This is so cool!
"Researchers led by Mary K. Crow, MD, of the Hospital for Special Surgery in New York City have found that virus-like endogenous elements that were long ago incorporated into the genome but that have no role in encoding for proteins may have a very different role: that of erroneously upregulating interferon in certain genetically predisposed individuals, ultimately leading to disease."
So, "junk DNA" includes virus like crap.
"Throughout genomic evolution, these potentially disruptive insertions have been tightly regulated, primarily through epigenetic methylation of DNA, and alterations in methylation in the L1 promoter region could permit increased expression and immune dysfunction, according to Crow."
Epigenetic changes can turn these stretches of otherwise non-encoding DNA on, leading to overproduction of interferon and lupus and similar diseases.
"The researchers first obtained biopsy samples of kidney tissues from 24 patients with lupus nephritis, and salivary gland tissue from 31 patients with Sjögren's syndrome, another condition associated with high expression of interferon." And what they found correlated with symptoms. They "found correlations between L1 mRNA expression and interferon-α2 in lupus kidney samples as well as in Sjögren's salivary gland samples."
They caught the retro-elements being transcribed. They _found_ the promoter region that turned it on. Exposure to cigarette smoke is believed to be something that can kickstart this whole process (there are surely others).
To be clear, this is obviously super _not cool_ when it happens to someone. However, it is incredibly amazing that someone has put the whole chain together to make sense of it all. And this was research led by a woman (ha!), in the context of history in the field of a bunch of men preaching the central dogma.
Not to mention a long history of mostly men doctors telling women with these kinds of diseases that it was all in their heads.
Functionally, this is _why we need women_ in STEM.
Also, this is yet another reason why (a) smoking is not a good idea and (b) letting smokers be around anyone else is an even worse idea (and not just when they are smoking -- the stuff is breathed out of their lungs for hours after the fact).