Temporal Regulation of Gene Expression in Post-Mitotic Cells is Revealed from a Synchronized Population of C. elegans Larvae

Abstract

Unsupervised Uniform Manifold Approximation and Projection (UMAP) plots of single cell sequencing data from synchronized Caenorhabditis elegans larvae yield tissue-specific data clusters, some of which are plotted as elongated archipelagos. These archipelagos likely represent a single cell type. I show that the pharyngeal archipelagos express a myriad of asynchronous temporally regulated genes, which likely accounts for their elongated topology. With one archipelago, I show that there is a high correlation between a) the base pair distance between the binding sites of an archipelago-specific transcription factor (HLH-6) and the transcriptional start site of the targeted genes and b) the timing of peak gene expression of those genes that are expressed in an archipelago-specific manner. Despite the correlation being made with only four genes, it prompts the hypothesis that the physical distance between a transcription factor and the relevant transcription start site may be an important factor in determining the temporal onset of transcription and transcript abundance.

Figure 1. Additional Temporal Regulation of Gene Expression in C. elegans Larvae is Revealed through the Intersection of Multiple mRNA Sequencing Datasets

A. A schematic illustrating the translation of C. elegans developmental time at 25 ^o C (top timeline) to ‘degrees’ as articulated by Hendriks et al. , (2014) (bottom timeline). On the top timeline, red vertical lines indicate the approximate time points at which Hendriks et al. sequenced mRNAs from whole animals. Longer vertical lines denote the transition from one stage to the next. On the bottom timeline, the 360 degrees is the timeline of a repeating pattern of larval gene expression that has a periodicity of ~eight hours. For example, genes that peak in expression at one time point (blue diagonal lines) were observed to peak again ~eight hours later (pink diagonal lines). E, embryogenesis (~14 hours); A, adulthood. See Hendriks et al. , (2014) for more details. B. UMAP plots of six major post-mitotic tissue types. Red arrows highlight obvious archipelagos. C. UMAP plots from the pharynx, excluding the gland cells cluster (topmost cluster in the top panel in ‘B’ ) and two smaller clusters (on the bottom right of the top panel in ‘B’ ). Each of the 14 exemplar genes shown are enriched in pharynx gene expression (see (Kamal et al. , 2022)) and peak in expression at different times (indicated by the degree in the upper right-hand corner of each panel) that illustrate how expression progresses along each archipelago over time. The black arrows in the upper left panel indicate the flow of time. D. UMAP plots of genes expressed within the pharynx gland cells archipelago. Gene names in green are characterized HLH-6 targets and described in more detail in panel ‘ D ’. The description is the same as for ‘C’ . The scale of expression intensity is shown below ‘ C’ and ‘D’ . All panels in B-D are unmanipulated screen shots from the VisCello server (see text for details). E. Four transcriptional targets of the HLH-6 and PHA-4 transcription (trnsc) factors and their associated properties. The source of the data in each column is as follows: a- (Hendriks et al. , 2014); b- (Cao et al. , 2017); c- (Smit et al. , 2008); d- (Smit et al. , 2008) and WormBase (WS284); e-(Smit et al. , 2008); f- (Smit ^{et al.} , 2008) and WormBase; g-i- WormBase. The bottom two rows show the correlation (r ² ) between the indicated data columns as calculated in excel.