Intro Epigenetics

Epigenetics. Or, how do you change DNA without changing DNA?

OK. That was too clever. What I mean is, how do cells permanently become determined to do only a subset of things without changing the DNA sequences?
We know that Immune cells actually do change their DNA sequence. But, that's really unusual. When epithelial cell divides, the two daughter cells know they are epithelial cells. This comes down to changes in how the DNA is packed and arranged in the nucleus. Whole regions of chromosomes are tightly packed in what we call "heterochromatin," which is differentiated from open "euchromatin," and is not actively transcribed.
Moreover, some of the changes are more subtle than that, but still maintained as the cells divide. So, the questions are:
  1. what are these stable "marks" on the DNA?
  2. How are they maintained?
  3. How are they removed?

That last one is really important. Because we know how that works, we now can convert adult cells into "Induced Pluripotent Stem Cells," IPSCs, which can do any job.

The answer to the first question basically is that there are changes made to the non-base-pairing sections of the DNA bases, usually addition of methyl groups at Cs in "CpG" islands, additions of methyl groups to the proteins that pack the DNA (histones)—these first two generally close down the DNA and make it less accessible to transcription. Additionally, there are added acetyl and phosphate groups added to the proteins, which tend to "open up" the DNA.

These are maintained by enzymes such as these:

which read the status of the DNA after replication and re-establish it.

The answer to the last question…well, we're leaving that open for now. If you know that certain cells can "reset" these marks, how would you go looking for them?