Epigenetics: Manipulating Gene Expression

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The modern definition of epigenetics is the study of changes in the regulation of gene activity and expression that are not dependent on gene DNA sequence. This means that while not all epigenetic mechanisms are genetically coded, some are inherited.

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Let's take a closer look at each mechanism and how we can study it in the laboratory.

1. DNA Methylation:

The first system, DNA methylation, involves adding a methyl group to the 5' carbon of the cytosine ring. It should be noted that it only affects cytosine when followed by guanine. Methylated DNA will wrap itself more tightly around the histones and is therefore inaccessible to transcription factors.

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2. Histone modification:

In contrast to DNA methylation, histone modification is a mechanism that adds functional groups to histone proteins instead of DNA molecules. There are four known types of modification: methylation, acetylation, phosphorylation, and ubiquitination. The effects of these four mechanisms are shown below:

There are two commonly used methods for studying histone modifications:

Western blot:

If we are interested in the nature and abundance of several modifications, the Western blot would be the most suitable choice. This method requires antibodies that can bind to the desired modification.

Square chips:

As already explained, histones are enveloped by DNA. Therefore we need to determine which part of the DNA makes up the envelope.

So if we are interested in determining the genomic position of histones, we can perform chromatin immunoprecipitation sequencing (ChiP-seq), a method that characterizes the interactions between DNA and DNA-binding proteins. This method also requires antibodies that can bind to the protein of interest.

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