cells.

The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. A recent paper in the November 2, 2016, online edition of the journal Genes & Development has described a crucial role of NPC components in the regulation of cell type-specifying genes and highlighted nuclear architecture as a regulatory layer of genome functions in cell fate.

Investigators at the Salk Institute for Biological Studies (La Jolla, CA, USA) employed a technique called DamID to determine where two nucleoporins, Nup153 and Nup93, came into contact with the genome in a human bone cancer cell line. DamID (DNA adenine methyltransferase identification) is a molecular biology protocol used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase. Binding of the protein of interest to DNA localizes the methyltransferase in the region of the binding site. Adenosine methylation does not occur naturally in eukaryotes and therefore adenine methylation in any region can be concluded to have been caused by the fusion protein, implying the region is located near a binding site.

Results revealed that the NPC components Nup93 and Nup153 bound to superenhancers (SE), which are regulatory structures that drive the expression of key genes that specify cell identity. Nucleoporin-associated SEs localized preferentially to the nuclear periphery, and the absence of Nup153 and Nup93 resulted in dramatic transcriptional changes of SE-associated genes.

"Our research shows that, far from being a passive enclosure as many biologists have thought, the nuclear membrane is an active regulatory structure," said senior author Dr. Martin W. Hetzer, research professor at the Salk Institute for Biological Studies. "Not only does it interact with portions of the genome to drive gene expression, but it can also contribute to disease processes when components are faulty. People have thought the nuclear membrane is just a protective barrier, which is maybe the reason why it evolved in the first place. But there are many more regulatory levels that we do not understand. And it is such an important area because so far, every membrane protein that has been studied and found to be mutated or mis-localized, seems to cause a human disease."

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Salk Institute for Biological Studies