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Structure-based discovery of a chemical probe targeting the Tudor domain of FMRP

ABSTRACT: Fragile X mental retardation protein (FMRP) is an RNA-binding protein whose loss of function is associated with neurodevelopmental disorders, including fragile X syndrome and autism, and whose aberrant overexpression has been linked to immune-related cancers. Here, we report XY6-1, a potent and selective antagonist that targets the tandem Tudor domain (TTD) of FMRP, a methylated-histone reader. Structural and mutagenesis analyses reveal that subtle differences in the shape of the aromatic cage contribute to the selective binding of XY6-1 to FMRP. Multiple orthogonal target engagement assays further demonstrate that XY6-1 specifically binds FMRP in cells and disrupts the interaction between FMRP-TTD and histone H3K79me3, thereby attenuating the DNA damage response (DDR), as evidenced by reduced γH2A.X levels. Collectively, this first-in-class chemical probe XY6-1, along with its fluorescent (XY6-1–FITC) and biotinylated (XY6-1–Biotin) derivatives and the negative control compound XY6-2, constitutes a valuable toolkit for elucidating the underexplored biological functions of FMRP.

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ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Kidney

SUBMITTER: boyi Li

LAB HEAD: Yunyuan Huang

PROVIDER: PXD072708 | Pride | 2026-07-30

REPOSITORIES: Pride

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Project description:Local translation at the synapse plays key roles in neuron development and activity-dependent synaptic plasticity. mRNAs are translocated from the neuronal soma to the distant synapses as compacted ribonucleoparticles referred to as RNA granules. These contain many RNA-binding proteins, including the Fragile X Mental Retardation Protein (FMRP), the absence of which results in Fragile X Syndrome, the most common inherited form of intellectual disability and the leading genetic cause of autism. Using FMRP as a tracer, we purified a specific population of RNA granules from mouse brain homogenates. Protein composition analyses revealed a strong relationship between polyribosomes and RNA granules. However, the latter have distinct architectural and structural properties, since they are detected as close compact structures as observed by electron microscopy, and converging evidence point to the possibility that these structures emerge from stalled polyribosomes. Time-lapse video microscopy indicated that single granules merge to form cargoes that are transported from the soma to distal locations. Transcriptomic analyses showed that a subset of mRNAs involved in cytoskeleton remodelling and neural development is selectively enriched in RNA granules. One third of the putative mRNA targets described for FMRP appear to be transported in granules and FMRP is more abundant in granules than in polyribosomes. This observation supports a primary role for FMRP in granules biology. Our findings open new avenues for the study of RNA granule dysfunctions in animal models of nervous system disorders, such as Fragile X syndrome. Fragile X syndrome is the most common form of inherited mental retardation affecting approximately 1 female out of 7000 and 1 male out of 4000 worldwide. The syndrome is due to the silencing of a single gene, the Fragile Mental Retardation 1 (FMR1), that codes for the Fragile X mental retardation protein (FMRP). This protein is highly expressed in brain and controls local protein synthesis essential for neuronal development and maturation as well as the formation of neural circuits. Several studies suggest a role for FMRP in the regulation of mRNA transport along axons and dendrites to distant synaptic locations in structures called RNA granules. Here we report the isolation of a particular subpopulation of these structures and the analysis of their architecture and composition in terms of RNA and protein. Also, using time-lapse video microscopy, we monitored granule transport and fusion throughout neuronal processes. These findings open new avenues for the study of RNA transport dysfunctions in animal models of nervous system disorders. The control or reference structure or subcellular fraction are the neuronal polyribosomes while the experimental or test structure or subcellular fraction are the neuronal granules. Three independant replicates were done for each structure. Microarray hybridization was done using a two-color design in full dye-swap.

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Structure-based discovery of a chemical probe targeting the Tudor domain of FMRP

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