Our Current Works
Once we collect all the puzzles from each team. We would like to combine them aiming to reveal the significance of epitranscriptomic regulation of RNA during brain developmental stages and in response to external environments which in turn impact cognitive functions.
By Mizuta Kotaro
01. Synaptic epitranscriptomics
Most RNAs in living organisms exhibit their functions through appropriate chemical modifications and higher-order structures. There are about 150 types of RNA chemical modifications and they have now been recognized as "epitranscriptomics," a new layer of gene expression regulation that bridges transcriptomics and proteomics. Recently, our laboratory has succeeded in large-scale sequencing of RNA modifications from synapses in mouse brains and provides an important insight into chemical modification on synaptic-transferred transcripts. In this research project, we aim to elucidate the process in which RNA chemical modification are involved and how the process affects synaptic function, using a multifaceted way including molecular biological, biochemical, and neuroscientific approaches.
Reference:
Merkurjev et al., Nat. Neurosci. 2018, 21, 1004.
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02. Decoding RNA N6-methyladenosine functions in the nervous system development
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Neurite development and synapse formation are essential processes for building neuronal networks and are highly dependent on post-transcriptional gene regulatory mechanisms. M6a epitranscriptomic RNA modification has emerged as a powerful post-transcriptional regulatory pathway in the brain. The lab focuses on the role of the major proteins directly interacting with m6a modifications, named the “readers”, which dictate the fate of the target mRNAs by regulating a wide array of processes such as translation, stability or localization.
Our investigations cover a large aspect of the molecular and cellular mechanisms regulated by the m6a readers from early neuronal differentiation to synapse plasticity. Specifically, we focus on the molecular mechanisms of endosome and RNA granule trafficking and remodeling, microtubules dynamics, and synaptic protein regulation
03. The role of N6-methyl-adenosine signals in building learned spatial cognitive maps in hippocampus
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We can go to our workplace and home without a map. We can also memorize directions to restaurants and other favorite places. It is thought that many of the navigations to these goals are forming cognitive maps in our brains and using these maps. In the hippocampus, there are cells called place cells that fire specifically when an animal is in a certain location, and it is thought that they encode spatial information and form and update cognitive maps. However, genetic regulation of the formation process of place cells has been rarely studied. To address this issue, we are carrying out experiments in which mice are allowed to explore within a virtual reality environment, and activity over 1000 pyramidal neurons in the hippocampus is recorded by two-photon calcium imaging [1-4]. By using this experimental system, genetic manipulation, and electrophysiological techniques, and behavioral test battery [5], we will clarify the relationship between the regulation of gene expression by m6A-modified RNA and spatial learning at the molecular, neural circuit, and behavioral levels.
References:
1. Sato M, Kawano M, Mizuta K, et al., Hippocampus-dependent goal localization by head-fixed mice in virtual reality. eNeuro4, (2017).
2. Sato M*, Mizuta K* (co-first author) et al., Distinct mechanisms of over-representation of landmarks and rewards in the hippocampus. Cell Reports 32, (2020).
3. Mizuta K, Nakai J, Hayashi Y, Sato M. Multiple coordinated cellular dynamics mediate CA1 map plasticity. Hippocampus, (2021).
4. Takamura R*, Mizuta K* (co-first author) et al., Modality specific impairment of hippocampal CA1 neurons of Alzheimer’s disease model mice. Journal of Neuroscience 41, (2021).
5. Sukegawa M, Yoshihara T, Hou S, Asano M, Hannan AJ, Wang DO. Long-lasting housing environment manipulation and acute loss of environmental enrichment impact BALB/c mice behaviour in multiple functional domains. Eur J Neurosci 55, (2022)
04. RNA adduction
Cellular RNA molecules can be chemically modified through two pathways: 1. through the functions of biological enzymes and biomolecules; 2. through reactions with cell-invading compounds/reagents with no requirement for biological enzymes. The latter is called “RNA adduction” for the purpose of distinction from biological “RNA modification”.Due to nucleophilicity of RNA molecules, they can react with a wide range of electrophilic molecules in a variety of natural sources. The invading pathways of the reactants, cellular metabolism, physiological and pathological functions of RNA adduction remain poorly understood. Recently, we reviewed endogenous and exogenous electrophiles that can potentially react to RNA molecules through alkylation.
Reference:
Zhou M, Wang DO, Li W, Zheng J*. RNA adduction derived from electrophilic species in vitro and in vivo. Chemico-Biological Interactions. 351, (2022)
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