Memory repression: how are genes involved?

By Easha Vigneswaran

Understanding how our brains control memory is a popular topic for scientists. Among the various issues concerning memories, something that has consistently been a point of interest is the way in which our brains repress certain memories. It is no surprise that there are many memories that have been confused with others and certain ones that have been simply erased from our brain. Scientists interested in the mechanisms that control memory function have found an enzyme that has been linked to memory repression or in some cases memory extinction.

Scientists have long been researching the interplay between genes and enzymes and how our brains control memory. It was in 2013 when researchers at MIT’s Picopower Institute for Learning and Memory found a group of enzymes that were responsible for the phenomenon neuroscientists have labelled as ‘Memory Extinction’. These group of enzymes are collectively called Ten eleven translocation enzymes or Tet (Rudenko, A et al., 2013). The family of enzymes are comprised of Tet1, Tet2 and Tet3, and have all been heavily linked to gene expression (Rasmussen, K.D et al., 2016). Over the last few years, Tet proteins have been thoroughly studied and are often observed as an influence in malignant cancers (An, J et al., 2017). At the time little was known about Tet’s neuronal influences and capabilities. 

Tet enzymes are a group of methylcytosine dioxygenases which catalyse the oxidation of 5-methylcytosine to 5-hydroxymethylacytosine (Rudenko, A et al., 2013). Enzymes are often involved in DNA methylation which is fundamental to the modification of genes and regulation of gene expression. However, Tet was found to be responsible for DNA demethylation. The presence of 5-hydroxymethylacytosine (5hmC) was observed as being involved in passive demethylation by inhibiting the effect of DNA methyltransferase (DNMT1), an enzyme necessary for the successful methylation of DNA (Smith, Z. D., and Meissner, A., 2013). The inhibition of DNMT which is responsible for DNA methylation was found to block adult rats’ ability to form behavioural memories but was also later found to affect concomitant memory (Miller, C.A et al.,2008). 

The researchers at MIT investigated their hypothesis by using Tet1 knock out (Tet1KO) mice to observe the effects of these genes on the brain. The scientists observed that the loss of Tet1 did not affect the morphology or anatomy of the brain however a reduction in 5hmC was observed (Rudenko, A et al., 2013). The team applied various tests on the Tet1KO mice to observe general behaviours including anxiety and depressive behaviours, however, no significant differences were identified between these mice and those still possessing the Tet1 gene.

Pre-existing research has indicated the effect DNA demethylation has on the mice’s cognitive abilities as discussed by Miller et al., in her 2008 paper. To explore this further the MIT research team performed tests to investigate learning and memory controlled by the hippocampus. The reason the hippocampus was focussed on is due to the fact that this part of the brain is responsible for the encoding of memories and is highly affected by many neurological and psychiatric disorders (Anand, K.S and Dhikav, V. 2012). 

To investigate the effect of Tet1 removal on the mice, the researchers conducted the Pavlovian fear conditioning test. The test uses behaviour testing to elicit fear through associative memory. A conditioned stimulus is applied which is generally an auditory tone-this is the conditioned stimulus. This is paired with an unconditioned stimulus like a foot shock (Bergstrom, H.C, 2011). In this instance, the researchers used a cage to deliver shock, in order to condition the mice to ‘fear’ this cage. Having performed the preliminary tests, the scientists found that associative memory function had initially not been impaired in both the Tet1 mice and Tet1KO mice (Rudenko, A et al., 2013).

Therefore, they extended their research to explore the effects of Tet 1 ablation on memory extinction. After twenty-four hours following the initial test on fear conditioning, Tet1 mice and Tet1KO mice both showed the same levels of freezing response (an indication of a fear response) of 65-75%. The experiment was repeated twenty-four hours later, and a new set of results were observed. They found that the Tet1 mice showed significantly lower levels of freezing response when exposed to the cage (~20%), indicating memory extinction, whereas Tet1KO mice retained a similar level of freezing response as before, indicating no memory extinction (Rudenko, A et al., 2013). The team hypothesised that Tet1 may be responsible for the way in which new memories are formed and the replacement of old ones hence why the Tet1KO mice remained fearful of the cage delivering the shock.

The team had further discovered within their numerous tests that the loss of Tet1 led to the downregulation of neuronal activity regulated genes specifically in the hippocampus and cortex. The highest levels of down regulation were observed in the neuronal PAS domain protein 4 (Npas4) a neuro-protective transcription factor important for the control of synaptic plasticity and memory function (Louis Sam Titus, A.S.C. et al., 2019). Due to Npas4’s importance as a transcription factor coding gene, the team performed tests on the gene’s promoter region. In the Tet1KO mice the Npas4 promoter-exon 1 is methylated in the cortex and hypermethylated in the hippocampus. High levels of 5mC and low levels of 5hmC were also observed thus supporting the idea that the presence of Tet increases 5hmC which is responsible for the inhibition of DNMT1 affecting DNA methylation levels (Rudenko, A et al., 2013).

The team concluded that Tet1 ablation was key to the downregulation of genes important in controlling memory extinction and synaptic plasticity. It appeared that Tet1 influences the methylation of the Npas4 gene which has further implications on genes downstream that are critical in cognitive function and the way in which memories are retained. The researchers at MIT did make a point that although the presence of Tet1 may be responsible for memory extinction, it is also vital for the methylation regulation to prevent excessive methylation thereby controlling gene expression (Rudenko, A et al., 2013).

Using this research, the MIT researchers proposed the potential clinical treatments that can be developed by exploiting the presence of Tet1 gene and its influence on memory extinction. Perhaps the over-expression of this gene may be considered as a way forward to treat people suffering with PTSD with the hope that it will suppress the existing memory of traumatic incidents.

References:

Rudenko, A., Dawlaty, M.M., Seo, J., Cheng, A. W., Meng, J., Le, T., Faull, K. F., Jaenisch, R., & Tsai, L. H. (2013). Tet1 is critical for neuronal activity-regulated gene expression and memory extinction. Neuron79(6), 1109–1122. Available from: https://doi.org/10.1016/j.neuron.2013.08.003

Rasmussen, K. D., & Helin, K. (2016). Role of TET enzymes in DNA methylation, development, and cancer. Genes & development30(7), 733–750. Available from: https://doi.org/10.1101/gad.276568.115 [Accessed 15th November 2020]

An, J., Rao, A. & Ko, M. (2017). TET family dioxygenases and DNA demethylation in stem cells and cancers. Experimental and Molecular Medicine. Available from: https://doi.org/10.1038/emm.2017.5

Smith, Z. D., & Meissner, A. (2013). The simplest explanation: passive DNA demethylation in PGCs. The EMBO journal32(3), 318–321. Available from: https://doi.org/10.1038/emboj.2012.349

Miller, C. A., Campbell, S. L., & Sweatt, J. D. (2008). DNA methylation and histone acetylation work in concert to regulate memory formation and synaptic plasticity. Neurobiology of learning and memory89(4), 599–603. Available from: https://doi.org/10.1016/j.nlm.2007.07.016

Anand, K. S., & Dhikav, V. (2012). Hippocampus in health and disease: An overview. Annals of Indian Academy of Neurology15(4), 239–246. Available from: https://doi.org/10.4103/0972-2327.104323

Bergstrom, H.C., McDonald, C.G., Johnson, L.R. (2011). Pavlovian Fear Conditioning Activates a Common Pattern of Neurons in the Lateral Amygdala of Individual Brains. PLOS ONE 6(1): e15698. Available from: https://doi.org/10.1371/journal.pone.0015698 Louis Sam Titus, A.S.C., Sharma, D., Kim, M.S. et al. (2019). The Bdnf and Npas4 genes are targets of HDAC3-mediated transcriptional repression. BMC Neurosci20, 65. Available from: https://doi.org/10.1186/s12868-019-0546-0

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