Transcription Factor Inhibition vs. Gene Methylation?

[icakeov]

I may mess up this question, and this is not my strong field of knowledge. I am wanting to understand different ways of genes not expressing themselves. So far I have come across two ways this happens (perhaps there are more?)
- "transcription factors that inhibit gene transcription"
- "genes are methylated, disabling transcription factors from expressing them"

I am mainly wanting to confirm that these are two different processes that act to suppress the expression of the genes. The second one is obviously in the domain of epigenetics and methylation.

My question is what exactly is the first one, where transcription factors themselves inhibit the expression. Would this still be considered in the domain of "epigenetics"? I am guessing not. Is this competition between transcription factors? Can this compete with epigenetic processes in any way? I am guessing if a gene is methylated and the transcription factor is coming to inhibit the gene, then it would be some sort of a double-whammy no-go? And vice versa, an expression of a gene has to satisfy both "not being methylated" and "transcription factor arriving 'uninhibited'" in order for it to be expressed?

Any feedback and thoughts appreciated, and forgive me for any mess-ups in the formulation of the question.

 

[BillTre]

Transcription has many moving parts and is very complicated.
There are therefore many ways it can be increased or decreased.
Methylation can have positive or negative effects. It can also be epigenetic (meaning inherited trait changes, not based on sequence changes, that might change back in one or more generations).
All these things are the result of interactions between many different kinds of molecules. Each interaction can be positively or negatively affected at different steps in the interaction pathway.

I would think of it in increasing levels of complexity:
DNA is like a string. Particular sequences are in different places along the string.
The string is twisted and folded up (or it wouldn't fit in a cell).
It gets wound around a set of proteins in certain ways. This makes to physically stronger and takes up less space.
Transcription happens when than RNNa polymerase enzyme finds the right sequence to trigger it to go into make RNA mode. In theory, it has to search the whole genome to find it, but much of the geneome may be excluded from the search in various ways (like being inactivated, very condensed so that the enzyme does not physically fit into the spaces where some of the sequences are).
There will also be chemical signals attracting or repelling particular molecular machines.
Some of these are just chemical modifications of the proteins associated with the DNA, or of the proteins associated with the proteins associated with the DNA. I think some of these patterns can be inherited.

Transcription factors can either promote of inhibit transcription. I believe that there are cases of the same molecule doing different things in different situations.

The more steps involved, the more possibilities for cybernetic complexities in the chemical interactions to emerge.

 

[icakeov]

Response much appreciated!
I guess we can at the least conclude is that methylation molecules and transcription factor molecules at the least are involved somewhere within the process of gene expression together, but whether they will play this part or that part at any point or another, and what we should call those, gets pretty messy pretty quickly.

 

[jim mcnamara]

See https://www.sciencedirect.com/science/article/abs/pii/S1367593108001191
Cell article abstract:
Cell 2018 Feb 8;172(4):650-665.
doi: 10.1016/j.cell.2018.01.029.