The Effects of Weak Genetic Perturbations on the Transcriptome of the Wing Imaginal Disc and Its Association With Wing Shape in Drosophila melanogaster

Abstract

A major objective of genomics is to elucidate the mapping between genotypic and phenotypic space as a step toward understanding how small changes in gene function can lead to elaborate phenotypic changes. One approach that has been utilized is to examine overall patterns of covariation between phenotypic variables of interest, such as morphology, physiology, and behavior, and underlying aspects of gene activity, in particular transcript abundance on a genome-wide scale. Numerous studies have demonstrated that such patterns of covariation occur, although these are often between samples with large numbers of unknown genetic differences (different strains or even species) or perturbations of large effect (sexual dimorphism or strong loss-of-function mutations) that may represent physiological changes outside of the normal experiences of the organism. We used weak mutational perturbations in genes affecting wing development in Drosophila melanogaster that influence wing shape relative to a co-isogenic wild type. We profiled transcription of 1150 genes expressed during wing development in 27 heterozygous mutants, as well as their co-isogenic wild type and one additional wild-type strain. Despite finding clear evidence of expression differences between mutants and wild type, transcriptional profiles did not covary strongly with shape, suggesting that information from transcriptional profiling may not generally be predictive of final phenotype. We discuss these results in the light of possible attractor states of gene expression and how this would affect interpretation of covariation between transcriptional profiles and other phenotypes.

BMP gradients: A paradigm for morphogen-mediated developmental patterning

“…A salient example of such redundancy is the ability of a membrane-tethered form of Wg alone to sustain viability and generate almost normal patterning (73), whereas it is nearly certain that diffusible forms of the protein also normally play a role in patterning. Additionally, new quantitative approaches integrated with cuttingedge imaging methods should be considered, such as using Bayesian statistical models to reveal potential links in gene regulatory networks by examining the effects of many (hundreds) modest perturbations of the system (e.g., heterozygosity or duplication of each gene in the network) on multiple gene expression markers in vivo across fields of developing cells [e.g., (112,113)]. …”

Causes and Consequences of Genetic Background Effects Illuminated by Integrative Genomic Analysis

“…We compared the results of our digital gene expression (DGE) experiment to two similar microarray experiments: one using Drosophila Genome Research Center arrays , and one using a custom Illumina array (Dworkin et al 2011). Raw array data are available at the National Center for Biotechnology Information Gene Expression Omnibus, NCBI GEO (GSE26706: GSM657471-GSM657487 and GSE13779: GSM346787-GSM346810).…”

“…First, we used two previously published microarray datasets comparing gene expression profiles between wild-type and sd E3 flies in both the SAM and ORE genetic backgrounds to identify genes whose expression levels are influenced by sd genotype, genetic background, and their interaction (Dworkin et al , 2011. Second, we examined the results of the screen for autosomal dominant modifiers of sd E3 mentioned earlier .…”

“…However, we may be able to gain additional insight by integrating data from a variety of approaches. For instance, gene expression studies can identify genes whose expression is affected by a focal mutation in a background-dependent manner (Dworkin et al , 2011, providing a complementary set of candidate loci. Then, using whole-genome resequencing to search for polymorphic transcription factor binding sites (TFBSs) could help explain these background-dependent effects on gene expression.…”

Regulation of BMP activity and range in Drosophila wing development

“…63,64], but have not been investigated for effects on the distribution of BMP activity. Cross-regulation is important for uniform growth [15,30,60], and will undoubtedly contribute to the stability of developmental outcome [65,66]. We anticipate that Drosophila physiology will continue as an experimental paradigm where integration of mathematical modeling, image analysis, and experimentation yield critical insights into the rich mechanisms at work in BMP signaling.…”