Biological consequences of dosage dependent gene regulatory systems

Birchler, James A.; Yao, Huilu; Chudalayandi, Siva

doi:10.1016/j.bbaexp.2006.12.002

Cited by 55 publications

(46 citation statements)

References 43 publications

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“…How is a new balance in regulatory proteins that forms a novel regulatory complex achieved? Birchler et al (2007) suggested that accumulating changes in cis-dominant regulatory regions of critical target loci may allow for a shift in the balance of regulators in the complex. A mutation in a cis-regulatory region could modify gene expression exclusively in a specific spatiotemporal domain (i.e.…”

Section: Recurring Wgds Facilitate Speciation and Increases In Morphomentioning

confidence: 99%

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Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

2009

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Whole genome duplications (WGDs) followed by diploidization, which includes gene loss, have been an important recurrent process in the evolution of higher eukaryotes. Gene retention is biased to specific functional gene categories during diploidization. Dosage-sensitive genes, which include transcription factors, are significantly over-retained following WGDs. By contrast, these same functional gene categories exhibit lower retention rates following smaller scale duplications (e.g., local and tandem duplicates, segmental duplicates, aneuploidy). In light of these recent observations, we review current theories that address the fate of nuclear genes following duplication events (i.e., Gain of Function Hypothesis, Subfunctionalization Hypothesis, Increased Gene Dosage Hypothesis, Functional Buffering Model, and the Gene Balance Hypothesis). We broadly review different mechanisms of dosage-compensation that have evolved to alleviate harmful dosage-imbalances. In addition, we examine a recently proposed extension of the Gene Balance Hypothesis to explain the shared single copy status for a specific functional class of genes across the flowering plants. We speculate that the preferential retention of dosage-sensitive genes (e.g., regulatory genes such as transcription factors) and gene loss following WGDs has played a significant role in the development of morphological complexity in eukaryotes and facilitating speciation, respectively. Lastly, we will review recent findings that suggest polyploid lineages had increased rates of survival and speciation following mass extinction events, including the Cretaceous-Tertiary (KT) extinction.

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Section: Recurring Wgds Facilitate Speciation and Increases In Morphomentioning

confidence: 99%

“…not globally). These changes would progressively occur to multiple target genes until a new balanced state of the regulatory complex is tolerated or selected to resolve the resulting intragenomic conflict (Birchler et al 2007).…”

Section: Recurring Wgds Facilitate Speciation and Increases In Morphomentioning

confidence: 99%

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

2009

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“…Aneuploidy is expected to result in lowered metabolic efficiency due to disturbances in the normal protein stoichiometry for affected dosage-sensitive genes (33)(34)(35)(36). One possible explanation for the repeated occurrence of homeologous substitutions is that the tetrasomic dosage might be maintained for genes present on both homeologs (37).…”

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confidence: 99%

Extensive chromosomal variation in a recently formed natural allopolyploid species,Tragopogon miscellus(Asteraceae)

Chester

Gallagher

Symonds

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

332

316

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Polyploidy, or whole genome duplication, has played a major role in the evolution of many eukaryotic lineages. Although the prevalence of polyploidy in plants is well documented, the molecular and cytological consequences are understood largely from newly formed polyploids (neopolyploids) that have been grown experimentally. Classical cytological and molecular cytogenetic studies both have shown that experimental neoallopolyploids often have meiotic irregularities, producing chromosomally variable gametes and progeny; however, little is known about the extent or duration of chromosomal variation in natural neoallopolyploid populations. We report the results of a molecular cytogenetic study on natural populations of a neoallopolyploid, Tragopogon miscellus, which formed multiple times in the past 80 y. Using genomic and fluorescence in situ hybridization, we uncovered massive and repeated patterns of chromosomal variation in all populations. No population was fixed for a particular karyotype; 76% of the individuals showed intergenomic translocations, and 69% were aneuploid for one or more chromosomes.

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“…These effects are often directly proportional to dosage (Huettel et al, 2008;Horiguchi et al, 2009), but compensatory or dosage-inverse changes have been observed as well (Birchler et al, 2001(Birchler et al, , 2007Huettel et al, 2008;Birchler and Veitia, 2010). Additionally, gene dosage effects can be exerted at the protein level, such as in stoichiometric alterations in the interaction of different subunits of a complex (Veitia et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

A System for Dosage-Based Functional Genomics in Poplar

et al. 2015

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Altering gene dosage through variation in gene copy number is a powerful approach to addressing questions regarding gene regulation, quantitative trait loci, and heterosis, but one that is not easily applied to sexually transmitted species. Elite poplar (Populus spp) varieties are created through interspecific hybridization, followed by clonal propagation. Altered gene dosage relationships are believed to contribute to hybrid performance. Clonal propagation allows for replication and maintenance of meiotically unstable ploidy or structural variants and provides an alternative approach to investigating gene dosage effects not possible in sexually propagated species. Here, we built a genome-wide structural variation system for dosage-based functional genomics and breeding of poplar. We pollinated Populus deltoides with gamma-irradiated Populus nigra pollen to produce >500 F1 seedlings containing dosage lesions in the form of deletions and insertions of chromosomal segments (indel mutations). Using high-precision dosage analysis, we detected indel mutations in ;55% of the progeny. These indels varied in length, position, and number per individual, cumulatively tiling >99% of the genome, with an average of 10 indels per gene. Combined with future phenotype and transcriptome data, this population will provide an excellent resource for creating and characterizing dosage-based variation in poplar, including the contribution of dosage to quantitative traits and heterosis.

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Biological consequences of dosage dependent gene regulatory systems

Cited by 55 publications

References 43 publications

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

Extensive chromosomal variation in a recently formed natural allopolyploid species,Tragopogon miscellus(Asteraceae)

A System for Dosage-Based Functional Genomics in Poplar

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