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The Gene Balance Hypothesis: Epigenetics and Dosage Effects in Plants

  • Xiaowen Shi
  • Chen Chen
  • Hua Yang
  • Jie Hou
  • Tieming Ji
  • Jianlin Cheng
  • Reiner A. Veitia
  • James A. BirchlerEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Aneuploidy Ploidy Copy number variants Quantitative traits Gene expression Dosage compensation Gene balance hypothesis 

Notes

Acknowledgment

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

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Xiaowen Shi
    • 1
  • Chen Chen
    • 2
  • Hua Yang
    • 1
  • Jie Hou
    • 2
  • Tieming Ji
    • 3
  • Jianlin Cheng
    • 2
  • Reiner A. Veitia
    • 4
    • 5
  • James A. Birchler
    • 1
    Email author
  1. 1.Division of Biological SciencesUniversity of MissouriColumbiaUSA
  2. 2.Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaUSA
  3. 3.Department of StatisticsUniversity of MissouriColumbiaUSA
  4. 4.Institut Jacques MonodParisFrance
  5. 5.Universite Paris-Diderot/Paris 7ParisFrance

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