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Is silencer the same as gene silencing? I know that gene silencing refers to those heterochromatin concentrated at the telomeres or centromere. It is also related to methylation. But what about a silencer. Are they the same? Or is silencer an opposite of enhancer (repressor)?

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You are a bit confused with your terms here. Remember, when you are talking about natural regulation of a transcriptome, you can control it at the level of the genome, transcriptome and the epigenome.

The Repressor protein is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. Depending on where it binds, it regulates at the level of the genome or transcriptome.

The Gene Silencer Region, is a DNA sequence in the geneome that that allows repressor proteins to bind to it. It is usually very near the promoter of the gene that it wants to control. This controls the expression of the gene at the level of the genome to repress the transcription of the gene. There exists a few types (Classc silencers, negative regulators and polycomb response) but lets not get into that).

An example is the regulatory element in the classical Lac operon.

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Gene Silencing as you call it is epigenetic in nature. I'll point you towards the wiki as it is quite big and diverse to explain it here: http://en.wikipedia.org/wiki/Gene_silencing

you can read more about it here:http://www.ncbi.nlm.nih.gov/books/NBK26872/

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  • $\begingroup$ Never heard of NRE; what is it? Is PRE Polycomb Response Element? or is it negatively regulated and positively regulated. Please expand the abbreviations. Plus, lac operon is not an example of a "silencer". It is just a case of simple transcriptional repression. Silencers, like enhancers operate from a long distance and have more global effects but they function oppositely to enhancers i.e. they reduce the transcriptional activity. $\endgroup$ – WYSIWYG May 6 '15 at 5:43
  • $\begingroup$ @WYSIWYG Doesn't the Lac operon contain a regulatory element that keeps it off normally (LacI)? Also edited the post for the acronyms. $\endgroup$ – Rover Eye May 6 '15 at 7:43
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    $\begingroup$ Yes it has a regulatory element at the promoter that is bound by LacI. These are usual cis elements and are frequently called operators; they only affect the proximal gene. Enhancers and Silencers control a bigger section of chromatin which may include many genes and they also sometimes interact with promoters via DNA looping. $\endgroup$ – WYSIWYG May 6 '15 at 9:09
  • $\begingroup$ @WYSIWYG Interesting. Never heard of it being called an operator before (was never taught that way) but thats a term. When you say tha Enhancers and Silencers control a larger section of the chromatin, I am assuming that you are saying that the enhancers are not gene specific right (in which case I undertsand)? Or are you saying that enhancers and silencers also control chromatin secondary structures (I have not really looked this up)? $\endgroup$ – Rover Eye May 6 '15 at 9:21
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    $\begingroup$ Enhancers and silencers regulate several genes and can interact with their promoters, cause epigenetic changes or both. Both processes lead to a change in chromatin structure. $\endgroup$ – WYSIWYG May 6 '15 at 11:37

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