Metabolic Enzyme Regulates Histone Acetylation and Spatial Memory

https://www.nature.com/articles/nature22405.pdf

Epigenetic modifications have been identified in cognitive processing, specifically in learning and memory. Lack of histone acetylation has been implicated in neurodevelopmental disorders, neurodegeneration, and aging.1 Expression of neuronal genes that are involved in chromatin modification processes, such as histone acetylation, have important involvement in storing and forming memories, mostly in the hippocampus. Transcription factor CREB, coactivator CREB binding protein (CBP)2, particularly histone acetyltransferase (HAT)3, and histone deacetylase inhibitors are all known to be required and helpful for consolidation of memories, though the mechanisms of histone acetylation are unknown. As known from Biochemistry 441, acetyl CoA has various roles in bodily metabolism in different pathways, so its importance in another mechanism of our body is not surprising. Sensing of metabolites, such as acetyl CoA levels, by acetyltransferases can alter the structure of chromatin and the expression of genes. Therefore, the enzymes responsible for the making of acetyl CoA, acetate-dependent acetyl-CoA synthetase 2 (ACSS2) and citrate-dependent ATP-citrate lyase (ACL), control the acetylation of histones as well as gene expression, but their role in post-mitotic neuronal cells and specifically in memory function is not established.

Mews et al. used the Cath-a-differentiated (CAD) cell line, a neuronal cell line from a mouse that demonstrates histochemical fluorescence, to look into the function of ACSS2. Earlier in Biochemistry 441, we read an article discussing a different type of cell differentiation and its role in metabolism.

ACSS2 remained in the cytoplasm when undifferentiated, but the moved to the nucleus and increased once differentiated from CAD cells into neurons, while ACL expression remained constant in the cytoplasm4. When neuron-specific protein markers were upregulated in differentiated neuronal cells, pre-differentiation knockdown of ACSS2 reduced expression of nuclear markers and ACL was not decreased, therefore ACSS2 has a significant role in neuronal differentiation. mRNA-seq identified 894 upregulated genes upon CAD neuronal differentiation and gene ontology analysis identified these genes were specific to each neuron4.

Mews et al. examined the acetylation of histones during differentiation by using chromatin immunoprecipitation with high-throughput DNA Sequencing (ChIP-sep) for histone H3 lysine 9 acetylation (H3K9ac), H4K5ac, and H4K12ac. The results indicated the 894 genes that were upregulated showed high levels of acetylation than all others. When reducing levels of ACSS2 and ACL using short hairpin RNAs before differentiation and RNA-seq and discovered that when ACSS2 was knocked down, levels of upregulation were lowered and showed a genome-wide defect, and when ACL was knocked down, there was no change in upregulation and cells showed lower global transcript levels4. The authors concluded that ACL has a non-specific effect on gene expression while ACSS2 has a specific requirement for upregulation of gene expression when CAD cells are differentiating into neurons4.

Mews et al. then used ChIP-seq to access the connection between ACSS2 and chromatin, and found a strong correlation using ACSS2 antibodies. The binding of ACSS2 correlated with an increase in histones in differentiated CAD cells. Being that genes proximal to ACSS2 peaks were linked to cell differentiation, chromatin-associated, neuronal gene promoter-proximal ACSS2 could very well be a source of acetyl-CoA to HAT enzymes4. ACSS2 binding was found to be connected to histone acetylation due to ACSS2 peaks directly overlapping with H3 and H4 acetylation peaks and the height of the peaks were correlating with each other, suggesting that H4 acetylation is the most responsive to acetyl CoA from ACSS2, specifically H4K12ac which is interestingly linked to ineffective forming of memories.5  The overlapping of peaks with different genes involved in memory are shown in the figure. Recruitment of ACSS2 by transcription factor binding demonstrated that the most enriched motif recruits CBP and E1A binding protein (p300), which are both acetyl-CoA dependent, meaning that ACSS2 in involved in HAT activity nearby. In fact, genes with the largest change in differential AcSS2 binding had the highest levels of histone acetylation and were neuron-specific. The CAD cell genomic data demonstrated that the enrichment of ACSS2 in differentiated neuronal cells is linked to higher levels of acetylation of histones and an involvement the upregulation of neuronal genes4.

Figure 1. ChIP–seq of ACSS2 and H3K9ac in mouse hippocampus. Overlap with three neuronal genes involved in memory.

Acetyl CoA levels in knocked down ACSS2 cells with ACSS2 inhibitor were decreased, supporting the idea that ACSS2 is a supplier to acetyl-CoA. Knocked down cells also showed reduced global histone acetylation levels in markers with transcriptional coactivators (CBP and P300) with roles in long term memory. ACSS2, CBP, and acetylated chromatin co-immunoprecipitated, showing that ACSS2 binds chromatin at active genes to drive the increase in the acetylation of histones when memories are forming4. ACSS2 inhibitor treatment reduced marker expression and histone acetylation, but didn’t lower ACSS2 levels or the ACL levels in mouse neurons. Using ChIP-seq, ACSS2 in the hippocampus and H3K9ac corresponded over three neuronal genes involved in memory formation. Genes enriched for H3k9ac were transcribed, but if enriched for ACSS2 and H3k9ac only then did they have the highest levels of expression4.

Spatial memory in the hippocampus occurs through epigenetic modifications, such as histone acetylation. ACSS2 could mediate histone acetylation in order to upregulate gene expression during the consolidation of memories6.  ACSS2 knockdown mice were found to have impaired spatial object memory, a lower discrimination index, and reduced total object exploration during an object-location memory test4. The authors concluded that AcSS2 has a role in dorsal hippocampus-meditated long-term spatial memory. Being that long-term spatial memory requires an increase in histone acetylation and immediate gene transcription and memory consolidation can be inhibited by stopping mRNA synthesis, Mews et al. used mRNA-seq on the dorsal hippocampus to access whether ACSS2 was involved in gene upregulation for hippocampal memory consolidation. Upregulation of early genes during the sensitive memory consolidation period was reduced when ACSS2 was knocked down. In addition, induction of early genes during the sensitive period was stopped by the knock down of ACSS2.4

In conclusion, the authors demonstrated a link between metabolism and neuronal plasticity, showing the function of ACSS2 as a chromatin-bound transcriptional coactivator, stimulating histone acetylation and upregulating gene expression, required for spatial memory. Post-mitotic neurons have a reliance on ACSS2 to be a supplier of the acetyl-CoA for the acetylation of histones, as HAT enzymes are controlled by changing acetyl CoA levels. The authors also show the role of ACSS2 of upregulation in early genes which can lead to a role in long-term memory consolidation. Understanding of epigenetic mechanisms that regulate neural functions can be linked to a better understanding of neuropsychiatric diseases. In fact, drug abuse is even linked to altering chromatin states7, so this new information can potentially be used to help in understanding drug addiction and treatment. Due to the complexity of understanding and memory, ACSS2 can be identified as enzymatic target to develop therapeutic agents to help to treat various different neurological and cognitive disorders, especially involving memory and learning.

References:

(1)          Gräff, J.; Tsai, L.-H. Histone Acetylation: Molecular Mnemonics on the Chromatin. Nat. Rev. Neurosci. 2013, 14 (2), 97–111.

(2)          Wood, M. A.; Kaplan, M. P.; Park, A.; Blanchard, E. J.; Oliveira, A. M. M.; Lombardi, T. L.; Abel, T. Transgenic Mice Expressing a Truncated Form of CREB-Binding Protein (CBP) Exhibit Deficits in Hippocampal Synaptic Plasticity and Memory Storage. Learn. Mem. 2005, 12 (2), 111–119.

(3)          Korzus, E.; Rosenfeld, M. G.; Mayford, M. CBP Histone Acetyltransferase Activity Is a Critical Component of Memory Consolidation. Neuron 2004, 42 (6), 961–972.

(4)          Mews, P.; Donahue, G.; Drake, A. M.; Luczak, V.; Abel, T.; Berger, S. L. Acetyl-CoA Synthetase Regulates Histone Acetylation and Hippocampal Memory. Nature 2017, 546 (7658), 381–386.

(5)          Peleg, S.; Sananbenesi, F.; Zovoilis, A.; Burkhardt, S.; Bahari-Javan, S.; Agis-Balboa, R. C.; Cota, P.; Wittnam, J. L.; Gogol-Doering, A.; Opitz, L.; et al. Altered Histone Acetylation Is Associated with Age-Dependent Memory Impairment in Mice. Science 2010, 328 (5979), 753–756.

(6)          Barrett, R. M.; Malvaez, M.; Kramar, E.; Matheos, D. P.; Arrizon, A.; Cabrera, S. M.; Lynch, G.; Greene, R. W.; Wood, M. A. Hippocampal Focal Knockout of CBP Affects Specific Histone Modifications, Long-Term Potentiation, and Long-Term Memory. Neuropsychopharmacology 2011, 36 (8), 1545–1556.

(7)          Walker, D. M.; Cates, H. M.; Heller, E. A.; Nestler, E. J. Regulation of Chromatin States by Drugs of Abuse. Curr. Opin. Neurobiol. 2015, 30, 112–121.

20 thoughts on “Metabolic Enzyme Regulates Histone Acetylation and Spatial Memory

  1. Hi Brittany! Thanks for sharing this unique example of epigenetic modifications that ties together metabolism and the limbic system. Identifying ACSS2 as a key regulator in genes critical for memory formation is a big step in understanding nervous system disease pathology and intervention. It was mentioned that along with ACSS2, ACL is responsible for acetyl CoA production and the acetylation of histones. Even though ACL is primarily in the cytoplasm during differentiation into neurons, can you please talk about why ACL was ruled out as an epigenetic regulator? As far as I know, the home of citrate lyase has always been the cytoplasm to make acetyl CoA for something like fatty acid synthesis. Why can’t the acetyl CoA made from citrate lyase go back into the nucleus and serve as an acetyl group source for histone acetylation?

    1. When doing RNAseq before differentiation, the authors stated that “the induction of neuronal genes was lost in the ACSS2 knockdown cells, whereas the same genes retained a strong correlation in transcriptional fold-change in ACL knockdown cells…The ACL-knockdown cells showed the same upward trend as wild-type cells, in contrast to the severe defect in ACSS2-knockdown cells.” The authors concluded that ACL’s effect on gene expression is broad and nonspecific, unlike ACSS2. Also, I am assuming it could, but ACL has a less specific effect on modifications. In addition, ACL can not be used when in a fasted state.

  2. Hi Brittany,
    This was an extremely intriguing article you seem to have found, and you reported it quite well! It was surprising to read about the biochemical pathways of memory formation, as it seems like a very hard subject to pinpoint. I was wondering if you could elaborate more on the possible drug-targets of ACSS2. More specifically, I’m curious if you think it would work in specific neuronal diseases involving spatial memory issues. I ask this because usually any neuronal diseases or impairments are fraught with a pleiotropic phenotype, of which it is hard for even the experts of the field to be able to target just one issue. Even though you report on ACSS2 being established as a major acetyl-CoA provider for the HATs of dorsal hippocampus cells, the experiments using CAD cells seem to indicate that ACSS2 regulation is also needed for general neuronal development. In other words, do you think a drug target of ACSS2 would have adverse effects on other sections of the brain, or could you envision a way to regulate ACSS2 activity localized to the dorsal hippocampus?

    1. As I mentioned above, this can certainly be used to better understanding of learning and memory in drug abuse. Because a lot of information isn’t available, it is hard to know how it could be a drug target. Possible upregulation can be used to help the process occur and maybe have the ability to treat diseases involving learning and memory, though I am unsure exactly how it can be used to treat something very specific. It also is most likely possible that ACSS2 can be needed for aspects of general neuronal development, though the authors link it specifically to memory and learning. I am unsure of what adverse effects it may be able to cause, though the possibility is there if upregulation of activity is not localized.

  3. Hello Brittney, thank you for the interesting paper! It continues to amaze me how much Acetyl-CoA does in our bodies. We often talk about ATP being the superhero of the body, but I am leading towards Acetyl-CoA claiming that title! One thing I was confused on was the authors referred to early genes and gave some examples but could explain what they mean by early genes? Are these just the first genes to become promoted to start forming memories or is this something different?

    1. I certainly agree with you Calvin. Team Acetyl CoA vs team ATP for the title. When the authors refer to early genes, they are referring to the transcription and expression of genes during the sensitive memory consolidation period. I hope this makes more sense now!

  4. Hi Brittany. I really enjoyed reading this article. When I read articles like this, or any research really, I usually think about it in a pharmacological way. Something like, “is there a drug that can alter something in this mechanism.” So while reading it, all I kept thinking about was finding a way to target this. I know I have issues remembering things, I would love to be able to remember more. We know, from the research that metabolic production of acetyl coenzyme A is linked to histone acetylation which is linked to differentiation in neurons and attenuation of the hippocampal gene expression that is involved in memory regulation. Have you thought of any methods as you were reading or can you propose any methods in which we can stimulate histone acetylation through drug therapy? Basically, have a way to increase histone acetylation so that it helps improve our memory? That would be a really cool drug to have, everyone can use a memory boost.

    1. I agree with you Endonita in that the first thing I think about when I read these is “drug target” or treatment. Certainly remembering more would be helpful to all of us, but treating a specific neurological disease would be the ideal application. I could just assume that something that can upregulate or better express ACSS2 would result in more histone acetylation and therefore more memory consolidation. I do not know how ACSS2 has the potential to be stimulated. We can only wait on drug companies to publish something pertaining to their method of targeting it.

  5. This was definitely a very interesting paper to read, especially since the epigenetic regulation being done during memory processing makes a lot of sense when combined with what I have learned about receptor up/downregulation at the synapse in response to higher or lower levels of signaling! I do have one question, and that is did they identify any specific genes that have also been implicated in learning and memory? One in particular I am curious about is the NMDA receptor since I have been taught that it is highly involved in learning and memory.

    1. I surely could use some more information regarding synaptic signaling and regulation so I would be eager to discuss this with you more deeply. Though, based on what I do know it does make sense. Arc, Egr2 and Nr2f2 genes were previously linked to learning and memory, and that is why they used these genes in experiments throughout this paper. The NMDA receptor was not mentioned in this paper, though maybe that could be used as a specific drug target in treating diseases of learning and memory.

  6. Hey Brittany! This paper seems to have found a new lens through which to look at acetyl-CoA synthesate 2, and your news and views version of the article was incredibly helpful in understanding this. The authors appear to have made a fairly reliable connection between acetyl-CoA synthetase 2 and epigenetic modification, but what exactly regulates acetyl-CoA synthetase? Epigenetic modification is complex and critical for cellular balance, so something must be acting as a covalent or allosteric regulator of this epigenetic action. Is there any evidence or speculation about this in the paper? Perhaps environmental cues are responsible?

    1. The authors did not mention what specifically regulates acetyl-CoA synthetase throughout the paper or in past papers that I saw, though finding a regulator of ACSS2 can evolve to be a potential drug treatment for diseases of learning and memory. But you are correct in that something must be regulating this epigenetic action, but no one is sure of what exactly just yet.

  7. Hi Brittany,
    Thank you for this interesting read! It’s amazing that the authors were able to actually show how acetyl CoA levels can affect things such as chromatin structure or gene expression and how this will then impact memory. The figure in your post depicts binding of ACSS2 and H3K9ac-H3 on three genes involved in memory. The authors mention that these genes are “canonical” neuronal genes involved in memory. Do you know if there are any diseases that result from malfunction of these genes? And do you think that a possible cause for this could be linked back to epigenetic modification?

    1. Though nothing is mentioned or known about the specific diseases involved, these genes are known to be upregulated following memory retrieval. The authors stated, “Remarkably, retrieval-associated induction of immediate-early genes did not occur during the sensitive reconsolidation period, whereas retrieval-linked downregulation during the same period was not affected by ACSS2 KD.” So it becomes unclear whether there is a strong connection between epigenetic modification and these specific genes. Though, there could be a link to epigenetic modification and disease relating to these specific genes.

  8. Hi Brittany,

    Thank you for your review, it was really helpful in understanding the paper. It is really interesting how ACSS2 is directly involved in the regulation of neuronal gene expression, especially with regard to cognition and long term-memory storage. In your assessment, how do you think this information might be applied in the clinical field? For example, in the case of individuals with impaired hippocampal long-term memory storage, do you think that targeting the enzyme and potentially stimulating its activity would be beneficial in improving memory? Further, would it be possible to put individuals on certain diets that might up-regulate ACSS2 activity and thus reverse hippocampal memory abnormalities?

    1. This information can give an overall better understanding of neuropsychiatric diseases. I believe this information can possibly link stimulation of ACSS2 as a drug target and have potential to aid in memory stimulation, though a lot more research needs to be done first. Because drug abuse is linked to altering of chromatin states, this information can help to better understand drug treatments but somehow altering chromatin states while using a drug target. I really am not sure if diets can affect the upregulation of ACSS2, though if a connection to diet is found for upregulation of ACSS2, then there is certainly a chance this may work to improve memory.

  9. Brittany – it is interesting to learn more about the connections between metabolic processes and the implications it may have on neuronal diseases. What kind of drug treatments do you propose can be developed from this information? Could ACSS2 somehow be genetically modified for overexpression in patients with neuronal damage?

    1. I think a lot more work needs to be done before any drug treatments can be formed. It may be possible to use ACSS2 as a drug target to treat diseases involved in memory. It can surely be possible to overexpress ACSS2, but how that can be applied is still to be discovered.

  10. This is a really cool paper Brittany! The role of proteins in memory consolidation seems so out of reach when looking at how other fields pursue brain functions and the mind. I was unaware of the current progress in mapping the specific genes involved in memory. That said, having a specific vital protein such as ACSS2 makes for a wonderful target for memory deficit linked pathologies. In addition, could this also be a target of enhancement. While morally ambiguous and debated, the ability to “enhance” someones cognitive abilities has always been desired. Authors cite this proteins function as necessary for initiation, but is there evidence that its expression or activity varies from specimen to specimen? This would provide a (controversial) link between a genetic basis and cognitive function. Very interesting, if a little scary.

  11. Hi Brittany, I really like how you were able to take something we learned in class and connect it to something we had never really talked about before. I was wondering if there was any information on how things we sense lead to the expression and activation of ACSS2 and other enzymes involved in gene regulation? Was there any mention of how this pathway connects to the pathway of our pheripheral neurons and the things we sense?

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