Computational protocol: Weak Polygenic Selection Drives the Rapid Adaptation of the Chemosensory System: Lessons from the Upstream Regions of the Major Gene Families

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Protocol publication

[…] To gain insights into the evolutionary impact of the cis-regulatory elements (CREs) that are located within the 5′ upstream regions, we gathered different sources of functional genomics data available for D. melanogaster. We collected information of the transcription factor binding sites () by mining the “TF_binding_sites”, “enhancer”, “silencer” and “insulator” keywords in the “feature” field of the FlyBase GFF file (D. melanogaster release 5.54). This data represents a valuable resource summarizing many functional assays currently conducted in D. melanogaster, mostly including CRE candidates inferred by chromatin immunoprecipitation techniques. We moreover downloaded the 30 chromatin states model, which classifies each D. melanogaster nucleotide position according to the combinatorial profile of 18 histone marks (). We utilized the chromatin model from the BG3 cell line, because as derives directly from neurons may provide a reasonable approximation of the high-order regulatory mechanisms acting at the chemosensory upstream regions.We used the 160 microarrays obtained by () to quantify the intra-specific transcriptional variability of the chemosensory genes. This data set encompasses transcriptional information for 40 DGRP lines, including two technical replicates for each male and female (ArrayExpress accession number: E-MEXP-1). We parsed and normalized the raw signal CEL files using the affy, affyPLM, drosophila2cdf, org.Dm.eg.db and drosophila2.db [R] packages of Bioconductor (). For each biallelic position, we classified the 40 DGRP lines as carriers of the ancestral or the derived allele, and computed the expression intensity ratio (EIR) between these two groups. The biallelic positions with an EIR significantly deviating from the genome-wide pattern (top-1% or bottom-1% outliers) were considered eQTLs. […]

Pipeline specifications

Software tools affy, affyPLM
Databases ArrayExpress FlyBase
Application Gene expression microarray analysis
Organisms Drosophila melanogaster