Ordered patterning of the sensory system is susceptible to stochastic features of gene expression

Sensory neuron numbers and positions are precisely organized to accurately map environmental signals in the brain. This precision emerges from biochemical processes within and between cells that are inherently stochastic. We investigated impact of stochastic gene expression on pattern formation, focusing on senseless (sens), a key determinant of sensory fate in Drosophila. Perturbing microRNA regulation or genomic location of sens produced distinct noise signatures. Noise was greatly enhanced when both sens alleles were present in homologous loci such that each allele was regulated in trans by the other allele. This led to disordered patterning. In contrast, loss of microRNA repression of sens increased protein abundance but not sensory pattern disorder. This suggests that gene expression stochasticity is a critical feature that must be constrained during development to allow rapid yet accurate cell fate resolution.

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• You should state whether an appropriate sample size was computed when the study was being designed • You should state the statistical method of sample size computation and any required assumptions • If no explicit power analysis was used, you should describe how you decided what sample (replicate) size (number) to use Please outline where this information can be found within the submission (e.g., sections or figure legends), or explain why this information doesn't apply to your submission: Sample size for all experiments is listed under 'Quantification and Statistical Analysis' in methods. For Fano factor and average protein, point-estimates and 95% confidence intervals were estimated by bootstrap technical replication. For all such pointestimates, adequate sample size was confirmed by normal distribution of bootstrapped replicates. For adult wing analysis, chemosensory bristle density distributions were checked for normality. For ectopic mechanosensory bristle analysis, sample sizes were computed for power 0.8 after a pilot study. To compare sens alleles between 57F5 vs 22A3, appropriate sample size was determined to be n ≥ 40. To statistically distinguish an effect of miR-9a for sens alleles at 22A3 with power 0.8, required sample size was estimated at n >34000 from pilot data. Since, this indicated a negligible effect, data were only gathered for n ≥ 60 for all genotypes.

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• Indicate how samples were allocated into experimental groups (in the case of clinical studies, please specify allocation to treatment method); if randomization was used, please also state if restricted randomization was applied • Indicate if masking was used during group allocation, data collection and/or data analysis Please outline where this information can be found within the submission (e.g., sections or figure legends), or explain why this information doesn't apply to your submission: Source data is provided in the data package uploaded on github. Calculation of all point-estimates and 95% confidence intervals is described in the methods section and/or relevant figure legends. Sample sizes are listed under 'Quantification and Statistical Analysis'. P-values and R 2 values are provided in figures and figure supplements. Odds ratio analysis reported in Figure 7 -source data 1. Where possible, data are plotted to show 95% confidence intervals of fit or point-estimate.
Groups were allocated according to genotype. Data were gathered in the same experimental run for multiple genotypes. For image data, all samples were masked during data collection. Segmentation, image processing and expression analysis were carried out for all groups identically with a computational pipeline. Sample labels were masked in all steps. For adult wing analysis, data were masked during imaging and bristle counting. For mRNA or protein decay analysis, data were grouped by time point.