I disagree with rg255 on this. Most if not all of posttranscriptional modification is encoded in the actual DNA sequence. Those microRNAs for example can be determined by reading the DNA bases or finding the encoded enzymes that do RNA editing (like C to U by TPR enzymes). The DNA sequence alread...
The expression of a gene is modified post transcription, not because a nucleotide was changed elsewhere in the genome, but because that nucleotide exists
e.g. expression of gene X may be regulated to be differently expressed in two cell types, each cell has the same sequence of DNA, but one part of that DNA gives instructions about regulation of gene X in specific cells - there are no differences in sequence between the cells, but there is a difference in expression, therefore it is epigenetic
if it creates variance in the genome, but does not come from variance in the sequence, it's epigenetic
the genomic variation is not generated by sequence variation - the machinery to create that variation can be coded within the sequence, but the genomic variation is not created by the existence of that segment of sequence
@rg255 Your point of view is correct but then that would mean that any mechanism of gene expression regulation arising because of the network dynamics should be considered epigenetic. I would agree with you on this definition but the very scientific community that works on these aspects considers only a few cases.
Just to note on your pubmed search, methylation research has a considerable headstart on miRNA regulation research having been discovered decades earlier.
@mimat could you explain to me why miRNA is not considered epigenetics? It's not a familiar back story for me
@rg255 I think that your point of view is correct. However, in that case we should also consider the gene regulatory programmes mediated by transcription factors as epigenetic as they do change the functionality of the genome without changing its function.
One can argue that these TFs were ultimately encoded by the genes but the same applies for histone modifiers and DNA methylases.
Since you also work with dynamical systems, you would understand that a state can be perpetuated just because of the dynamics of the system.
I say that, if ncRNAs are epigenetic, then so should be TFs. Why should something be non-epigenetic just solely because of its molecular nature.
However, the community does not consider TFs as epigenetic while considering other mechanisms of gene regulation, which is simply flawed.
In that case the concerned research should be called "chromatin biology" and not epigenetics.
Discussion between WYSIWYG and rg255
Discussion between WYSIWYG and rg255