Dataset Information

Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness.

ABSTRACT: The regulatory logic of time- and tissue-specific gene expression has mostly been dissected in the context of the smallest DNA fragments that, when isolated, recapitulate native expression in reporter assays. It is not known if the genomic sequences surrounding such fragments, often evolutionarily conserved, have any biological function or not. Using an enhancer of the even-skipped gene of Drosophila as a model, we investigate the functional significance of the genomic sequences surrounding empirically identified enhancers. A 480 bp long "minimal stripe element" is able to drive even-skipped expression in the second of seven stripes but is embedded in a larger region of 800 bp containing evolutionarily conserved binding sites for required transcription factors. To assess the overall fitness contribution made by these binding sites in the native genomic context, we employed a gene-replacement strategy in which whole-locus transgenes, capable of rescuing even-skipped(-) lethality to adulthood, were substituted for the native gene. The molecular phenotypes were characterized by tagging Even-skipped with a fluorescent protein and monitoring gene expression dynamics in living embryos. We used recombineering to excise the sequences surrounding the minimal enhancer and site-specific transgenesis to create co-isogenic strains differing only in their stripe 2 sequences. Remarkably, the flanking sequences were dispensable for viability, proving the sufficiency of the minimal element for biological function under normal conditions. These sequences are required for robustness to genetic and environmental perturbation instead. The mutant enhancers had measurable sex- and dose-dependent effects on viability. At the molecular level, the mutants showed a destabilization of stripe placement and improper activation of downstream genes. Finally, we demonstrate through live measurements that the peripheral sequences are required for temperature compensation. These results imply that seemingly redundant regulatory sequences beyond the minimal enhancer are necessary for robust gene expression and that "robustness" itself must be an evolved characteristic of the wild-type enhancer.

SUBMITTER: Ludwig MZ

PROVIDER: S-EPMC3213169 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness.

Ludwig Michael Z MZ Manu Kittler Ralf R White Kevin P KP Kreitman Martin M

PLoS genetics 20111110 11

The regulatory logic of time- and tissue-specific gene expression has mostly been dissected in the context of the smallest DNA fragments that, when isolated, recapitulate native expression in reporter assays. It is not known if the genomic sequences surrounding such fragments, often evolutionarily conserved, have any biological function or not. Using an enhancer of the even-skipped gene of Drosophila as a model, we investigate the functional significance of the genomic sequences surrounding empi ...[more]

PMID: 22102826

Similar Datasets

Project description:Most cases of alternative reproductive tactics (ARTs) are thought to represent conditional strategies, whereby high-status males express highly competitive phenotypes, whereas males below a certain status threshold resort to sneaky tactics. The underlying evolutionarily stable strategy (ESS) model assumes that males of high competitive ability achieve higher fitness when expressing the territorial phenotype, whereas the less competitive males are more fit as sneakers, caused by fitness functions for the ARTs having different slopes and intersecting at a threshold value of competitive ability. The model, however, is notoriously difficult to test as it requires access to low-status territorials and high-status sneakers, that rarely occur in nature. Here, we test the conditional ESS in the androdimorphic acarid mite Sancassania berlesei, where large males tend to develop into an armoured, aggressive 'fighter' morph, while small males become unarmoured, non-aggressive 'scramblers'. In addition to body size, male morph is affected by pheromones produced by big populations, with fighters being suppressed in dense colonies. By manipulating pheromone concentration, we obtained high-status scramblers and low-status fighters. We also estimated status- and size-dependent fitness functions for male morphs across a range of population sizes. Fighters had the highest fitness in small populations and their fitness declined with increasing density, whereas the reverse was true for scramblers, providing support for condition-dependent ESS with respect to demography. However, whereas male fitness increased with body size, the fitness functions did not differ significantly between morphs. Thus, although we found evidence for the intersection of morph fitness functions with respect to demography, we did not find such an intersection in relation to male body size. Our results highlight how demography can exert selection pressures shaping the evolution of the conditional strategy in species with ARTs.

Project description:Mutation is the ultimate source of genetic variation, the bedrock of evolution. Yet, predicting the consequences of new mutations remains a challenge in biology. Gene expression provides a potential link between a genotype and its phenotype. But the variation in gene expression created by de novo mutation and the fitness consequences of mutational changes to expression remain relatively unexplored. Here, we investigate the effects of >2600 de novo mutations on gene expression across the transcriptome of 28 mutation accumulation lines derived from two independent wild-type genotypes of the green algae Chlamydomonas reinhardtii. We observed that the amount of genetic variance in gene expression created by mutation (Vm) was similar to the variance that mutation generates in typical polygenic phenotypic traits and approximately 15-fold the variance seen in the limited species where Vm in gene expression has been estimated. Despite the clear effect of mutation on expression, we did not observe a simple additive effect of mutation on expression change, with no linear correlation between the total expression change and mutation count of individual MA lines. We therefore inferred the distribution of expression effects of new mutations to connect the number of mutations to the number of differentially expressed genes (DEGs). Our inferred DEE is highly L-shaped with 95% of mutations causing 0-1 DEG while the remaining 5% are spread over a long tail of large effect mutations that cause multiple genes to change expression. The distribution is consistent with many cis-acting mutation targets that affect the expression of only one gene and a large target of trans-acting targets that have the potential to affect tens or hundreds of genes. Further evidence for cis-acting mutations can be seen in the overabundance of mutations in or near differentially expressed genes. Supporting evidence for trans-acting mutations comes from a 15:1 ratio of DEGs to mutations and the clusters of DEGs in the co-expression network, indicative of shared regulatory architecture. Lastly, we show that there is a negative correlation with the extent of expression divergence from the ancestor and fitness, providing evidence of the deleterious effects of perturbing gene expression.

Dataset Information

Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness.

Publications

Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets