Epigenetics is not magic.

My god, epigenetics is a woo-magnet.

Its not epigenetics fault, its just science.

But the word 'epigenetics' gets put on this ('chambery thing' heh.).

And this.

And this.

And... well, just Google it. Find your own favorite bit of self-help/explain all/magic epigenetic crap.

Attention woo-meisters:

Its science and its cool because its science.


THIS is epigenetics:

KAP1 controls endogenous retroviruses in embryonic stem cells
Almost half of the mammalian genome is derived from virus-like entities called retroelements, many of them the result of the incorporation of endogenous retroviruses. Didier Trono and colleagues use a combination of genetic, functional and biochemical analyses to demonstrate that KRAB-associated protein 1 (KAP1)-mediated epigenetic regulation is involved in the early embryonic silencing of intracisternal A particles (IAPs), a still active and highly polymorphic subset of endogenous retroviruses. This work establishes a role for the KAP1 co-repressor in the control of endogenous retroelements during early embryonic development.

This paper is awesome. They did so much work, and only 13 authors. Theres no way I could cover it all in a blog post-- but I can give you all the jist of it.

ERVs and ERV-like-thingies, IAPs, are trouble for developing babbies. If these chunks of pirate DNA are hopping and plopping around a genome, they might cause cancer in grown adults (exogenous retroviruses do cause cancer in adults), but they would immediately kill a developing babby.

Well, apparently, one of the ways genomes have evolved to keep some kinds of pirate DNA silent during the crucial process of development is epigenetics. Not 'BIRD SONGS ARE EPIGENETICS! DIIIIRP!', but real 'science' epigenetics-- You have a family of proteins in your genome, KRABs. KRABs are sequence specific, and nestle up next to DNA with their particular sequence. We have a ton of KRABs in our genome (at least 250-ish), and theyve been under strong evolutionary stress over the course of our evolution. For some of them, we know what that stress was: they recognize ERV and IAP sequences. But KRABs themselves have no 'function'. They just recognize sequence.

KAP-1 (aka TRIM28) sees the KRABs. KAP-1 is the opposite of KRABs-- they have a function, but not really any specificity. It dunno where to go. BUT, if it finds a KRAB, it knows just what to do!

KAP-1 trundles over to a KRAB with a chromatin remodeling complex (histone methyltransferases, heterochromatin proteins, histone deacetylases), thus silences the surrounding DNA, thus keeps ERVs/IAPs silent.

They figured out some of the protein players in epigenetic control of ERVs.


Remember this post the next time you read some feather-brained article on epigenetics. Does what theyre writing, what theyre saying, look like this?

More like this

I'm certain epigenetics has an assortment of computational methods under its belt, and if not it's probably an area of research with lots of potential.

By Tyler DiPietro (not verified) on 21 Jan 2010 #permalink

When it gets right down to it, these "epigenetics iz everywhere, liek a rainbow of new-age grooviness" stories are about as uncomforting as one of those radium-filled "health belts" that they used to sell in the early 20th century.
I don't think I'd want epigenetic mechanisms to be so free and easy that they'd be switching our genes on and off depending on the weather, our moods, or our immediate social circumstances.
Altering gene expression at the drop of a hat just sounds too dangerous -- and anyway, aren't there a lot of nice, nongenetic/epigenetic systems (like the CNS, hormones, etc.) to take care of most of the day-to-day stuff?
All in all, I'd feel much more warm, cozy, and comfortable thinking that epigenetic mechanism are very conservative, and keep their activities confined to the long-term, serious stuff, rather than going all new-age-y on us at the slightest provocation.

By TotallyUncool (not verified) on 21 Jan 2010 #permalink

Is epigenetics going to be the new quantum physics?

Because my money was on dark matter.

Sure they're magic!

Sequencio! Silencio! Geminio!

Well, at least what we'll be able to do biologically in 40 years from now will look like magic. Screw you, warp drive! Biology's where it's at and going to be! Maybe we'll pack a light lunch for quantum computing as well.

People will look funny in the midst of tooth bud therapy. Human hexapods still unlikely. Chromatophores... not yet. All science fiction underestimates the length of time technology takes.

With the way histones work, it's no wonder the secrets of cloning and tissue differentiation didn't give themselves up so easily. Wish my 'histonomics' post from years ago didn't disappear down my web host's memory hole - I was salivating over the upcoming histone acetylation/methylation research and frustrated by the then-lack of explanations and diagrams.

I wonder how much ES research it's going to take before we can practically manipulate differentiated cells into ES substitutes?

Intelligent Design, my arse.

They just silence the stuff, rather than get rid of it? Makes perfect sense.

Having grown increasingly fascistoid, I'd like to know if there's some way to encourage these babby-killing thingummabobs. Something to put in the water supply, if necessary. (I might be nice and just put it in bottled water.)

I was stuck on a plane a while back and found myself reading the SkyMall catalogue. Midway through the general silliness, I saw an "electronic feng shui compass" which, it was said, used "aerospace" technology to measure the energy fields around your furniture. "Aerospace?" thought I. "Fuck that. I'm not buying an electronic feng shui compass unless it uses goddamn quantum physics and comes with its own tachyons."

Looks like I'll have to add "epigenetics" to that list.

ERV you just don't understand. Because the way DNA folds up on itself and thereby controlling gene regulation as a consequence, it means that the universe specifically cares about me and God exists as an energy making the universe as one.

See this "just science" talk is the kind of thing that suggests because particles can entangle for short times and therefore be the same particle over potentially vast distances it must be the case that the universe has a oneness and everything is interconnected from the moment of the big bang.

Sheesh, next you'll tell me that because subatomic particles react differently when they are measured that it's just one odd thing to do with pure science and doesn't actually suggest that the conscious mind changes the nature of reality by acting as a conduit of universal uncreated quantum consciousness.

Holographic Quantum Epigenetics. That's the FUTURE!

Thinks hey, that's a good idea -- better steal it before someone else does...

Don't forget to pre-order a copy of my new book, The Fengshui of Holographic Quantum Epigenetics, available just as soon as I finish pasting it together from random phrases on the Internet!

By TotallyUncool (not verified) on 23 Jan 2010 #permalink

I think you're full of yourself and right at the same time. Child abuse has been shown to effect genetic expression so if you're faulting people for thinking that there is a connection between life experience and health you're just being arrogant. Woo sucks and I don't go near new age authors even with a 10-foot clown pole but they are onto something, obviously, without a doubt. The only way the woosters will ever start using science to tests themselves is if we can open up a dialouge that goes beyond mocking tones of ethical superiority.

Time to write a book: "Holistic Epigenetic Meditation: How to Transcend Disease and Suffering by Transforming Your Holographic Mind."

By James Turpin (not verified) on 12 Aug 2010 #permalink

"ERVs and ERV-like-thingies, IAPs, are trouble for developing babbies." There's much still to be discovered about this, and it's an exciting field. I really suspect that autism is a result of epigenetic changes occurring while the baby is still in the womb. As you probably know, methylation is central in the body for silencing active endogenous retroviruses, and although it's far from a cure for autism, many find symptom alleviation by raising natural SAM-e levels, and thereby boosting the methylation process.

Children of ME patients very often have autism, and it may very well be a result of illness in the parent, which in turn kickstarts the epigenetic changes while the mother is still being pregnant.

One question, since you work with ERVS, can epigenetic changes come from the father as well (via the genes in the sperm), or does is the only parent it can come from the mother? (of course excluding environmental epigenetic changes after the birth has taken place).