Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants

Abstract

Determining the molecular properties of neurons is essential to understand their development, function and evolution. Using Targeted DamID (TaDa), we characterize RNA polymerase II occupancy and chromatin accessibility in selected Ionotropic receptor (Ir)-expressing olfactory sensory neurons in Drosophila. Although individual populations represent a minute fraction of cells, TaDa is sufficiently sensitive and specific to identify the expected receptor genes. Unique Ir expression is not consistently associated with differences in chromatin accessibility, but rather to distinct transcription factor profiles. Genes that are heterogeneously-expressed across populations are enriched for neurodevelopmental factors, and we identify functions for the POU-domain protein Pdm3 as a genetic switch of Ir neuron fate, and the atypical cadherin Flamingo in segregation of neurons into discrete glomeruli. Together this study reveals the effectiveness of TaDa in profiling rare neural populations, identifies new roles for a transcription factor and a neuronal guidance molecule, and provides valuable datasets for future exploration.

Olfactory Receptor Gene Regulation in Insects: Multiple Mechanisms for Singular Expression

“…Moreover, the presence of a motif in a CRE for a given gene does not necessarily mean that the corresponding TF is required (and vice versa) ( Jafari et al, 2012 ; Figure 2A ). While some TFs have lineage-specific expression and function ( Li et al, 2020 ; Arguello et al, 2021 ), many have broad expression in OSNs despite very selective requirements in receptor regulation ( Jafari et al, 2012 ; Li et al, 2020 ). The lack of correlation between the presence of a TF binding motif in a CRE and TF requirement for a given receptor might reflect differences in in vitro and in vivo binding specificities for TFs and/or an indirect requirement for trans -acting factors in controlling receptor expression.…”

“…The lack of correlation between the presence of a TF binding motif in a CRE and TF requirement for a given receptor might reflect differences in in vitro and in vivo binding specificities for TFs and/or an indirect requirement for trans -acting factors in controlling receptor expression. Indeed, temporal manipulation of TF function indicates that several of these proteins have multiple roles in OSN development, for example, during SOP lineage specification ( Bai and Carlson, 2010 ; Jafari et al, 2012 ; Chai et al, 2019 ; Arguello et al, 2021 ; Mika et al, 2021 ). Moreover, many TFs are expressed and required in late pupal/adult stages implying roles in both initiation and maintenance of correct receptor expression ( Bai and Carlson, 2010 ; Jafari et al, 2012 ; Arguello et al, 2021 ; Mika et al, 2021 ).…”

“…Indeed, temporal manipulation of TF function indicates that several of these proteins have multiple roles in OSN development, for example, during SOP lineage specification ( Bai and Carlson, 2010 ; Jafari et al, 2012 ; Chai et al, 2019 ; Arguello et al, 2021 ; Mika et al, 2021 ). Moreover, many TFs are expressed and required in late pupal/adult stages implying roles in both initiation and maintenance of correct receptor expression ( Bai and Carlson, 2010 ; Jafari et al, 2012 ; Arguello et al, 2021 ; Mika et al, 2021 ). The biochemical properties of TF/CRE interactions that promote stable receptor expression in a given OSN type remain, however, largely elusive.…”

“…Despite these insights, a global time course of chromatin state at active and silenced endogenous receptor loci in specific neuron populations is lacking, constrained by the ability to obtain enough cells of a given class for ChIP-sequencing-based methods. A low-resolution assessment of chromatin structure in several individual mature Ir -expressing OSN populations has been made using Chromatin Accessibility Targeted DamID (CATaDa) ( Arguello et al, 2021 ), which exploits cell-type specific expression of the E. coli Dam methylase to avoid a need for cell sorting ( Aughey et al, 2018 ). This analysis revealed that access to the DNA at different receptor genes is globally similar between neuron populations, suggesting that the specificity of transcriptional activation in a given neuron is not reliant upon uniquely accessible enhancers (at least in the analyzed Ir populations) ( Arguello et al, 2021 ).…”

“…A low-resolution assessment of chromatin structure in several individual mature Ir -expressing OSN populations has been made using Chromatin Accessibility Targeted DamID (CATaDa) ( Arguello et al, 2021 ), which exploits cell-type specific expression of the E. coli Dam methylase to avoid a need for cell sorting ( Aughey et al, 2018 ). This analysis revealed that access to the DNA at different receptor genes is globally similar between neuron populations, suggesting that the specificity of transcriptional activation in a given neuron is not reliant upon uniquely accessible enhancers (at least in the analyzed Ir populations) ( Arguello et al, 2021 ). Although direct comparison is currently hard, this situation might contrast with that in mammals, where all but the chosen receptor gene are maintained in a heterochromatic, silenced state ( Dalton and Lomvardas, 2015 ; Monahan and Lomvardas, 2015 ).…”