Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors

Elife. 2019 Jul 19;8:e46726. doi: 10.7554/eLife.46726.


Single-cell transcriptomes are established by transcription factors (TFs), which determine a cell's gene-expression complement. Post-transcriptional regulation of single-cell transcriptomes, and the RNA binding proteins (RBPs) responsible, are more technically challenging to determine, and combinatorial TF-RBP coordination of single-cell transcriptomes remains unexplored. We used fluorescent reporters to visualize alternative splicing in single Caenorhabditis elegans neurons, identifying complex splicing patterns in the neuronal kinase sad-1. Most neurons express both isoforms, but the ALM mechanosensory neuron expresses only the exon-included isoform, while its developmental sister cell the BDU neuron expresses only the exon-skipped isoform. A cascade of three cell-specific TFs and two RBPs are combinatorially required for sad-1 exon inclusion. Mechanistically, TFs combinatorially ensure expression of RBPs, which interact with sad-1 pre-mRNA. Thus a combinatorial TF-RBP code controls single-neuron sad-1 splicing. Additionally, we find 'phenotypic convergence,' previously observed for TFs, also applies to RBPs: different RBP combinations generate similar splicing outcomes in different neurons.

Keywords: C. elegans; RNA; developmental biology; genetics; genomics; single neuron; splicing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Caenorhabditis elegans
  • Gene Expression Regulation*
  • Genes, Reporter
  • Intracellular Signaling Peptides and Proteins / biosynthesis*
  • Microscopy, Fluorescence
  • Neurons / enzymology*
  • Protein Serine-Threonine Kinases / biosynthesis*
  • RNA Splicing*
  • RNA-Binding Proteins / metabolism*
  • Transcription Factors / metabolism*


  • Intracellular Signaling Peptides and Proteins
  • RNA-Binding Proteins
  • Transcription Factors
  • sad-1 protein, C elegans
  • Protein Serine-Threonine Kinases