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Evaluation of the role of functional constraints on the integrity of an ultra conserved region in the genus Drosophila

ABSTRACT: Our results indicate that even in highly rearranged genomes like those of Diptera, unusually high levels of gene order conservation cannot be systematically attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE31120 | GEO | 2011/08/03

SECONDARY ACCESSION(S): PRJNA144959

REPOSITORIES: GEO

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Evaluation of the role of functional constraints on the integrity of an ultra conserved region in the genus Drosophila

Project description:Our results indicate that even in highly rearranged genomes like those of Diptera, unusually high levels of gene order conservation cannot be systematically attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought. 6 genotypes (REC, INV1, INV2, SIM1, REV1, and REV2) and 2 sexes (male and female) were investigated in this study, each with 3 biological replicates (A,B,and C), so a total of 36 (6x2x3) hybridizations were conducted. Differential analysis between genotypes or sexes were analyzed.

2011-08-02 | E-GEOD-31120 | biostudies-arrayexpress

Evaluation of the role of functional constraints on the integrity of an ultraconserved region in the genus Drosophila.

Project description: Not available

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Functional and cellular constraints that shaped the PPARg binding landscape in human and mouse macrophages

Project description:This SuperSeries is composed of the following subset Series: GSE25137: Functional and cellular constraints that shaped the PPARg binding landscape in human and mouse macrophages: human expression GSE25426: Functional and cellular constraints that shaped the PPARg binding landscape in human and mouse macrophages: human ChIP-Seq Refer to individual Series

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High-throughput laboratory evolution reveals global evolutionary constraints for antibiotic resistance

Project description:Understanding constraints which shape antibiotic resistance is key for predicting and controlling drug resistance. Here, we performed high-throughput laboratory evolution of Escherichia coli. The transcriptome, resistance, and genomic profiles for the evolved strains in 48 environments were quantitatively analyzed. By analyzing the quantitative datasets through interpretable machine learning techniques, the emergence of low dimensional phenotypic states within the 192 strains was observed. Further analysis revealed the underlying biological processes responsible for the distinct states. We also report a novel constraint which leads to decelerated evolution. These findings bridge the genotypic, gene expression, and drug resistance space, and lead to a comprehensive understanding of constraints for antibiotic resistance.

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Targets and genomic constraints of ectopic Dnmt3b expression

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Evolution of microrna expression at the onset of drosophila metamorphosis by miRNA

Project description:We found two lines of evidence suggesting that miRNA abundance has been shaped by different evolutionary regimes at the two developmental stages. Attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought.

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Evolution of microRNA expression at the onset of drosophila metamorphosis by mRNA

Project description:We found two lines of evidence suggesting that miRNA abundance has been shaped by different evolutionary regimes at the two developmental stages attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought.

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Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast

Project description:Gene expression evolution can be caused by changes in cis- or trans-regulatory elements or both. As cis and trans regulation operate through different molecular mechanisms, cis and trans mutations may show different inheritance patterns and may be subjected to different selective constraints. To investigate these issues, we obtained and analyzed gene expression data from two Saccharomyces cerevisiae strains and their hybrid, using high-throughput sequencing. Our data indicate that compared to other types of genes, those with antagonistic cis-trans interactions are more likely to exhibit over- or under-dominant inheritance of expression level. Moreover, in accordance with previous studies, genes with trans variants tend to have a dominant inheritance pattern while cis variants are enriched for additive inheritance. In addition, cis regulatory differences contribute more to expression differences between species than within species, whereas trans regulatory differences show a stronger association between divergence and polymorphism. Our data indicate that in the trans component of gene expression differences genes subjected to weaker selective constraints tend to have an excess of polymorphism over divergence compared to those subjected to stronger selective constraints. In contrast, in the cis component, this difference between genes under stronger and weaker selective constraint is mostly absent. To explain these observations, we propose that purifying selection more strongly shapes trans polymorphism than cis polymorphism. Study the gene expression patterns in two strains of yeast (BY and RM)

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Developmental constraints shape the evolution of the nematode mid-developmental transition

Project description:Evolutionary theory assumes that genetic variation is uniform and gradual in nature, yet morphological and gene expression studies have revealed that different life-stages exhibit distinct levels of cross-species conservation. In particular, a stage in mid-embryogenesis is highly conserved across species of the same phylum, suggesting that this stage is subject to developmental constraints, either by increased purifying selection or by a strong mutational bias. An alternative explanation, however, holds that the same ‘hourglass’ pattern of variation may result from increased positive selection at the earlier and later stages of development. To distinguish between these scenarios, we examined gene expression variation in a population of the nematode C. elegans using an experimental design that eliminated the influence of positive selection. By measuring gene expression for all genes throughout development in twenty strains, we found that variations were dramatically uneven throughout development, with a significant depletion during mid-embryogenesis. In particular, the family of homeodomain transcription factors, whose expression generally coincides with mid-embryogenesis, evolved under high constraint. Our data further shows that genes responsible for the integration of germ layers during morphogenesis are the most constrained class of genes. Together, these results provide the first evidence for developmental constraints as the mechanism underlying the hourglass model of animal evolution. Understanding the pattern and mechanism of developmental constraints provides a framework to understand how evolutionary processes have interacted with embryogenesis and led to the diversity of animal life on earth.

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Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

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