Biology subjects

Nassim-Assir, B.

Publications and source records attributed to Nassim-Assir, B..

4 recordsLinked to original sources

bioRxiv2026

Local consequences of FMRP loss: cell type-specific mRNA and protein profiles of Fmr1-KO synapses

Brain function relies on billions of neurons interconnected by synapses with unique molecular composition specialized for cell type, brain region, and their role in circuit dynamics. Pathological synaptic dysfunctions - so-called synaptopathies - underlie many neurodevelopmental disorders (NDDs), including Fragile X Syndrome (FXS). While synaptic deficits are well documented in FXS, molecular studies have largely relied on bulk brain homogenates or synaptic fractions, which typically represent ''average'' molecular identities, potentially masking synapse type-specific alterations. To provide synapse type resolution, we use fluorescence-activated synaptosome sorting coupled to RNA-sequencing and mass spectrometry to isolate and profile cortical excitatory and inhibitory synapses of hemizygous and heterozygous Fmr1-deficient mice. We found that full or partial FMRP loss leads to cell type- and compartment-specific molecular remodeling (syndive.org), affecting mRNAs and proteins related to synaptic organization and metabolic pathways. Strikingly, only a minority of dysregulated mRNAs/proteins were shared across excitatory and inhibitory synapses - the substantial majority were uniquely regulated at one subtype. Indeed, FMRP loss often resulted in opposing protein changes in each synapse type. Changes in mRNA or protein abundance were also not well coordinated, consistent with substantial post-transcriptional regulation, including changes to the translational and ubiquitin-dependent protein degradation machinery. For example, our data suggest a disturbed, cell type-distinct coordination of protein degradation via CAND1 as one key consequence of FMRP loss. Furthermore, we observed differences in male (Fmr1-/y) and female (Fmr1-/+) transcriptomes, where, for example, FMRP dosage was coupled to reciprocal regulation of the NDD-risk gene Trpc4 in both synapse types.

neuroscience↗

bioRxiv2025

Localized mRNAs and protein synthesis in cortical layer 1

Cortical layer 1 plays an essential role for brain function, integrating many streams of information and undergoing synaptic plasticity during learning. Yet, we understand little of the underlying molecular processes, and whether they are specialized to achieve layer-specific functions. Here, we show that layer 1 and its synapses are metabolically active. Using laser capture RNA-sequencing and fluorescence in situ hybridization, we report an abundance of synaptic transcripts localized to layer 1. We purified layer 1 excitatory and inhibitory synapses and characterized their enriched transcriptomes, identifying candidate proteins that can be locally synthesized to maintain and regulate synaptic transmission in layer 1. Furthermore, we find significant differences between the transcriptome of synapses in layer 1 and in deeper, somatic layers, suggesting that local translation might confer specialized function. Finally, by comparing our tissue data with the transcriptome from the hippocampal CA1 strata, we discover a strong similarity between cortical layer 1 and stratum lacunosum moleculare, suggesting that these distal layers share a common molecular environment. Together, our results establish that local protein synthesis is an important mechanism for layer 1, and provide the first comprehensive characterization of the transcripts localized to layer 1 and its synapses.

neuroscience↗

bioRxiv2022

An Abundance of Free Proteasomal Regulatory (19S) Particles Regulate Neuronal Synapses Independent of the Proteasome

The major protein-degradation machine, the proteasome, functions at brain synapses and regulates long-term information storage. Here we found that the two essential subcomplexes of the proteasome, the regulatory (19S) and catalytic (20S) particles that recognize and degrade substrates, are differentially distributed within individual rat cortical neurons. Using superresolution microscopy, we discovered a surprising abundance of free particles (19S) near synapses. The free neuronal 19S particles bind and deubiquitylate Lys63-ubiquitin, a non-proteasome targeting ub-linkage. Pull-down assays revealed a significant over-representation of synaptic molecules as Lys63 interactors. Inhibition of 19S deubiquitylase activity significantly altered excitatory synaptic transmission and reduced the synaptic availability of AMPA receptors at multiple trafficking points in a proteasome-independent manner. Together, these results reveal a moonlighting function of the regulatory proteasomal subcomplex near synapses. One-Sentence SummaryThe 19S subcomplex of the major protein-degradation machine, the proteasome, functions without its 20S partner to populate and regulate synapses.

neuroscience↗

bioRxiv2020

The mRNA translation landscape in the synaptic neuropil.

To form and modify synaptic connections and store information, neurons continuously remodel their proteomes. The impressive length of dendrites and axons imposes unique logistical challenges to maintain synaptic proteins at locations remote from the transcription source (the nucleus). The discovery of thousands of mRNAs near synapses suggested that neurons overcome distance and gain autonomy by producing proteins locally1. It is not known, however if, how and when localized mRNAs are translated into protein. To investigate the translational landscape in neuronal subregions, we performed simultaneous RNA-seq and Ribo-seq from microdissected rodent brain slices to identify and quantify the transcriptome and translatome in cell bodies as well as dendrites and axons (neuropil). More than 4800 transcripts were translated in synaptic regions. Thousands of transcripts were differentially translated between somatic and synaptic regions, with scaffold and signaling molecules mostly arising from local sources. Furthermore, specific mRNA features were identified that regulate the efficiency of mRNA translation. The findings overturn the view that local translation is a minor source of synaptic protein2 and indicate that on-site translational control is an important mechanism to control synaptic strength.

neuroscience↗