Subcellular sequencing of single neurons reveals the dendritic transcriptome of GABAergic interneurons

Pérez, Julio; Dieck, Susanne tom; Álvarez-Castelao, Beatriz; Tushev, Georgi; Chan, I.C.W.; Schuman, Erin M.

doi:10.7554/elife.63092

Cited by 63 publications

(58 citation statements)

References 58 publications

(59 reference statements)

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“…The most abundant RNA species in all samples were derived from mitochondrialencoded genes such as Mt-Rnr1, Mt-Rnr2, and Mt-Nd1 (Figure 3I). Although mRNAs encoding ribosomal proteins and nuclear-encoded mitochondrial proteins have been observed in axons (Aschrafi et al, 2016;Briese et al, 2016;Gumy et al, 2011;Shigeoka et al, 2016Shigeoka et al, , 2019Taylor et al, 2009), these mRNAs are also present in dendrites (Fusco et al, 2021;Perez et al, 2021), the synaptic neuropil (Biever et al, 2020;Cajigas et al, 2012), and perisynaptic astrocyte processes (Mazaré et al, 2020). Given the ambiguous cellular and subcellular contribution to the mRNA content of our FASS samples, it is unclear whether any FASS-enriched mRNAs are derived from DA synaptosomes.…”

Section: Lack Of Evidence For Axonal Translation In Striatal Ribotag Ipsmentioning

confidence: 94%

Subcellular and regional localization of mRNA translation in midbrain dopamine neurons

Hobson

Kong

Angelo

et al. 2021

Preprint

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Local translation within excitatory and inhibitory neurons is involved in neuronal development and synaptic plasticity. Despite the extensive dendritic and axonal arborizations of central monoaminergic neurons, the subcellular localization of protein synthesis is not well-characterized in these populations. Here, we investigated mRNA localization and translation in midbrain dopaminergic (mDA) neurons, cells with enormous axonal and dendritic projections, both of which exhibit stimulation-evoked dopamine (DA) release. Using highly-sensitive ribosome-bound RNA-sequencing and imaging approaches in mDA axons, we found no evidence for axonal mRNA localization or translation. In contrast, mDA neuronal dendritic projections into the substantia nigra reticulata (SNr) contain ribosomes and mRNAs encoding the major components of DA synthesis, release, and reuptake machinery. Surprisingly, we also observed dendritic localization of mRNAs encoding synaptic vesicle-related proteins, including those involved in vesicular exocytic fusion. Our results are consistent with a role for local translation in the regulation of DA release from dendrites, but not from axons. Our translatome data further defined a molecular signature of the sparse mDA neurons resident in the SNr, including enrichment of Atp2a3/SERCA3, an ER calcium pump previously undescribed in mDA neurons.

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Section: Lack Of Evidence For Axonal Translation In Striatal Ribotag Ipsmentioning

confidence: 94%

Subcellular and regional localization of mRNA translation in midbrain dopamine neurons

Hobson

Kong

Angelo

et al. 2021

Preprint

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“…(A) Overlap of RP mRNAs detected in neuronal processes from three different studies: dendritic arbors ((Perez et al, 2021), in purple), purified synaptosomes ((Hafner et al, 2019), in green), developing axons ((Poulopoulos et al, 2019), in yellow) of rodent neurons. See also Table S1 for additional studies and data.…”

Section: Resultsmentioning

confidence: 99%

“…Advances in transcriptome-wide profiling methods have led to the elucidation of thousands of mRNAs localized to neuronal processes. In addition to many neuronal/synaptic transcripts, the RP mRNAs have been surprisingly detected in many preparations enriched for axons and dendrites (Figure 1A and Table S1; see also (Andreassi et al, 2010;Biever et al, 2020;Briese et al, 2016;Cajigas et al, 2012;Gioio et al, 2004;Gumy et al, 2011;Hafner et al, 2019;Middleton et al, 2019;Moccia et al, 2003b;Perez et al, 2021;Poulopoulos et al, 2019;Saal et al, 2014;Shigeoka et al, 2016;Taylor et al, 2009;Tushev et al, 2018;Zivraj et al, 2010). To evaluate whether the mRNAs for the ribosome are specifically enriched in dendrites and axons, we compared the dendritic enrichment of RP mRNAs to mRNAs that code for proteins in other ubiquitous macromolecular complexes.…”

Section: Rp Mrna Localization and Translation In Dendritesmentioning

confidence: 99%

“…As ribosome biogenesis is believed to require the step-wise incorporation of all ribosomal proteins, it remains unclear how heterogeneous ribosomes are formed. Additionally, many transcriptomics studies have detected RP mRNAs remote from the site of ribosome biogenesis, including in distal neuronal processes, potentially challenging our common understanding of assembled ribosome as a static structure (Andreassi et al, 2010; Biever et al, 2020; Briese et al, 2016; Cajigas et al, 2012; Gioio et al, 2004; Hafner et al, 2019; Mardakheh et al, 2015; Mazaré et al, 2020; Middleton et al, 2019; Misra et al, 2016; Moccia et al, 2003a; Moor et al, 2017; Perez et al, 2021; Poulopoulos et al, 2019; Saal et al, 2014; Shigeoka et al, 2016; Taylor et al, 2009; Tushev et al, 2018; Zivraj et al, 2010). Indeed, the cytosolic incorporation of some RPs in developing Xenopus retinal ganglion cell axons was recently observed (Shigeoka et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Neuronal ribosomes dynamically exchange ribosomal proteins in a context-dependent manner

Fusco

Desch

Doerrbaum

et al. 2021

Preprint

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Owing to their morphological complexity and dense network connections, neurons modify their proteomes locally, using mRNAs and ribosomes present in the neuropil (tissue enriched for dendrites and axons). Although ribosome biogenesis largely takes place in the nucleus and perinuclear region, neuronal ribosomal protein (RP) mRNAs have been frequently detected remotely, in dendrites and axons. Here, using imaging and ribosome profiling, we directly detected the RP mRNAs and their translation in the neuropil. Combining brief metabolic labeling with mass spectrometry, we found that a group of RPs quickly associated with translating ribosomes in the cytoplasm and that this incorporation is independent of canonical ribosome biogenesis. Moreover, the incorporation probability of some RPs was regulated by location (neurites vs. cell bodies) and changes in the cellular environment (in response to oxidative stress). Our results suggest new mechanisms for the local activation, repair and/or specialization of the translational machinery within neuronal processes, potentially allowing remote neuronal synapses a rapid solution to the relatively slow and energy-demanding requirement of nuclear ribosome biogenesis.

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“…Lastly, it remains unclear how RNA editing may play out across distinct cellular compartments and locations. Recent work has found discrete gene expression differences across synapses, dendrites, axons and neuronal bodies 43,44 , and RNA editing may represent a driver of activity-induced RNA localization 1,2,11 .…”

Section: Discussionmentioning

confidence: 99%

Cellular and genetic drivers of RNA editing variation in the human brain

Cuddleston

Fan

et al. 2021

Preprint

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Posttranscriptional adenosine-to-inosine modifications amplify the functionality of RNA molecules in the brain, yet the cellular and genetic regulation of RNA editing is poorly described. We quantified base-specific RNA editing across three major cell populations from the human prefrontal cortex: glutamatergic neurons, medial ganglionic eminence GABAergic neurons, and oligodendrocytes. We found more selective editing and RNA hyper-editing in neurons relative to oligodendrocytes. The pattern of RNA editing was highly cell type-specific, with 189,229 cell type-associated sites. The cellular specificity for thousands of sites was confirmed by single nucleus RNA-sequencing. Importantly, cell type-associated sites were enriched in GTEx RNA-sequencing data, edited ~twentyfold higher than all other sites, and variation in RNA editing was predominantly explained by neuronal proportions in bulk brain tissue. Finally, we discovered 661,791 cis-editing quantitative trait loci across thirteen brain regions, including hundreds with cell type-associated features. These data reveal an expansive repertoire of highly regulated RNA editing sites across human brain cell types and provide a resolved atlas linking cell types to editing variation and genetic regulatory effects.

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Subcellular sequencing of single neurons reveals the dendritic transcriptome of GABAergic interneurons

Cited by 63 publications

References 58 publications

Subcellular and regional localization of mRNA translation in midbrain dopamine neurons

Subcellular and regional localization of mRNA translation in midbrain dopamine neurons

Neuronal ribosomes dynamically exchange ribosomal proteins in a context-dependent manner

Cellular and genetic drivers of RNA editing variation in the human brain

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