A new study from Fudan University, in China has identified novel activities for KDM5C, and RACK7, both of which are proteins involved in the epigenetic regulation of genes. These two proteins have been shown to form a complex, which at times can occupy the enhancer site of many genes, causing a “break” in gene transcription.
What Are Enhancers?
Enhancers are short regions of DNA (50-1500 base pairs), which can be bound by proteins called activators. Once bound by these activators, enhancers will promote the transcription of specific genes that they correspond to. Enhancers are particularly interesting because they do not need to be found anywhere near the gene that they regulate. They can be located hundreds of thousands of base pairs away, they can either be upstream or downstream of the gene they regulate, and they can be facing either forwards or backwards. In essence, their location relative to the gene they regulate has limited effect on their function. The reason for this is simple. Once activators have bound to enhancers, they will recruit other proteins necessary to initiate transcription. Once these other factors have been recruited, the enhancer will bend DNA in such a way that it finds the gene it is meant to regulate. The factors it has recruited will then bind to that gene and begin transcription of DNA to RNA .
Histone Demethylase KDM5C
KDM5C is a histone demethylase. This means that it will remove a methyl group from various histones (the proteins on which DNA is wrapped around) throughout the genome. Histone methylation and demethylation is one of the most important types of epigenetic modifications. Depending on the type of methylation, it can either cause increases or decreases in gene expression. Furthermore, these histone methylation marks can often be inherited from cell to cell within the body .
Since little was known about RACK7, except that it could potentially “read” chromatin (meaning it can look for specific histone marks and bind to them), the group from Fudan University sought to further elucidate its functions. Using a genome wide analysis, they found that RACK7 actually binds to DNA in about 15,000 different places. Further analysis indicated that the vast majority of RACK7 binding sites were actually active enhancers. Using mass spectrometry, the group was able to identify KDM5C in association with RACK7 at these binding sites, indicating that they were capable of forming a complex. This association was not expected, as KDM5C is normally thought of as a protein that is primarily involved in histone demethylation.
The group then investigated the function of this complex. In order to do that, they repressed expression of both proteins, and analyzed the regions to which the complex bound. What they found was that different types of histone methylation marks were either increased or decreased, indicating that this complex is important for maintaining proper methylation of histones. They also found increased expression of genes associated with the bound enhancers, which suggests that this complex is important for regulating gene expression .
Taken together, these results indicate that the RACK7-KDM5C complex acts as a cellular on and off switch for enhancers. This result is unexpected because KDM5C was previously thought to be primarily a regulator of histone methylation, and was not thought to associate with enhancers. It is important to consider that proteins that are canonically thought to have a particular function can often complex with other proteins and perform other important tasks that are necessary for proper cellular function. These types of studies further our understanding of the human genome and help us understand that biology is a lot more complex than “one structure one function,” and that even secondary interactions can often be vitally important.