Abstract
Protein subcellular localization is fundamental to the establishment of the body axis, cell migration, synaptic plasticity, and a vast range of other biological processes. Protein localization occurs through three mechanisms: protein transport, mRNA localization, and local translation. However, the relative contribution of each process to neuronal polarity remains unknown. Using neurons differentiated from mouse embryonic stem cells, we analyze protein and RNA expression and translation rates in isolated cell bodies and neurites genome-wide. We quantify 7323 proteins and the entire transcriptome, and identify hundreds of neurite-localized proteins and locally translated mRNAs. Our results demonstrate that mRNA localization is the primary mechanism for protein localization in neurites that may account for half of the neurite-localized proteome. Moreover, we identify multiple neurite-targeted non-coding RNAs and RNA-binding proteins with potential regulatory roles. These results provide further insight into the mechanisms underlying the establishment of neuronal polarity.
Highlights
Protein subcellular localization is fundamental to the establishment of the body axis, cell migration, synaptic plasticity, and a vast range of other biological processes
We find that almost half of the neurite-enriched proteome is encoded by neurite-localized mRNAs, revealing that mRNA localization is a key mechanism of protein localization to neurites
We found transcripts known to be preferentially localized, such as syntaxin-3 (Stx3)[22], glutamate receptor-1 (Gria1)[5], calcium channel Ryr[25], inositol 1,4,5-trisphosphate receptor type 1 (Itpr1)[5], neuregulins (Nrg[123] and Nrg224), voltage-dependent L-type calcium channel subunit α-1D (Cacna1d)[5], ephrin type-A receptor 2 (Epha2)[25], unconventional myosin-Ic (Myo1c)[26], low-density lipoprotein receptor adapter protein 1 (Ldlrap1)[27], vang-like protein (Vangl)[28], and transcripts encoding mitochondrial proteins[6, 10], consistent with previous works
Summary
Them and (3) as a part of trafficking messenger ribonucleoprotein complexes or vesicles. Previous studies have focused on the identification of the RNAs, largely leaving out analysis of the local proteome, or detecting the mere presence of mRNAs or proteins in neurites rather than relative enrichment. We quantify 7,323 proteins and measure the levels and translation rates of the entire transcriptome. Using this approach, we identify hundreds of localized and locally translated transcripts, as well as localized proteins, and independently validate a number of candidates with important neuronal fuctions. As RBPs are key factors in RNA metabolism, we identify 29 neurite-targeted RBPs, including both known components of the mRNA localization machinery and potential novel factors in mRNA transport and local translation. We identify dozens of neurite-targeted non-coding RNAs, including 12 long non-coding RNAs (lncRNAs) and 41 circular RNAs (circRNAs), with potential roles in neuronal polarity
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