One Hundred Years of Gene Balance: How Stoichiometric Issues Affect Gene Expression, Genome Evolution, and Quantitative Traits

A century ago experiments with the flowering plant <i>Datura stramonium</i> and the fruit fly <i>Drosophila melanogaster</i> revealed that adding an extra chromosome to a karyotype was much more detrimental than adding a whole set of chromosomes. This phenomenon was referred to as gene balance and has been recapitulated across eukaryotic species. Here, we retrace some developments in this field. Molecular studies suggest that the basis of balance involves stoichiometric relationships of multi-component interactions. This concept has implication for the mechanisms controlling gene expression, genome evolution, sex chromosome evolution/dosage compensation, speciation mechanisms, and the underlying genetics of quantitative traits.

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Dosage Compensation Systems

Introduction to Epigenetics - Learning Materials in Biosciences ◽

10.1007/978-3-030-68670-3_4 ◽

2021 ◽

pp. 67-89

Author(s):

Renato Paro ◽

Ueli Grossniklaus ◽

Raffaella Santoro ◽

Anton Wutz

Keyword(s):

Gene Expression ◽

X Chromosome ◽

Dosage Compensation ◽

Molecular Mechanisms ◽

Sex Chromosome ◽

Fruit Fly ◽

X Chromosomes ◽

Compensation Systems ◽

A Cell ◽

Males And Females

AbstractThis chapter provides an introduction to chromosome-wide dosage compensation systems. We will examine the evolution of dosage compensation, which is thought to be driven by the appearance of differentiated sex chromosomes. In a subset of species with X chromosomal sex determination or XY sex chromosome systems, expression of X-linked genes is regulated by chromosome-wide modifications that equalize gene expression differences between males and females. The molecular mechanisms of X chromosome-wide dosage compensation have been studied in flies, worms, and mammals. Each of these species uses a distinct dosage compensation strategy with a different molecular mechanism. In the wormCaenorhabditis elegans, gene expression on the two X chromosomes of hermaphrodites is reduced to a level that approximates a single X chromosome in males. The fruit flyDrosophila melanogasterachieves dosage compensation by increased transcription of the single X chromosome in males to a level that is similar to the two X chromosomes in females. Lastly, in mammals, one of the two X chromosomes in female cells is transcriptionally inactive and a single X chromosome is transcribed in both sexes. Studies of dosage compensation systems provide insights into how epigenetic regulation controls gene expression and chromatin organization differentially within a cell.

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Do the microRNAs we eat affect gene expression?

Nature ◽

10.1038/d41586-020-01767-x ◽

2020 ◽

Vol 582 (7812) ◽

pp. S10-S11 ◽

Cited By ~ 1

Author(s):

Kristina Campbell

Keyword(s):

Gene Expression ◽

Affect Gene Expression

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Faculty Opinions recommendation of Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.14061961.15528062 ◽

2012 ◽

Author(s):

Job Dekker

Keyword(s):

Gene Expression ◽

Noncoding Rnas ◽

Affect Gene Expression

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Phenotypic plasticity

10.1093/oso/9780198797500.003.0005 ◽

2018 ◽

Author(s):

Karen D. Williams ◽

Marla B. Sokolowski

Keyword(s):

Gene Expression ◽

Phenotypic Plasticity ◽

Environmental Change ◽

Behavioral Plasticity ◽

Behavioral Flexibility ◽

Insect Behavior ◽

Behavioral Variability ◽

Gene By Environment Interactions ◽

Affect Gene Expression

Why is there so much variation in insect behavior? This chapter will address the sources of behavioral variability, with a particular focus on phenotypic plasticity. Variation in social, nutritional, and seasonal environmental contexts during development and adulthood can give rise to phenotypic plasticity. To delve into mechanism underlying behavioral flexibility in insects, examples of polyphenisms, a type of phenotypic plasticity, will be discussed. Selected examples reveal that environmental change can affect gene expression, which in turn can affect behavioral plasticity. These changes in gene expression together with gene-by-environment interactions are discussed to illuminate our understanding of insect behavioral plasticity.

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Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids

Nature Ecology & Evolution ◽

10.1038/s41559-021-01523-y ◽

2021 ◽

Vol 5 (10) ◽

pp. 1382-1393

Author(s):

Xinyu Jiang ◽

Qingxin Song ◽

Wenxue Ye ◽

Z. Jeffrey Chen

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Small Rnas ◽

Structural Variation ◽

Self Incompatibility ◽

Polyploid Evolution ◽

Genomic Variations ◽

Conserved Gene ◽

Arabidopsis Suecica ◽

Affect Gene Expression

AbstractDuring evolution successful allopolyploids must overcome ‘genome shock’ between hybridizing species but the underlying process remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized and natural Arabidopsis suecica (TTAA) allotetraploids derived from Arabidopsisthaliana (TT) and Arabidopsisarenosa (AA). A. suecica shows conserved gene synteny and content with more gene family gain and loss in the A and T subgenomes than respective progenitors, although A. arenosa-derived subgenome has more structural variation and transposon distributions than A. thaliana-derived subgenome. These balanced genomic variations are accompanied by pervasive convergent and concerted changes in DNA methylation and gene expression among allotetraploids. The A subgenome is hypomethylated rapidly from F1 to resynthesized allotetraploids and convergently to the T-subgenome level in natural A. suecica, despite many other methylated loci being inherited from F1 to all allotetraploids. These changes in DNA methylation, including small RNAs, in allotetraploids may affect gene expression and phenotypic variation, including flowering, silencing of self-incompatibility and upregulation of meiosis- and mitosis-related genes. In conclusion, concerted genomic and epigenomic changes may improve stability and adaptation during polyploid evolution.

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Schistosoma mansoni and Echinostoma caproni excretorysecretory products differentially affect gene expression in Biomphalaria glabrata embryonic cells

Parasitology ◽

10.1017/s0031182003004049 ◽

2003 ◽

Vol 127 (6) ◽

pp. 533-542 ◽

Cited By ~ 27

Author(s):

C. COUSTAU ◽

G. MITTA ◽

C. DISSOUS ◽

F. GUILLOU ◽

R. GALINIER ◽

...

Keyword(s):

Gene Expression ◽

Schistosoma Mansoni ◽

Biomphalaria Glabrata ◽

Embryonic Cells ◽

Echinostoma Caproni ◽

Affect Gene Expression

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Mammalian linker-histone subtypes differentially affect gene expression in vivo

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0736105100 ◽

2003 ◽

Vol 100 (10) ◽

pp. 5920-5925 ◽

Cited By ~ 82

Author(s):

R. Alami ◽

Y. Fan ◽

S. Pack ◽

T. M. Sonbuchner ◽

A. Besse ◽

...

Keyword(s):

Gene Expression ◽

Linker Histone ◽

Affect Gene Expression

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Interactions Among Dosage-Dependent Trans-Acting Modifiers of Gene Expression and Position-Effect Variegation in Drosophila

Genetics ◽

10.1093/genetics/150.1.251 ◽

1998 ◽

Vol 150 (1) ◽

pp. 251-263 ◽

Cited By ~ 3

Author(s):

Utpal Bhadra ◽

Manika Pal Bhadra ◽

James A Birchler

Keyword(s):

Gene Expression ◽

Quantitative Traits ◽

Position Effect ◽

Position Effect Variegation ◽

Developmental Transitions ◽

Eye Color ◽

Dosage Effects ◽

Effect Variegation ◽

Hierarchical Manner ◽

Color Gene

Abstract We have investigated the effect of dosage-dependent trans-acting regulators of the white eye color gene in combinations to understand their interaction properties. The consequences of the interactions will aid in an understanding of aneuploid syndromes, position-effect variegation (PEV), quantitative traits, and dosage compensation, all of which are affected by dosage-dependent modifiers. Various combinations modulate two functionally related transcripts, white and scarlet, differently. The overall trend is that multiple modifiers are noncumulative or epistatic to each other. In some combinations, developmental transitions from larvae to pupae to adults act as a switch for whether the effect is positive or negative. With position-effect variegation, similar responses were found as with gene expression. The highly multigenic nature of dosage-sensitive modulation of both gene expression and PEV suggests that dosage effects can be progressively transduced through a series of steps in a hierarchical manner.

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