Seeing double: appreciating genetic redundancy.

Pickett, F. Bryan; Meeks-Wagner, D. Ry

doi:10.1105/tpc.7.9.1347

Cited by 152 publications

(88 citation statements)

References 51 publications

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“…Over time, one of the duplicates may be lost or both duplicates may be retained and diverge in sequence and function, leading to subfunctionalization or neofunctionalization, with corresponding changes in the degree of genetic redundancy (Pickett and Meeks-Wagner, 1995;Briggs et al, 2006;Pérez-Pérez et al, 2009;Chen et al, 2010).…”

Section: Discussion Molecular Dissection Of Duplicate Gene Functionmentioning

confidence: 99%

“…Because redundancy is assessed by comparing differences in single and multiple mutants, conclusions regarding genetic redundancy are necessarily dependent on the nature of the phenotypic analysis performed (Pickett and Meeks-Wagner, 1995;Pérez-Pérez et al, 2009;Lloyd and Meinke, 2012).…”

Section: Redundancy Is Relativementioning

confidence: 99%

“…However, this approach relies on the availability of mutants that exhibit observable differences in phenotype. Unfortunately, the majority of single-gene mutants lack detectable alterations, due to genetic redundancy, other compensatory mechanisms, or difficulties in phenotypic assessment, which limits the usefulness of a genetic approach for defining gene function (Pickett and Meeks-Wagner, 1995;Bouché and Bouchez, 2001;Hanada et al, 2009a;Pérez-Pérez et al, 2009;Lloyd and Meinke, 2012).…”

Section: Introductionmentioning

confidence: 99%

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Tissue-Specific Profiling Reveals Transcriptome Alterations inArabidopsisMutants Lacking Morphological Phenotypes

et al. 2013

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Traditional genetic analysis relies on mutants with observable phenotypes. Mutants lacking visible abnormalities may nevertheless exhibit molecular differences useful for defining gene function. To examine this, we analyzed tissue-specific transcript profiles from Arabidopsis thaliana transcription factor gene mutants with known roles in root epidermis development, but lacking a single-gene mutant phenotype due to genetic redundancy. We discovered substantial transcriptional changes in each mutant, preferentially affecting root epidermal genes in a manner consistent with the known double mutant effects. Furthermore, comparing transcript profiles of single and double mutants, we observed remarkable variation in the sensitivity of target genes to the loss of one or both paralogous genes, including preferential effects on specific branches of the epidermal gene network, likely reflecting the pathways of paralog subfunctionalization during evolution. In addition, we analyzed the root epidermal transcriptome of the transparent testa glabra2 mutant to clarify its role in the network. These findings provide insight into the molecular basis of genetic redundancy and duplicate gene diversification at the level of a specific gene regulatory network, and they demonstrate the usefulness of tissue-specific transcript profiling to define gene function in mutants lacking informative visible changes in phenotype.

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Section: Discussion Molecular Dissection Of Duplicate Gene Functionmentioning

confidence: 99%

Section: Redundancy Is Relativementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Tissue-Specific Profiling Reveals Transcriptome Alterations inArabidopsisMutants Lacking Morphological Phenotypes

et al. 2013

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“…Loss-of-function mutants in most of these genes do not have defects during zygotic embryo development, perhaps indicating the presence of redundant factors, as is common with ;90% of gene functions protected by redundancy (Pickett and Meeks-Wagner, 1995;Meinke et al, 2003). Loss-of-function mutants that show ectopic embryo development, but again, often without obvious zygotic phenotypes, have also been isolated.…”

Section: Introductionmentioning

confidence: 97%

Global Identification of Targets of theArabidopsisMADS Domain Protein AGAMOUS-Like15

et al. 2009

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AGAMOUS-Like15 (AGL15) is a MADS domain transcriptional regulator that promotes somatic embryogenesis by binding DNA and regulating gene expression. Chromatin immunoprecipitation (ChIP) analysis previously identified DNA fragments with which AGL15 associates in vivo, and a low-throughput approach revealed a role for AGL15 in gibberellic acid catabolism that is relevant to embryogenesis. However, higher throughput methods are needed to identify targets of AGL15. Here, we mapped AGL15 in vivo binding sites using a ChIP-chip approach and the Affymetrix tiling arrays for Arabidopsis thaliana and found that ;2000 sites represented in three biological replicates of the experiment are annotated to nearby genes. These results were combined with high-throughput measurement of gene expression in response to AGL15 accumulation to discriminate responsive direct targets from those further downstream in the network. LEAFY COTYLE-DON2, FUSCA3, and ABA INSENSITIVE3, which encode B3 domain transcription factors that are key regulators of embryogenesis, were identified and verified as direct target genes of AGL15. Genes identified as targets of the B3 genes are also targets of AGL15, and we found that INDOLEACETIC ACID-INDUCED PROTEIN30 is involved in promotion of somatic embryo development. The data presented here and elsewhere suggest that much cross-regulation occurs in gene regulatory networks underpinning embryogenesis.

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“…With the subsequent evolution of genetic redundancies (Nowak et al, 1997, Pickett and Meeks-Wagner, 1995, Tautz, 1992, Wagner, 1996, Wilkins, 1997 and other mechanisms supporting reliability of developmental outcome (e.g., Rutherford and Lindquist, 1998), a closer linkage between genetic change and phenotypic change was established. In particular, with evolution under selective criteria favoring the maintenance of morphological phenotype in the face of environmental or metabolic variability (see Baldwin, 1896, Schmalhausen, 1949, Waddington, 1942, Riedl, 1978, SalazarCiudad et al, 2001a organisms would come to be characterized by a closer mapping of genotype to phenotype, giving rise to the familiar Mendelian world.…”

Section: Introductionmentioning

confidence: 99%

Before programs: The physical origination of multicellular forms

Newman¹,

Forgács²,

Müller³

2006

Int. J. Dev. Biol.

159

118

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By examining the formative role of physical processes in modern-day developmental systems, we infer that although such determinants are subject to constraints and rarely act in a "pure" fashion, they are identical to processes generic to all viscoelastic, chemically excitable media, non-living as well as living. The processes considered are free diffusion, immiscible liquid behavior, oscillation and multistability of chemical state, reaction-diffusion coupling and mechanochemical responsivity. We suggest that such processes had freer reign at early stages in the history of multicellular life, when less evolution had occurred of genetic mechanisms for stabilization and entrenchment of functionally successful morphologies. From this we devise a hypothetical scenario for pattern formation and morphogenesis in the earliest metazoa. We show that the expected morphologies that would arise during this relatively unconstrained "physical" stage of evolution correspond to the hollow, multilayered and segmented morphotypes seen in the gastrulation stage embryos of modern-day metazoa as well as in Ediacaran fossil deposits of 600 Ma. We suggest several ways in which organisms that were originally formed by predominantly physical mechanisms could have evolved genetic mechanisms to perpetuate their morphologies.

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Seeing double: appreciating genetic redundancy.

Cited by 152 publications

References 51 publications

Tissue-Specific Profiling Reveals Transcriptome Alterations inArabidopsisMutants Lacking Morphological Phenotypes

Tissue-Specific Profiling Reveals Transcriptome Alterations inArabidopsisMutants Lacking Morphological Phenotypes

Global Identification of Targets of theArabidopsisMADS Domain Protein AGAMOUS-Like15

Before programs: The physical origination of multicellular forms

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