Structural and Dynamic Insights into Redundant Function of YTHDF Proteins

Li, Yaozong; Bedi, R.K.; Moroz, Elena; Caflisch, Amedeo

doi:10.1021/acs.jcim.0c01029

Cited by 46 publications

(95 citation statements)

References 22 publications

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“…Whilst the best characterised m 6 A-binding proteins (readers), which recognise specific chemical modifications and direct binding events [3,4], belong to the YTH domain family of proteins [5][6][7]. Among them, the cytoplasmic YTHDF1, YTHDF2 and YTHDF3 proteins have similar sequence identity and binding affinities toward preferred RNA motifs [8,9] and recent studies support dosage dependent redundancy in their function to regulate m 6 A dependent mRNA stability and translation [10][11][12]. The mechanisms which govern this redundancy in a spatiotemporal manner, and hence define the exact role of individual YTHDF reader and eraser proteins in subcellular structures, is still largely unknown.…”

Section: Introductionmentioning

confidence: 99%

Modifying the m6A brain methylome by ALKBH5-mediated demethylation: a new contender for synaptic tagging

et al. 2021

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Synaptic plasticity processes, which underlie learning and memory formation, require RNA to be translated local to synapses. The synaptic tagging hypothesis has previously been proposed to explain how mRNAs are available at specific activated synapses. However how RNA is regulated, and which transcripts are silenced or processed as part of the tagging process is still unknown. Modification of RNA by N6-methyladenosine (m6A/m) influences the cellular fate of mRNA. Here, by advanced microscopy, we showed that m6A demethylation by the eraser protein ALKBH5 occurs at active synaptic ribosomes and at synapses during short term plasticity. We demonstrated that at activated glutamatergic post-synaptic sites, both the YTHDF1 and YTHDF3 reader and the ALKBH5 eraser proteins increase in co-localisation to m6A-modified RNAs; but only the readers showed high co-localisation to modified RNAs during late-stage plasticity. The YTHDF1 and YTHFDF3 readers also exhibited differential roles during synaptic maturation suggesting that temporal and subcellular abundance may determine specific function. m6A-sequencing of human parahippocampus brain tissue revealed distinct white and grey matter m6A methylome profiles indicating that cellular context is a fundamental factor dictating regulated pathways. However, in both neuronal and glial cell-rich tissue, m6A effector proteins are themselves modified and m6A epitranscriptional and posttranslational modification processes coregulate protein cascades. We hypothesise that the availability m6A effector protein machinery in conjunction with RNA modification, may be important in the formation of condensed synaptic nanodomain assemblies through liquid-liquid phase separation. Our findings support that m6A demethylation by ALKBH5 is an intrinsic component of the synaptic tagging hypothesis and a molecular switch which leads to alterations in the RNA methylome, synaptic dysfunction and potentially reversible disease states.

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Section: Introductionmentioning

confidence: 99%

Modifying the m6A brain methylome by ALKBH5-mediated demethylation: a new contender for synaptic tagging

et al. 2021

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“…In the past, the MD simulations have been successfully applied many times in studies of protein/RNA complexes, 16 including the YTH domain. 14,[17][18] By providing essentially infinite temporal and spatial resolution, the MD can extend upon the information from ensemble-averaged experimental data. It is particularly well-suited for studies of hydration and its structural role in biomolecular complexes.…”

Section: Introductionmentioning

confidence: 99%

Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration

et al. 2021

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The YTH domain of YTHDC1 belongs to a class of protein "readers", recognizing the N6methyladenosine (m 6 A) chemical modification in mRNA. Static ensemble-averaged structures revealed details of N6-methyl recognition via a conserved aromatic cage. Here, we performed molecular dynamics (MD) simulations along with nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) to examine how dynamics and solvent interactions contribute to the m 6 A recognition and negative selectivity towards unmethylated substrate. The structured water molecules surrounding the bound RNA and the methylated substrate's ability to exclude bulk water molecules contribute to the YTH domain's preference for m 6 A. Intrusions of bulk water deep into the binding pocket disrupt binding of unmethylated adenosine. The YTHDC1's preference for the 5′-Gm 6 A-3′ motif is partially facilitated by a network of water-mediated interactions between the 2-amino group of the guanosine and residues in the m 6 A binding pocket. The 5′-Im 6 A-3′ (where I is inosine) motif can be recognized too but disruption of the water network lowers affinity. The D479A mutant also disrupts the water network and destabilizes m 6 A binding. Our interdisciplinary study of YTHDC1 protein/RNA complex reveals an unusual physical mechanism by which solvent interactions contributes towards m 6 A recognition.

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“…(N) YTH-YTHDF2 in the free state (Upper; Li et al, 2014 ); YTHDF2, predicted from “AlphaFold” (Lower). (O) YTHDF3 YTH domain in complex with m 6 A RNA (Upper; Li et al, 2020 ); YTHDF3, predicted from “AlphaFold” (Lower). (P) YTHDC1 with m 6 A (Upper; Li Y. et al, 2021 ); YTHDC1, predicted from “AlphaFold” (Lower).…”

Section: Rna N6-methyladenosine Methylation Modification Proteinmentioning

confidence: 99%

“…YTH domain-containing RNA-binding protein includes YTH domain-containing family protein 1/2/3 (YTHDF1/2/3) ( Figures 2 , 3M–O ; Li et al, 2014 , 2020 ; Xu et al, 2015 ) and YTH domain-containing protein 1/2 (YTHDC1/2) ( Figures 2 , 3P,Q ; Ma et al, 2019 ; Li Y. et al, 2021 ). Their YTH domains are capable of combining with the m 6 A RRACH sites to mediate RNA-specific binding, while their proline/glutamine/asparagine-enriched (P/Q/N-rich) domains regulate the subcellular localization of target RNA ( Liao et al, 2018 ; Patil et al, 2018 ).…”

Section: Rna N6-methyladenosine Methylation Modification Proteinmentioning

confidence: 99%

RNA N6-Methyladenosine Modifications and Its Roles in Alzheimer’s Disease

Zhang

Guo

et al. 2022

Front. Cell. Neurosci.

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The importance of epitranscriptomics in regulating gene expression has received widespread attention. Recently, RNA methylation modifications, particularly N6-methyladenosine (m6A), have received marked attention. m6A, the most common and abundant type of eukaryotic methylation modification in RNAs, is a dynamic reversible modification that regulates nuclear splicing, stability, translation, and subcellular localization of RNAs. These processes are involved in the occurrence and development of many diseases. An increasing number of studies have focused on the role of m6A modification in Alzheimer’s disease, which is the most common neurodegenerative disease. This review focuses on the general features, mechanisms, and functions of m6A methylation modification and its role in Alzheimer’s disease.

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Structural and Dynamic Insights into Redundant Function of YTHDF Proteins

Cited by 46 publications

References 22 publications

Modifying the m6A brain methylome by ALKBH5-mediated demethylation: a new contender for synaptic tagging

Modifying the m6A brain methylome by ALKBH5-mediated demethylation: a new contender for synaptic tagging

Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration

RNA N6-Methyladenosine Modifications and Its Roles in Alzheimer’s Disease

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