Angled DNA Double Helix
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Researchers have provided an insight into how a virus-like element has been able to write a  major part of the human genome, which could provide in-roads into treatments for autoimmune diseases, cancer, and aging.

Approximately half a million copies of LINE-1 (L1) exist in the human genome, which the team dubs an “ancient genetic parasite” in the journal Nature.

The retrotransposon is one of the most common elements in human DNA and makes up a large part of the “dark genome”—the 98 percent of DNA that does not encode proteins.

It is able to do this through a “copy and paste” mechanism that is catalyzed by its multifunctional enzyme, a reverse transcriptase called open reading frame 2 protein (ORF2p).

Taylor et al. have now discovered the structures of the human ORF2p “core” and offer key mechanistic insights into L1 polymerization and insertion.

“Our integrated analyses reveal the inner workings of the molecular machine that has written nearly half of the human genome,” the researchers report.

“Understanding L1 structure and function is important both in evolution and, increasingly, in human disease.

“Accumulating evidence links L1 activity and the host response to common pathologies including cancer, aging, neurodegeneration, and autoimmunity.”

In certain disease conditions, LINE-1 escapes repression and generates RNA molecules that migrate to the cytosol, encoding proteins that can transfer LINE-1 RNA back to the nucleus.

Here, through reverse transcription, they can create and insert a new LINE-1 DNA copy into the genome that can cause mutations and damage.

Reverse transcription also happens in the cytoplasm, where it creates RNA-DNA hybrids that can trigger inflammation.

The detailed structure of the LINE-1 reverse transcriptase could therefore enable the development of specific inhibitors that could be used against autoimmune diseases, cancer and neurodegeneration.

Taylor and team elucidated the human ORF2p “core” of residues 238-1061, including the RT domain, using X-ray crystallography and cryo‐electron microscopy to determine its 3D structure in multiple conformational states.

This revealed two novel folded domains, extensive contacts to RNA templates, and associated adaptations that contribute to the L1 unique replication cycle.

Computer models of full-length ORF2p revealed a dynamic closed ring conformation that appeared to open during the process.

The researchers note that ORF2p reverse transcriptase and endonuclease activities have been implicated in the pathophysiology of cancer, autoimmunity, and aging, making ORF2p a potential therapeutic target.

However, a lack of structural and mechanistic knowledge has hampered efforts to rationally exploit it.

The team suggests: “Our structural elucidation of ORF2p will facilitate rational design of new therapeutics and lays the groundwork for future studies needed to dissect and improve our understanding of the L1 insertion mechanism, its evolution, and its roles in disease.”

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