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

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 comb...

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Autores principales: Thompson, Morgan, Bixby, Ryan, Dalton, Robert, Vandenburg, Alexa, Calarco, John A, Norris, Adam D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6641836/
https://www.ncbi.nlm.nih.gov/pubmed/31322498
http://dx.doi.org/10.7554/eLife.46726
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author Thompson, Morgan
Bixby, Ryan
Dalton, Robert
Vandenburg, Alexa
Calarco, John A
Norris, Adam D
author_facet Thompson, Morgan
Bixby, Ryan
Dalton, Robert
Vandenburg, Alexa
Calarco, John A
Norris, Adam D
author_sort Thompson, Morgan
collection PubMed
description 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.
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spelling pubmed-66418362019-07-22 Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors Thompson, Morgan Bixby, Ryan Dalton, Robert Vandenburg, Alexa Calarco, John A Norris, Adam D eLife Developmental Biology 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. eLife Sciences Publications, Ltd 2019-07-19 /pmc/articles/PMC6641836/ /pubmed/31322498 http://dx.doi.org/10.7554/eLife.46726 Text en © 2019, Thompson et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Developmental Biology
Thompson, Morgan
Bixby, Ryan
Dalton, Robert
Vandenburg, Alexa
Calarco, John A
Norris, Adam D
Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors
title Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors
title_full Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors
title_fullStr Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors
title_full_unstemmed Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors
title_short Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors
title_sort splicing in a single neuron is coordinately controlled by rna binding proteins and transcription factors
topic Developmental Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6641836/
https://www.ncbi.nlm.nih.gov/pubmed/31322498
http://dx.doi.org/10.7554/eLife.46726
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