Development of any tissue or organ is associated with dynamic changes of gene expression patterns. In general, studies investigating the transcriptome at single cell level observe a global reduction in numbers of genes expressed per cell while development proceeds from the embryo towards adulthood. We hypothesize that the decrease in genes per cell counts may not solely correspond to a fraction of genes simply being shut off once development is completed, but rather due to well-coordinated modulation of gene expression from constitutively ON, at varying levels, towards a binary ON/OFF mode, also known as bursting. We specifically addressed this hypothesis in the maturing mouse organ of Corti.
Gene expression in mammalian cells is modulated by various factors including promoter activity, transcription rates, and transcript lifetime. Thus far, these parameters were assessable through low throughput measures such as single molecule in situ hybridization, which allows single transcript counting. Using high-multiplexed single cell qRT-PCR, we analyzed in parallel the expression of 96 candidate genes from flow-sorted pillar and Deiters’ cells at three time points during late organ of Corti development and maturation. Concordant with the general view, we measured a decrease in the number of detectable genes expressed as supporting cells differentiated. Comparing mRNA-expression levels from select candidate genes with protein and fluorescent reporter expression levels we found evidence for the occurrence of distinctive modes of gene expression in the adult organ of Corti. Specifically, we found that expression of various genes changed from a continuous expression to a previously described “bursting mode” that is characterized by undulating transcript levels over time. We applied a novel data analysis strategy to predict bursting rate, bursting intensity and length of each bursting event for the 96 genes analyzed.
The results of this study contribute to the rapidly growing field of single cell analysis and highlight that the maturation state of a cell needs to be considered in comparative studies using single cell transcriptomic data. Moreover, our results show that substantial changes in gene expression regulation exist between neonatal and mature organ of Corti supporting cell types. Our data analysis strategy allows the quantitative assessment of transcription kinetics with single cell and single gene resolution with a throughput of up-to 300 genes per cell. A fundamental understanding of the changes that happen when organ of Corti supporting cells mature from neonatal stages is going to be useful for the development of regenerative therapies.