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The Gene Balance Hypothesis: Epigenetics and Dosage Effects in Plants

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Plant Epigenetics and Epigenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2093))

Abstract

Dosage effects in plants are caused by changes in the copy number of chromosomes, segments of chromosomes, or multiples of individual genes. Genes often exhibit a dosage effect in which the amount of product is closely correlated with the number of copies present. However, when larger segments of chromosomes are varied, there are trans-acting effects across the genome that are unleashed that modulate gene expression in cascading effects. These appear to be mediated by the stoichiometric relationship of gene regulatory machineries. There are both positive and negative modulations of target gene expression, but the latter is the plurality effect. When this inverse effect is combined with a dosage effect, compensation for a gene can occur in which its expression is similar to the normal diploid regardless of the change in chromosomal dosage. In contrast, changing the whole genome in a polyploidy series has fewer relative effects as the stoichiometric relationship is not disrupted. Together, these observations suggest that the stoichiometry of gene regulation is important as a reflection of the mode of assembly of the individual subunits involved in the effective regulatory macromolecular complexes. This principle has implications for gene expression mechanisms, quantitative trait genetics, and the evolution of genes depending on the mode of duplication, either segmentally or via whole-genome duplication.

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Acknowledgment

Research supported by the National Science Foundation Grant IOS-1545780 Plant Genome (JB, JC), NSF 1615789 (TJ), and NSF 1853556 (TJ).

Author information

Authors and Affiliations

  1. Division of Biological Sciences, University of Missouri, Columbia, MO, USA

    Xiaowen Shi, Hua Yang & James A. Birchler

  2. Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA

    Chen Chen, Jie Hou & Jianlin Cheng

  3. Department of Statistics, University of Missouri, Columbia, MO, USA

    Tieming Ji

  4. Institut Jacques Monod, Paris, France

    Reiner A. Veitia

  5. Universite Paris-Diderot/Paris 7, Paris, France

    Reiner A. Veitia

Authors
  1. Xiaowen Shi
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  2. Chen Chen
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  3. Hua Yang
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  4. Jie Hou
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  5. Tieming Ji
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  6. Jianlin Cheng
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  7. Reiner A. Veitia
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  8. James A. Birchler
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Corresponding author

Correspondence to James A. Birchler .

Editor information

Editors and Affiliations

  1. Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland

    Charles Spillane

  2. Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland

    Peter McKeown

Software Implementation

Software Implementation

Source code for ratio distribution and scatter plots is available through GitHub (https://github.com/chrischen1/Ratio-Distribution-Analysis-Demo).

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Shi, X. et al. (2020). The Gene Balance Hypothesis: Epigenetics and Dosage Effects in Plants. In: Spillane, C., McKeown, P. (eds) Plant Epigenetics and Epigenomics . Methods in Molecular Biology, vol 2093. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0179-2_12

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  • DOI: https://doi.org/10.1007/978-1-0716-0179-2_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0178-5

  • Online ISBN: 978-1-0716-0179-2

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