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Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells

Planarian flatworms have an indefinite capacity to regenerate missing or damaged body parts owing to a population of pluripotent adult stems cells called neoblasts (NBs). Currently, little is known about the importance of the epigenetic status of NBs and how histone modifications regulate homeostasi...

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Autores principales: Dattani, Anish, Kao, Damian, Mihaylova, Yuliana, Abnave, Prasad, Hughes, Samantha, Lai, Alvina, Sahu, Sounak, Aboobaker, A. Aziz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169894/
https://www.ncbi.nlm.nih.gov/pubmed/30143598
http://dx.doi.org/10.1101/gr.239848.118
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author Dattani, Anish
Kao, Damian
Mihaylova, Yuliana
Abnave, Prasad
Hughes, Samantha
Lai, Alvina
Sahu, Sounak
Aboobaker, A. Aziz
author_facet Dattani, Anish
Kao, Damian
Mihaylova, Yuliana
Abnave, Prasad
Hughes, Samantha
Lai, Alvina
Sahu, Sounak
Aboobaker, A. Aziz
author_sort Dattani, Anish
collection PubMed
description Planarian flatworms have an indefinite capacity to regenerate missing or damaged body parts owing to a population of pluripotent adult stems cells called neoblasts (NBs). Currently, little is known about the importance of the epigenetic status of NBs and how histone modifications regulate homeostasis and cellular differentiation. We have developed an improved and optimized ChIP-seq protocol for NBs in Schmidtea mediterranea and have generated genome-wide profiles for the active marks H3K4me3 and H3K36me3, and suppressive marks H3K4me1 and H3K27me3. The genome-wide profiles of these marks were found to correlate well with NB gene expression profiles. We found that genes with little transcriptional activity in the NB compartment but which switch on in post-mitotic progeny during differentiation are bivalent, being marked by both H3K4me3 and H3K27me3 at promoter regions. In further support of this hypothesis, bivalent genes also have a high level of paused RNA Polymerase II at the promoter-proximal region. Overall, this study confirms that epigenetic control is important for the maintenance of a NB transcriptional program and makes a case for bivalent promoters as a conserved feature of animal stem cells and not a vertebrate-specific innovation. By establishing a robust ChIP-seq protocol and analysis methodology, we further promote planarians as a promising model system to investigate histone modification–mediated regulation of stem cell function and differentiation.
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spelling pubmed-61698942019-04-01 Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells Dattani, Anish Kao, Damian Mihaylova, Yuliana Abnave, Prasad Hughes, Samantha Lai, Alvina Sahu, Sounak Aboobaker, A. Aziz Genome Res Research Planarian flatworms have an indefinite capacity to regenerate missing or damaged body parts owing to a population of pluripotent adult stems cells called neoblasts (NBs). Currently, little is known about the importance of the epigenetic status of NBs and how histone modifications regulate homeostasis and cellular differentiation. We have developed an improved and optimized ChIP-seq protocol for NBs in Schmidtea mediterranea and have generated genome-wide profiles for the active marks H3K4me3 and H3K36me3, and suppressive marks H3K4me1 and H3K27me3. The genome-wide profiles of these marks were found to correlate well with NB gene expression profiles. We found that genes with little transcriptional activity in the NB compartment but which switch on in post-mitotic progeny during differentiation are bivalent, being marked by both H3K4me3 and H3K27me3 at promoter regions. In further support of this hypothesis, bivalent genes also have a high level of paused RNA Polymerase II at the promoter-proximal region. Overall, this study confirms that epigenetic control is important for the maintenance of a NB transcriptional program and makes a case for bivalent promoters as a conserved feature of animal stem cells and not a vertebrate-specific innovation. By establishing a robust ChIP-seq protocol and analysis methodology, we further promote planarians as a promising model system to investigate histone modification–mediated regulation of stem cell function and differentiation. Cold Spring Harbor Laboratory Press 2018-10 /pmc/articles/PMC6169894/ /pubmed/30143598 http://dx.doi.org/10.1101/gr.239848.118 Text en © 2018 Dattani et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Research
Dattani, Anish
Kao, Damian
Mihaylova, Yuliana
Abnave, Prasad
Hughes, Samantha
Lai, Alvina
Sahu, Sounak
Aboobaker, A. Aziz
Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
title Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
title_full Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
title_fullStr Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
title_full_unstemmed Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
title_short Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
title_sort epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169894/
https://www.ncbi.nlm.nih.gov/pubmed/30143598
http://dx.doi.org/10.1101/gr.239848.118
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