What is epigenetics, exactly...

What is epigenetics, exactly? From the wikipedia article it seems like it's quasi-heritable traits that arise from different generations being exposed to the same environmental factors, or some shit, but I'm not well versed in biology and know very little about genetics so I'm probably not getting it.

Is it encoded in the junk dna?

>modification of the genome that leaves the original genetic material intact but that alters expression of this via methylation of base pairs and modification of histone proteins.

This is the simple version

This, only thing to add is they result in heritable phenotypes

Uh... could you dumb it down some more?

hurr little pokey bits sticky to dna

The genome is a collection of all the 'genes' you have. The language of the genome is your genetic material, otherwise known as DNA.

Transcription of genes can be turned off with a region called a promoter. Think of it like a club promoter, he's not gonna be promoting any clubs if you sew his mouth shut. The thread you sewed his mouth shut with is the methyl groups in this analogy.

Now we go to the histone, the histone is like a person who doing that burrito thing with their bed sheets, the bed sheets being the DNA. In this analogy this person is trapped forever in their bed sheets because those bed sheets have fused with their skin. They scream in eternal agony, but no one will ever hear.

Make sense?

Not him but I can try

If you add methyl groups (CH3) to chromatin, the genetic material of cells, or change histone proteins (positively-charged proteins that negatively-charged DNA are attracted to) so they have a different conformations (open confirmation allows transcription to occur, closed conformation makes it very hard to transcribe the DNA), the level at which a gene is expressed is changed. When DNA is replicated, these changes are also replicated and these changes are carried in the daughter cells.

fairly rarely, most marks are wiped off intergenerationally

Gene expression is physical. It requires that proteins be able to physically access, to touch, the genes in question. When you stick shit onto the bases or the histones (big rocks that DNA is wrapped around), you, through some still-debated mechanisms, alter the accessibility of the genes.
Normally this wouldn't really matter for your kids, but there are some patterns of modifications that are passed on after replication.

Yeah, I should have said "can result" rather

How can I use this to my advantage though

starve your enemies when they are young and their grandchildren will be fat

Soo, does this mean the 3D shape changes a bit?

some marks activate (stabilize an open, accessible shape) while others silence (stabilize a closed, inaccessible state)

Why does it have to be a methyl group and not literally anything else?

Cytosine (and also adenine) can be methylated due to its ring structure, other groups can be added to DNA bases and affect them in different ways (e.g. nitrous acid replacing amino groups with keto groups change cytosine into uracil or adenine into hypoxanthine).

Thank you so much. That really clears things up. I think I'm going to screencap this in case I want to research it more, as this is a great introduction.

So epigenetic traits are not actually passed down, typically? Does that mean I was partly right that they generally come from environmental/outside factors?

>simple version
>simpler
two twins, almost exact clones with dna, separated at birth

Twin A becomes a circus performer.
Twin B becomes a smoker.

+40yrs

A's offspring develop stronger bone density and higher "IQ" from the lifestyle A lead (ex/food/mental awareness)

B's offspring have bodies that don't retain iron well and have a harder time with paying attention.

In conclusion A & B contributed differing sets of dna through the years of built up habits and activities, EVEN THO they started with IDENTICAL dna from the start.

The idea of genes only appeared in order to "prove" abstract thought experiments like "inheritance" or "evolution".

There are two domains of epigenetics and they are distinct.

First, genetics is the study of the transmission of information (inheritance genes) from one organism to another. This includes mother/father --> offspring and stem cell --> differentiated cell.

As we came to understand the physical basis for most genes in DNA, then all 'genes' came to be defined as DNA differences. The problem is that this didn't explain all forms of inheritance and didn't explain why a tissue like the liver doesn't become another cell type like blood. Some kind of information is being transmitted, and we knew that the DNA remains unchanged, mostly. So this discrepancy was called epi-genetics, or the transmission of information that is not associated with DNA changes.

Epigenetics is not DNA-methylation or histone modifications alone, those are simply some of the mechanisms with which epigenetic information exists and is transmitted. mRNA, piRNA, protein concentrations, metabolic substrates all can carry information that is non-DNA and will effect progeny in both domains of epigenetics.

Now the two domains are somatic epigenetics and trans-generational epigenetics and they are distinct.

Somatic epigenetics is very well supported, it's all the things which mother cells pass on to their daughter cells that define what that cell can be and what it will do. This is where things like DNA methylation really shine and are highly informative.

Trans-generational epigenetics also 100% exists. There are tightly controlled experiments which show that certain traits such as Agouti mouse-coat colour are passed on from mother/father to progeny mice and this change is not a difference in DNA, it arises from a difference in piRNA concentration in the mothers eggs. That is just about all of the good evidence for trans-generational epigenetic inheritance in mammals. ALL of the human data is suggestive at best, and misleading at worst.

2/2 cont'd

It's critical to not confuse somatic epigenetics and trans-generational epigenetics these are two completely distinct concepts. For instance, histones must be replaced every cell division, but they may influence the state of the histones which replace them after a cell division and that would be a form of somatic epigenetics.

Histone marks in any tissue have zero 'epigenetic' influence in trans-generational epigenetics and are unrelated.

The most important concept to consider here is that for cells to make up an entire organism they are reduced to two cells; sperm and egg. Those are the only two cells which can possibly carry transgenerational information. DNA methylation and histone modifications are completely stripped in these cells (global reset) except for a few exceptional locus.

Epigenetics is fascinating but don't believe 99% of the pop-science bullshit associated with it. Even most non-genetics biologists have a shitty understanding of it.

So what governs trans-gen epigenetics? Or is that not yet known?

Just a buzzword racial iq deniers throw around. There's no research to support any of it

>quasi
Stopped reading there. KYS my man.
This is so fucking wrong on so many levels. KILL YOUR FUCKING SELF YOU FUCKING WORTHLESS RETARD.

Geneticist here.

You know how DNA is a ladder, and the information bits are on the inside and lock together, epigenetic modifications are things stuck to the outside. Lets talk about how that works.

Straighten out the DNA ladder, yeah, thats it, then imagine it as train tracks. Enzymes ride along those tracks to read DNA and do, well, pretty much everything. Now, epigenetic effects add stuff, either to prevent trains from moving so quickly along the tracks, encourage them to take that track, or to keep them from moving there at all. These modifications are made to basically fine-tune your genetics based on environmental factors, diet, and stress level.

Now, how is this inherited? Remember how your DNA is inherited, well, so are the things stuck to the sides. However, since they're less important, they're much more likely to fall off or be removed on accident (or on purpose) during DNA replication.

Any questions?

Different guy, but its not yet known. Measuring epigenetic factors is much harder than measuring genetic ones, mainly because DNA is in discrete units and epigenetic factors tend to be a bit more fuzzy.

The activity of DNA methyl/acetyl transferases as well as histone methyl/acetyl transferases results in the passing down of epigenetic modifications after replication of DNA. Remember that DNA replication is semi conservative not just for the DNA molecules themselves but also the histones.

If the methyl/acetyl transferases notice an epigenetic modification on one strand of DNA, for the sake of conservation they add this same change to the newly replicated strand.

Also OP, a general rule which you are probably aware of is that methylation generally silences gene expression whereas acetylation increases expression.

Methylation of DNA essentially jams up the transcriptional machinery, while acetylation speeds it up. Methylation of the histones tightens the chromatin structure making it less accessible for transcription whereas acetylation loosens it making it more accessible.

Cool! So it's a bit like the DNA is a magnetic tape and the enzymes are like the tape head, reading and writing information onto the tape? Or is that taking it a bit to far? I think I've got the epigenetic mechanism down, but your post made me realize I didn't actually know how DNA information works.
Thank you.

What's the evidence that histone modifications are semi-conservative? I've never seen an experiment what demonstrates this, let alone one which shows that histones are inherited locally.

Also, as I mentioned here: Your answer is 100% incorrect. DNA methylation and histone modifications in no way whatsoever explain trans-generational epigenetics, only somatic epigenetics.

DNA methylation is globally erased in germ cells except for imprinted loci. Sperm cells lose histones and maternal cells have already all but differentiated by the time a female is born so new information is not imparted into them. Unless you know of some experiments I haven't read which show otherwise.

People say

"epigenetics is the future of genetics/biology!"

When they're just blowing smoke out their asses. The only people remotely interested in epigenetics to the degree they're hyped are psychologists, and even then, neural mapping is more of a focus.

They are interesting, and mapping epigenes, while a daunting task, can prove useful, but they're just another molecular mechanism or tool that exists in biology, like any other phenomenon.

CRISPRfag here though so I just think there are more interesting things to look forward to.

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