The mechanism that regulates memory gene activity

Summary: DNA methylation regulates the expression of PKMzeta, a gene involved in long-term memory formation. Reduced levels of PKMzeta in the brain are associated with Alzheimer’s disease and other memory deficit disorders.

Source: FAPESP

The PKMzeta protein is known to be associated with the formation of long-term memory. Neurological disorders such as Alzheimer’s disease, as well as depression and aging, correlate with reduced levels of this protein in the brain.

Researchers affiliated with institutions in Brazil and the United States have now discovered a mechanism that helps explain the link and could pave the way for future medical innovations.

Their study is reported in an article published in the journal Biochimica et Biophysica Acta (BBA) – Mechanisms of gene regulation.

To understand the mechanism, the researchers used epigenetics, the science of how environmental stimuli activate or inhibit gene expression without altering DNA sequence.

An epigenetic technique often used by researchers is DNA methylation gene silencing, in which methyl groups are added to a specific section of a gene to prevent its transcription. For example, methylating a gene’s DNA sequence can turn the gene off so that it doesn’t make a protein.

In the article, the authors recall that in the central nervous system the CREB1 protein normally binds to a section of the gene PKMzeta so that it expresses the protein of the same name. The study showed, however, that hypermethylating this part of the gene resulted in significantly lower levels of the PKMzeta protein.

“Our analysis revealed that DNA methylation regulates the expression of this gene, which plays a role in several pathologies,” said Deborah Schechtman, the paper’s final author and professor at the Institute of Chemistry at University of São Paulo (IQ-USP) in Brazil. .

“I believe that when basic science is done well, it provides vital information for the development of advanced drugs and therapies.”

The study was supported by FAPESP via five projects (19/06982-6, 15/24046-5, 15/17812-3, 20/13929-1 and 20/16204-8).

Inside the DNA

Dimitrius Pramio, first author of the paper and a doctoral candidate in biochemistry at IQ-USP, described the materials used in the study, some of which were obtained through partnerships with Yale University and SUNY Upstate Medical. University in the United States. “Materials included databases, human cells isolated from patients or modified in the laboratory, and animal cells,” he said.

Several tests have been conducted to see if the methylation of the gene PKMzeta would lead to lower levels of the protein it produces, using drugs that interfere with DNA methylation and the CRISPR gene-editing technique. In this case, the alterations made to the gene PKMzeta prevented proper binding of the CREB1 protein. “Production of the PKMzeta protein indeed dropped as a result,” Schechtman said.

It shows a brain
The study showed, however, that hypermethylating this part of the gene resulted in significantly lower levels of the PKMzeta protein. Image is in public domain

The results confirmed that the gene in question requires CREB1 to trigger the production of the PKMzeta protein and that DNA methylation explains the drop in levels of the protein.

The authors also analyzed the role of other genes in the central nervous system to see if they were inhibited by this DNA hypermethylation process that prevented CREB1 binding. “We wanted to know if the process had gone more holistically,” Schechtman said.

If the expression of genes other than PKMzeta is affected by this DNA methylation pattern, this should be particularly relevant for brain alterations possibly associated with pathologies, and the authors showed that the mechanism is not limited to the PKMzeta protein.

Next steps

Several points emerge from this study. One would be to analyze other genes affected by this DNA methylation process that inhibits the binding of CREB1, with the aim of seeing what role they play in the organism, as well as their possible association with diseases. .

Another possibility would be to try to understand what the PKMzeta protein actually does in the central nervous system. “We know it’s involved in memory, but how does it work in detail? It’s a relevant question,” Schechtman said.

For Pramio, it is also important to test the mechanism in more precise models. For example, specific regions of the brain could be analyzed, as could animal models of diseases such as Alzheimer’s disease and depression.

“Other studies have shown that the use of certain antidepressants in animal models of depression restores the expression of the gene PKMzeta when it’s inhibited, but they haven’t studied DNA methylation,” he said.

Other conditions could also be considered. Schechtman, for example, works on chronic pain, and it is possible that the gene PKMzeta could be involved in such conditions due to its participation in synaptic remodeling of neurons. “Many questions and hypotheses were raised by the study,” she said.

According to Pramio, progress in these lines of research could contribute in the future to the development of new treatments, which would be particularly important for depression and Alzheimer’s disease, given the challenges posed to doctors by these disorders.

About this genetics and memory research news

Author: Heloise Reinert
Source: FAPESP
Contact: Heloisa Reinert – FAPESP
Picture: Image is in public domain

Original research: Free access.
“DNA methylation of the promoter region at the CREB1 binding site is a brain-specific epigenetic regulatory mechanism of PKMζ” by Deborah Schechtman et al. Biochimica et Biophysica Acta (BBA) – Mechanisms of gene regulation


DNA methylation of the promoter region at the CREB1 binding site is a brain-specific epigenetic regulatory mechanism of PKMζ

Protein kinase M zeta, PKMζ, is a brain-enriched kinase with a well-characterized role in long-term potentiation (LTP), the activity-dependent enhancement of synapses involved in long-term memory formation. However, little is known about the molecular mechanisms that maintain the tissue specificity of this kinase. Here, we characterized the epigenetic factors, primarily DNA methylation, regulating PKMζ expression in the human brain.

THE PRKCZ The gene has an upstream promoter regulating protein kinase Cζ (PKCζ), and an internal promoter driving the expression of PKMζ. A demethylated region, including a canonical CREB binding site, located at the internal promoter was observed only in human CNS tissues.

Induction of site-specific hypermethylation of this region resulted in decreased CREB1 binding and downregulation of PKMζ expression. Of note, CREB binding sites were absent in the promoter upstream of PRKCZ locus, suggesting a specific mechanism for regulating PKMζ expression.

These observations were validated using a human neuronal differentiation system from induced pluripotent stem cells (iPSC). Binding of CREB1 at the inner promoter was only detected in differentiated neurons, where PKMζ is expressed.

The same epigenetic mechanism in the context of the CREB binding site has been identified in other genes involved in neuronal differentiation and LTP. Moreover, aberrant DNA hypermethylation at the internal promoter level has been observed in cases of Alzheimer’s disease, in correlation with a decrease in the expression of PKMζ in the brain of the patients.

Altogether, we present a conserved epigenetic mechanism regulating the expression of PKMζ and other enhanced genes in the CNS with possible implications in neuronal differentiation and Alzheimer’s disease.

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