The best answer to this question is “there is no clear consensus definition of what ‘epigenetics’ means.” For this reason, at Cell Reports we discourage the use of the term and require that the authors define it as soon as possible in their paper.
Perhaps someday, even soon, this will change and the scientific world will agree that ‘epigenetics’ means ‘modification of chromatin’ or something like that, but if anything is clear it is this: no such consensus exists.
Am I much out of line if I think of epigenetics as any factors of inheritance over and above the actual DNA base pair transcription?
You’re not out of line until you claim (which you didn’t) that this is the definition of epigenetics.
Let’s also remember that “epigenetics” was a word long before anyone knew about methylation or even that DNA was the genetic material. Cell-to-cell adhesion, cell migration, extracellular matrices, differential proliferation, and apoptosis are all epigenetic processes.
Also, for “transcription”, read “replication”.
//When 5-methylcytosine is deaminated into uracil, this error can be corrected by base-excision repair, before or after the uracil gets replaced with a thymine, so the G-U or G-T pair is fixed back to a G-C pair.//
No. If this erroneous G-T pair ends up to replication, it will result in A-T pair due to cellular machinery maintainig the genetic integrity. This is why there are ~32,000 disease-causing GC>AT point mutations in human genome.
Or it gets repaired back to a GC pair via the mechanism I described.
I’m not disagreeing that deamination of 5meC CAN result in a C>T transition mutation, I was pointing out that your claim that it’s an inevitability is incorrect, because repair mechanisms do in fact exist that can fix it.
“However, if a cell replicates before the mismatch can be repaired, a C>T mutation will become encoded into its genome.”
‘If’ is the key word.
Please read my previous comments.
In your first comment on the subject, you said there was no repair mechanism to stop deaminated 5meC resulting in a C>T mutation. I pointed out that a repair mechanism does in fact exist. If you agreed, why didn’t you say so?