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Are enhancers and silencers considered as epigenetic modifications? I am confused as it seems like enhancers and silencers are sequences on the DNA and how they work is through binding with proteins, while epigenetic changes seem to be changes made to the bases for instance adding a methyl group.

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No.

Epigenetic information is (by definition) NOT included in the nucleotide sequence, but affects genetic expression.

Enhancers/silencers are themselves nucleotide sequences, and therefore not epigenetic information.

Methylation is an example of epigenetic information, but a DNA sequence itself is genetic information, even if it affects a gene.

CgATgCCAg= Genetic

Acetylation of a histone/DNA methylation= epigenetic

Hope that helps!

Further reading: http://www.whatisepigenetics.com/fundamentals/

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Strictly speaking, enhancers and silencers are not themselves epigenetic modifications. Rather, they are genetic elements that directly regulate gene expression through their interactions with various proteins.

An epigenetic modification is a chemical change to DNA bases, generally through either methylation or acetylation.

Enhancer and silencer sequences can be, and often are, epigenetically altered by the addition or removal of these chemical groups. This is not uncommon along the course of development for many genes, whose expression must be regulated differently at various stages of development. Enhancers and silencers are also epigenetically regulated in different cell types, which enables cells to use the same genes found in every cell to maintain different cell type identities.

So in short, enhancers and silencers are genetic regulatory elements, but they are very often epigenetically modified. Hope that helps.

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So there are certain combinations of marks we've found that tend to mark regions of DNA that will enhancer/silence expression of reporter genes when we stick them into plasmids and do reporter gene experiments. People often define regions and call them 'enhancers' using these biochemical marks alone, but it's an approximation. There's no guarantee all such regions will be enhancers/silencers, and there's certainly no guarantee that all enhancers/silencers will have the marks.

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Epigenetics is defined as heritable changes in gene activity and expression that occur without alteration in DNA sequence (not encoded in the sequence), and it is influenced by chemical modification of the DNA like in the case of methylation. Enhancers and silencers are sequences of DNA, like genes, but they do not encode for proteins, rather they have gene-regulatory effects. An enhancer/silencer can be methylated and thus be epigenetically controlled.

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