Biology subjects

Christine Queitsch

Publications and source records attributed to Christine Queitsch.

10 recordsLinked to original sources

bioRxiv2016

The variable ELF3 polyglutamine tract mediates complex epistatic interactions in Arabidopsis thaliana.

Short tandem repeats are hypervariable genetic elements that occur frequently in coding regions. Their high mutation rate readily generates genetic variation contributing to adaptive evolution and human diseases. We recently proposed that short tandem repeats are likely to engage in epistasis because they are well-positioned to compensate for genetic variation arising at other loci due to their high mutation rate. We previously reported that natural ELF3 polyglutamine variants cause reciprocal genetic incompatibilities in two divergent Arabidopsis thaliana backgrounds. Here, we dissected the genetic architecture of this incompatibility and used a yeast two-hybrid strategy to identify proteins whose physical interactions with ELF3 were modulated by polyglutamine tract length. Using these two orthogonal approaches, we identify specific genetic interactions and physical mechanisms by which the ELF3 polyglutamine tract may mediate the observed genetic incompatibilities. Our work elucidates how short tandem repeat variation, which is generally underascertained in population-scale sequencing, can contribute to phenotypic variation. Furthermore, our results support our proposal that highly variable STR loci can contribute disproportionately to the epistatic component of heritability.

Genetics↗

bioRxiv2016

Redundancy, feedback, and robustness in the Arabidopsis thaliana BZR/BEH gene family

Organismal development is remarkably robust, tolerating stochastic errors to produce consistent, so-called canalized adult phenotypes. The mechanistic underpinnings of developmental robustness are poorly understood, but recent studies implicate certain features of genetic networks such as functional redundancy, connectivity, and feedback. Here, we examine the BRZ/BEH gene family, whose function is crucial for embryonic stem development in the plant Arabidopsis thaliana, to test current assumptions on functional redundancy and trait robustness. Our analyses of BRZ/BEH gene mutants and mutant combinations revealed that functional redundancy among gene family members does not contribute to trait robustness. Connectivity is another commonly cited determinant of robustness; however, we found no correlation between connectivity among gene family members or their connectivity with other transcription factors and effects on robustness. Instead, we found that only BEH4, the most ancient family member, modulated developmental robustness. We present evidence that regulatory cross-talk among gene family members is integrated by BEH4 and promotes wild-type levels of developmental robustness. Further, the chaperone HSP90, a known determinant of developmental robustness, appears to act via BEH4 in maintaining robustness of embryonic stem length. In summary, we demonstrate that even among closely related transcription factors, trait robustness can arise through the activity of a single gene family member, challenging common assumptions about the molecular underpinnings of robustness.

Genetics↗

bioRxiv2016

ELF3 polyQ variation in Arabidopsis thaliana reveals a PIF4-independent role in thermoresponsive flowering.

Plants have evolved elaborate mechanisms controlling developmental responses to environmental stimuli. A particularly important stimulus is temperature. Previous work has identified the interplay of PIF4 and ELF3 as a central circuit underlying thermal responses in Arabidopsis thaliana. However, thermal responses vary widely among strains, possibly offering mechanistic insights into the wiring of this circuit. ELF3 contains a polyglutamine (polyQ) tract that is crucial for ELF3 function and varies in length across strains. Here, we use transgenic analysis to test the hypothesis that natural polyQ variation in ELF3 is associated with the observed natural variation in thermomorphogenesis. We found little evidence that the polyQ tract plays a specific role in thermal responses beyond modulating general ELF3 function. Instead, we made the serendipitous discovery that ELF3 plays a crucial, PIF4-independent role in thermoresponsive flowering under conditions more likely to reflect field conditions. We present evidence that ELF3 acts through the photoperiodic pathway, pointing to a previously unknown symmetry between low and high ambient temperature responses. Moreover, in analyzing two strain backgrounds with vastly different thermal responses, we demonstrate that responses may be shifted rather than fundamentally rewired across strains. Our findings tie together disparate observations into a coherent framework in which multiple pathways converge in accelerating flowering in response to temperature, with some such pathways modulated by photoperiod.

Plant Biology↗

bioRxiv2015

Evolutionary assembly patterns of prokaryotic genomes

Evolutionary innovation must occur in the context of some genomic background, which limits available evolutionary paths. For example, protein evolution by sequence substitution is constrained by epistasis between residues. In prokaryotes, evolutionary innovation frequently happens by macrogenomic events such as horizontal gene transfer (HGT). Previous work has suggested that HGT can be influenced by ancestral genomic content, yet the extent of such gene-level constraints has not yet been systematically characterized. Here, we evaluated the evolutionary impact of such constraints in prokaryotes, using probabilistic ancestral reconstructions from 634 extant prokaryotic genomes and a novel framework for detecting evolutionary constraints on HGT events. We identified 8,228 directional dependencies between genes, and demonstrated that many such dependencies reflect known functional relationships, including, for example, evolutionary dependencies of the photosynthetic enzyme RuBisCO. Modeling all dependencies as a network, we adapted an approach from graph theory to establish chronological precedence in the acquisition of different genomic functions. Specifically, we demonstrated that specific functions tend to be gained sequentially, suggesting that evolution in prokaryotes is governed by functional assembly patterns. Finally, we showed that these dependencies are universal rather than clade-specific and are often sufficient for predicting whether or not a given ancestral genome will acquire specific genes. Combined, our results indicate that evolutionary innovation via HGT is profoundly constrained by epistasis and historical contingency, similar to the evolution of proteins and phenotypic characters, and suggest that the emergence of specific metabolic and pathological phenotypes in prokaryotes can be predictable from current genomes.

Evolutionary Biology↗

bioRxiv2015

A Two-State Epistasis Model Reduces Missing Heritability of Complex Traits

Despite decade-long efforts, the genetic underpinnings of many complex traits and diseases remain largely elusive. It is increasingly recognized that a purely additive model, upon which most genome-wide association studies (GWAS) rely, is insufficient. Although thousands of significant trait-associated loci have been identified, purely additive models leave much of the inferred genetic variance unexplained. Several factors have been invoked to explain the missing heritability, including epistasis. Accounting for all possible epistatic interactions is computationally complex and requires very large samples. Here, we propose a simple two-state epistasis model, in which individuals show either high or low variant penetrance with respect to a certain trait. The use of this model increases the power to detect additive trait-associated loci. We show that this model is consistent with current GWAS results and improves fit with heritability observations based on twin studies. We suggest that accounting for variant penetrance will significantly increase our power to identify underlying additive loci.

Genetics↗

bioRxiv2014

A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana

Efforts to identify loci underlying complex traits generally assume that most genetic variance is additive. Here, we examined the genetics of Arabidopsis thaliana root length and found that the narrow-sense heritability for this trait was statistically zero. This low additive genetic variance likely explains why no associations to root length could be found using standard additive-model-based genome-wide association (GWA) approaches. However, the broad-sense heritability for root length was significantly larger, and we therefore also performed an epistatic GWA analysis to map loci contributing to the epistatic genetic variance. This analysis revealed four interacting pairs involving seven chromosomal loci that passed a standard multiple-testing corrected significance threshold. Explorations of the genotype-phenotype maps for these pairs revealed that the detected epistasis cancelled out the additive genetic variance, explaining why these loci were not detected in the additive GWA analysis. Small population sizes, such as in our experiment, increase the risk of identifying false epistatic interactions due to testing for associations with very large numbers of multi-marker genotypes in few phenotyped individuals. Therefore, we estimated the false-positive risk using a new statistical approach that suggested half of the associated pairs to be true positive associations. Our experimental evaluation of candidate genes within the seven associated loci suggests that this estimate is conservative; we identified functional candidate genes that affected root development in four loci that were part of three of the pairs. In summary, statistical epistatic analyses were found to be indispensable for confirming known, and identifying several new, functional candidate genes for root length using a population of wild-collected A. thaliana accessions. We also illustrated how epistatic cancellation of the additive genetic variance resulted in an insignificant narrow-sense, but significant broad-sense heritability that could be dissected into the contributions of several individual loci using a combination of careful statistical epistatic analyses and functional genetic experiments.\n\nAuthor summaryComplex traits, such as many human diseases or climate adaptation and production traits in crops, arise through the action and interaction of many genes and environmental factors. Classic approaches to identify contributing genes generally assume that these factors contribute mainly additive genetic variance. Recent methods, such as genome-wide association studies, often adhere to this additive genetics paradigm. However, additive models of complex traits do not reflect that genes can also contribute with non-additive genetic variance. In this study, we use Arabidopsis thaliana to determine the additive and non-additive genetic contributions to the phenotypic variation in root length. Surprisingly, much of the observed phenotypic variation in root length across genetically divergent strains was explained by epistasis. We mapped seven loci contributing to the epistatic genetic variance and validated four genes in these loci with mutant analysis. For three of these genes, this is their first implication in root development. Together, our results emphasize the importance of considering both non-additive and additive genetic variance when dissecting complex trait variation, in order not to lose sensitivity in genetic analyses.

Genomics↗

bioRxiv2014

MIPSTR: a method for multiplex genotyping of germ-line and somatic STR variation across many individuals

Abstract Short tandem repeats (STRs) are highly mutable genetic elements that often reside in functional genomic regions. The cumulative evidence of genetic studies on individual STRs suggests that STR variation profoundly affects phenotype and contributes to trait heritability. Despite recent advances in sequencing technology, STR variation has remained largely inaccessible across many individuals compared to single nucleotide variation or copy number variation. STR genotyping with short-read sequence data is confounded by (1) the difficulty of uniquely mapping short, low-complexity reads and (2) the high rate of STR amplification stutter. Here, we present MIPSTR, a robust, scalable, and affordable method that addresses these challenges. MIPSTR uses targeted capture of STR loci by single-molecule Molecular Inversion Probes (smMIPs) and a unique mapping strategy. Targeted capture and mapping strategy resolve the first challenge; the use of single molecule information resolves the second challenge. Unlike previous methods, MIPSTR is capable of distinguishing technical error due to amplification stutter from somatic STR mutations. In proof-of-principle experiments, we use MIPSTR to determine germ-line STR genotypes for 102 STR loci with high accuracy across diverse populations of the plant A. thaliana. We show that putatively functional STRs may be identified by deviation from predicted STR variation and by association with quantitative phenotypes. Employing DNA mixing experiments and a mutant deficient in DNA repair, we demonstrate that MIPSTR can detect low-frequency somatic STR variants. MIPSTR is applicable to any organism with a high-quality reference genome and is scalable to genotyping many thousands of STR loci in thousands of individuals.

Genomics↗

bioRxiv2014

The conserved PFT1 tandem repeat is crucial for proper flowering in Arabidopsis thaliana

It is widely appreciated that short tandem repeat (STR) variation underlies substantial phenotypic variation in organisms. Some propose that the high mutation rates of STRs in functional genomic regions facilitate evolutionary adaptation. Despite their high mutation rate, some STRs show little to no variation in populations. One such STR occurs in the Arabidopsis thaliana gene PFT1 (MED25), where it encodes an interrupted polyglutamine tract. Though the PFT1 STR is large ([~]270 bp), and thus expected to be extremely variable, it shows only minuscule variation across A. thaliana strains. We hypothesized that the PFT1 STR is under selective constraint, due to previously undescribed roles in PFT1 function. We investigated this hypothesis using plants expressing transgenic PFT1 constructs with either an endogenous STR or with synthetic STRs of varying length. Transgenic plants carrying the endogenous PFT1 STR generally performed best across adult PFT1-dependent traits, in terms of complementing a pft1 null mutant. In stark contrast, transgenic plants carrying a PFT1 transgene lacking the STR entirely phenocopied a pft1 loss-of-function mutant for flowering time phenotypes, and were generally hypomorphic for other traits, establishing the functional importance of this domain. Transgenic plants carrying various synthetic constructs occupied the phenotypic space between wild-type and pft1-loss-of-function mutants. By varying PFT1 STR length, we discovered that PFT1 can act as either an activator or repressor of flowering in a photoperiod-dependent manner. We conclude that the PFT1 STR is constrained to its approximate wild-type length by its various functional requirements. Our study implies that there is strong selection on STRs not only to generate allelic diversity, but also to maintain certain lengths pursuant to optimal molecular function.

Genetics↗

bioRxiv2014

Hsp90 promotes kinase evolution

Heat-shock protein 90 (Hsp90) promotes the maturation and stability of its client proteins, including many kinases. In doing so, Hsp90 may allow its clients to accumulate mutations as previously proposed by the capacitor hypothesis. If true, Hsp90 clients should show increased evolutionary rate compared to non-clients; however, other factors, such as gene expression and protein connectivity, may confound or obscure the chaperones putative contribution. Here, we compared the evolutionary rates of many Hsp90 clients and non-clients in the human protein kinase superfamily. We show that Hsp90 client status promotes evolutionary rate independently of, but in a small magnitude similar to that of gene expression and protein connectivity. Hsp90s effect on kinase evolutionary rate was detected across mammals, specifically relaxing purifying selection. Hsp90 clients also showed increased nucleotide diversity and harbored more damaging variation than non-client kinases across humans. These results are consistent with the central argument of the capacitor hypothesis that interaction with the chaperone allows its clients to harbor genetic variation. Hsp90 client status is thought to be highly dynamic with as few as one amino acid change rendering a protein dependent on the chaperone. Contrary to this expectation, we found that across protein kinase phylogeny Hsp90 client status tends to be gained, maintained, and shared among closely related kinases. We also infer that the ancestral protein kinase was not an Hsp90 client. Taken together, our results suggest that Hsp90 played an important role in shaping the kinase superfamily.

Evolutionary Biology↗

bioRxiv2014

The overdue promise of short tandem repeat variation for heritability.

Short tandem repeat (STR) variation has been proposed as a major explanatory factor in the heritability of complex traits in humans and model organisms. However, we still struggle to incorporate STR variation into genotype-phenotype maps. Here, we review the promise of STRs in contributing to complex trait heritability, and highlight the challenges that STRs pose due to their repetitive nature. We argue that STR variants are more likely than single nucleotide variants to have epistatic interactions, reiterate the need for targeted assays to accurately genotype STRs, and call for more appropriate statistical methods in detecting STR-phenotype associations. Lastly, somatic STR variation within individuals may serve as a read-out of disease susceptibility, and is thus potentially a valuable covariate for future association studies.

Genetics↗