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Heart disease, leukemia links to dysfunctional nucleus
Using a suite of molecular technologies, Salk Institute scientists discovered two proteins sitting in the nuclear envelope that work together with the membrane to trigger key genes in DNA. Better understanding these intra cellular functions gives insight into diseases such as leukemia, heart disease and aging that appear related to dysfunction within the nuclear membrane.
Historically, the nuclear membrane's main purpose was thought to be keeping contents of the nucleus separated from the rest of the cell. Within the membrane, at least thirty different proteins — called nucleoporins — form openings (pores) in the membrane and control what goes in or out of the nucleus. But as the Hetzer lab shows, these nuclear pore complexes (NPCs), are not mere gateways into the nucleus, but regulators of DNA on the inside.
The work was conducted by Salk Institute scientists, and detailed in the November 2 issue of Genes & Development
"Discovering that key regulatory regions of the genome are actually positioned at nuclear pores was very unexpected," according to Arkaitz Ibarra PhD, Molecular and Cell Biology Laboratory, Salk Institute and first author of the paper. "And even more importantly, nuclear pore proteins are critical for the function of those genomic sites."
Curious about all regions of DNA with which nucleoporins interact, the team examined a human bone cancer cell line. Using a molecular biology technique called DamID, they pinpointed two nucleoporins — Nup153 and Nup93 — and where they came into contact with the genome. Using several other sequencing techniques, they identified which genes were being affected in those regions — and how.
They discovered Nup153 and Nup93 interacted with stretches of the genome called super-enhancers, known to help determine cell identity. As every cell in our body has the same DNA, what differentiates a muscle cell from a liver cell or a nerve cell — is which genes are turned on or expressed within that cell.
Experiments in a lung cancer cell line validated the bone cancer results. Nucleoporins in the NPC were found to interact with multiple super-enhancer regions and drive gene expression. Experiments that altered NPC proteins made related gene expression faulty, even while still performing their primary role as gatekeepers of the cell membrane.
"It was incredible to find that we could perturb the proteins without affecting their gateway role, but still have nearby gene expression go awry," says Ibarra.
"People have thought the nuclear membrane is just a protective barrier — which is maybe the reason it evolved in the first place. But there are many more regulatory levels we don't understand. It is 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," adds Hetzer.
The work was funded by the Human Frontier Science Program, National Institutes of Health grant R01GM098749, NIH Transformative Research Award R01NS096786, the Glenn Foundation for Medical Research, the NOMIS Foundation, the Keck Foundation and American Cancer Society Award number P30CA014195.
About the Salk Institute for Biological Studies:
A super-enhancer driven cell identity gene (RED DOT) localized in close proximity to the
nuclear envelope (GREEN) in the nucleus of a human primary lung fibroblasts (BLUE).
Image Credit: Salk Institute for Biological Studies