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Modular, cascade-like transcriptional program of regeneration in Stentor

The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis in a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological st...

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Autores principales: Sood, Pranidhi, Lin, Athena, Yan, Connie, McGillivary, Rebecca, Diaz, Ulises, Makushok, Tatyana, Nadkarni, Ambika V, Tang, Sindy KY, Marshall, Wallace F
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9371601/
https://www.ncbi.nlm.nih.gov/pubmed/35924891
http://dx.doi.org/10.7554/eLife.80778
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author Sood, Pranidhi
Lin, Athena
Yan, Connie
McGillivary, Rebecca
Diaz, Ulises
Makushok, Tatyana
Nadkarni, Ambika V
Tang, Sindy KY
Marshall, Wallace F
author_facet Sood, Pranidhi
Lin, Athena
Yan, Connie
McGillivary, Rebecca
Diaz, Ulises
Makushok, Tatyana
Nadkarni, Ambika V
Tang, Sindy KY
Marshall, Wallace F
author_sort Sood, Pranidhi
collection PubMed
description The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis in a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half regenerates an intact cell. We used RNA sequencing (RNAseq) to assay the dynamic changes in Stentor’s transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression including kinases, RNA -binding proteins, centriole biogenesis factors, and orthologs of human ciliopathy genes. By comparing transcriptional profiles of different regeneration events, we identified distinct modules of gene expression corresponding to oral apparatus regeneration, posterior holdfast regeneration, and recovery after wounding. By measuring gene expression after blocking translation, we show that the sequential waves of gene expression involve a cascade mechanism in which later waves of expression are triggered by translation products of early-expressed genes. Among the early-expressed genes, we identified an E2F transcription factor and the RNA-binding protein Pumilio as potential regulators of regeneration based on the expression pattern of their predicted target genes. RNAi-mediated knockdown experiments indicate that Pumilio is required for regenerating oral structures of the correct size. E2F is involved in the completion of regeneration but is dispensable for earlier steps. This work allows us to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures.
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spelling pubmed-93716012022-08-12 Modular, cascade-like transcriptional program of regeneration in Stentor Sood, Pranidhi Lin, Athena Yan, Connie McGillivary, Rebecca Diaz, Ulises Makushok, Tatyana Nadkarni, Ambika V Tang, Sindy KY Marshall, Wallace F eLife Cell Biology The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis in a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half regenerates an intact cell. We used RNA sequencing (RNAseq) to assay the dynamic changes in Stentor’s transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression including kinases, RNA -binding proteins, centriole biogenesis factors, and orthologs of human ciliopathy genes. By comparing transcriptional profiles of different regeneration events, we identified distinct modules of gene expression corresponding to oral apparatus regeneration, posterior holdfast regeneration, and recovery after wounding. By measuring gene expression after blocking translation, we show that the sequential waves of gene expression involve a cascade mechanism in which later waves of expression are triggered by translation products of early-expressed genes. Among the early-expressed genes, we identified an E2F transcription factor and the RNA-binding protein Pumilio as potential regulators of regeneration based on the expression pattern of their predicted target genes. RNAi-mediated knockdown experiments indicate that Pumilio is required for regenerating oral structures of the correct size. E2F is involved in the completion of regeneration but is dispensable for earlier steps. This work allows us to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures. eLife Sciences Publications, Ltd 2022-08-04 /pmc/articles/PMC9371601/ /pubmed/35924891 http://dx.doi.org/10.7554/eLife.80778 Text en © 2022, Sood et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Cell Biology
Sood, Pranidhi
Lin, Athena
Yan, Connie
McGillivary, Rebecca
Diaz, Ulises
Makushok, Tatyana
Nadkarni, Ambika V
Tang, Sindy KY
Marshall, Wallace F
Modular, cascade-like transcriptional program of regeneration in Stentor
title Modular, cascade-like transcriptional program of regeneration in Stentor
title_full Modular, cascade-like transcriptional program of regeneration in Stentor
title_fullStr Modular, cascade-like transcriptional program of regeneration in Stentor
title_full_unstemmed Modular, cascade-like transcriptional program of regeneration in Stentor
title_short Modular, cascade-like transcriptional program of regeneration in Stentor
title_sort modular, cascade-like transcriptional program of regeneration in stentor
topic Cell Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9371601/
https://www.ncbi.nlm.nih.gov/pubmed/35924891
http://dx.doi.org/10.7554/eLife.80778
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