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Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation

Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variation present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA (rDNA) copy...

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Autores principales: Li, Bo, Kremling, Karl A.G., Wu, Penghao, Bukowski, Robert, Romay, Maria C., Xie, En, Buckler, Edward S., Chen, Mingsheng
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/PMC6169892/
https://www.ncbi.nlm.nih.gov/pubmed/30166407
http://dx.doi.org/10.1101/gr.229716.117
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author Li, Bo
Kremling, Karl A.G.
Wu, Penghao
Bukowski, Robert
Romay, Maria C.
Xie, En
Buckler, Edward S.
Chen, Mingsheng
author_facet Li, Bo
Kremling, Karl A.G.
Wu, Penghao
Bukowski, Robert
Romay, Maria C.
Xie, En
Buckler, Edward S.
Chen, Mingsheng
author_sort Li, Bo
collection PubMed
description Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variation present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA (rDNA) copy number and ribosomal RNA (rRNA) expression for a population of maize inbred lines and investigated the potential role of rDNA and rRNA dosage in regulating global gene expression. Extensive variation was found in both ribosomal DNA copy number and ribosomal RNA expression among maize inbred lines. However, rRNA abundance was not consistent with the copy number of the rDNA. We have not found that the rDNA gene dosage has a regulatory role in gene expression; however, thousands of genes are identified to be coregulated with rRNA expression, including genes participating in ribosome biogenesis and other functionally relevant pathways. We further investigated the potential roles of copy number and the expression level of rDNA on agronomic traits and found that both correlated with flowering time but through different regulatory mechanisms. This comprehensive analysis suggested that rRNA expression variation is a valuable source of functional diversity that affects gene expression variation and field-based phenotypic changes.
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spelling pubmed-61698922019-04-01 Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation Li, Bo Kremling, Karl A.G. Wu, Penghao Bukowski, Robert Romay, Maria C. Xie, En Buckler, Edward S. Chen, Mingsheng Genome Res Research Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variation present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA (rDNA) copy number and ribosomal RNA (rRNA) expression for a population of maize inbred lines and investigated the potential role of rDNA and rRNA dosage in regulating global gene expression. Extensive variation was found in both ribosomal DNA copy number and ribosomal RNA expression among maize inbred lines. However, rRNA abundance was not consistent with the copy number of the rDNA. We have not found that the rDNA gene dosage has a regulatory role in gene expression; however, thousands of genes are identified to be coregulated with rRNA expression, including genes participating in ribosome biogenesis and other functionally relevant pathways. We further investigated the potential roles of copy number and the expression level of rDNA on agronomic traits and found that both correlated with flowering time but through different regulatory mechanisms. This comprehensive analysis suggested that rRNA expression variation is a valuable source of functional diversity that affects gene expression variation and field-based phenotypic changes. Cold Spring Harbor Laboratory Press 2018-10 /pmc/articles/PMC6169892/ /pubmed/30166407 http://dx.doi.org/10.1101/gr.229716.117 Text en © 2018 Li 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
Li, Bo
Kremling, Karl A.G.
Wu, Penghao
Bukowski, Robert
Romay, Maria C.
Xie, En
Buckler, Edward S.
Chen, Mingsheng
Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
title Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
title_full Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
title_fullStr Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
title_full_unstemmed Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
title_short Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
title_sort coregulation of ribosomal rna with hundreds of genes contributes to phenotypic variation
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169892/
https://www.ncbi.nlm.nih.gov/pubmed/30166407
http://dx.doi.org/10.1101/gr.229716.117
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