Spatial organization of the transcriptome in individual neurons

Abstract

Neurons are highly polarized cells with complex neurite morphology. Spatial organization and local translation of RNAs in dendrites and axons play an important role in many neuronal functions. Here we performed super-resolution spatial profiling of RNAs inside individual neurons at the genome scale using multiplexed error-robust fluorescence in situ hybridization (MERFISH), and mapped the spatial organization of up to ∼4,200 RNA species (genes) across multiple length scales, ranging from sub-micrometer to millimeters. Our data generated a quantitative intra-neuronal atlas of RNAs with distinct transcriptome compositions in somata, dendrites, and axons, and revealed diverse sub-dendritic distribution patterns of RNAs. Moreover, our spatial analysis identified distinct groups of genes exhibiting specific spatial clustering of transcripts at the sub-micrometer scale that were dependent on protein synthesis and differentially dependent on synaptic activity. Overall, these data provide a rich resource for characterizing the subcellular organization of the transcriptome in neurons with high spatial resolution.

Large protein complex interfaces have evolved to promote cotranslational assembly

“…A wide array of ribosome-associated chaperones are vital for nascent chain homeostasis 4,5,[81][82][83] and the degree to which they choreograph assembly steps is yet to be elucidated. Furthermore, because interface size alone does not fully explain the range of affinities observed in a growing number of complexes [46][47][48][49] , it will be exciting to see whether binding affinity plays a role in colocalising mRNA molecules in eukaryotic cells 13,14,19,21,84,85 .…”

“…This process is highly effective because it takes advantage of the fact that homomeric subunits are identical; hence nascent chains are essentially colocalised by the nature of their synthesis. On the other hand, heteromers, products of distinct genes that stably interact, can only employ the trans mode of assembly in eukaryotes, providing mechanisms that colocalise their transcripts exist [19][20][21] . Although .…”

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

“…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 .…”

MERFISH Enables Mapping of Cellular Diversity with Spatial Context at Subcellular Resolution

“…Furthermore, MERFISH's robust experimental design requires no intermediate steps that could cause bias in transcript detection, such as enzymatic amplification. This gives MERFISH an unparalleled target detection efficiency of 95 percent in cell culture [9] and 70 percent in tissue [10].…”

“…More recently, in a 2020 preprint, Wang et al used MER-FISH to conduct quantitative, high-resolution spatial profiling of ∼4,200 RNA species within mouse hippocampal neurons to MERFISH Method form a cell atlas of the distinct transcriptomic regions inside individual neurons [10]. The authors detected approximately 11,000 RNA molecules per cell and found that cell bodies, axons, dendrites, and even smaller dendritic regions, had their own distinct transcriptional profiles.…”