Transcriptomics,Genomics

Dataset Information

52

Regulatory divergence in Drosophila melanogaster and D. simulans: a genome-wide analysis of allele-specific expression


ABSTRACT: Species-specific regulation of gene expression contributes to the development and maintenance of reproductive isolation and to species differences in ecologically important traits. A better understanding of the evolutionary forces which shape regulatory variation and divergence can be developed by comparing expression differences among species and interspecific hybrids. Once expression differences are identified, the underlying genetics of regulatory variation or divergence can be explored. With the goal of associating cis and/or trans components of regulatory divergence with differences in gene expression, overall and allele-specific expression levels were assayed genome-wide in female adult heads of D. melanogaster, D. simulans and their F1 hybrids. A greater proportion of cis differences than trans differences were identified for genes expressed in heads and, in accordance with previous studies, cis differences also explained a larger number of species differences in overall expression level. Regulatory divergence was found to be prevalent among genes associated with defense, olfaction, and among genes downstream of the Drosophila sex determination hierarchy. In addition, two genes, with critical roles in sex determination and micro RNA processing, Sxl and loqs, were identified as misexpressed in hybrid female heads, potentially contributing to hybrid incompatibility. Overall design: Females heads from two species, D. melanogaster and D. simulans, and their F1 hybrid were compared. Genomic DNA was used as a control.

INSTRUMENT(S): [Dm35b_MR] Affymetrix Drosophila Tiling 1.0R Array

SUBMITTER: Rob J Kulathinal 

PROVIDER: GSE17453 | GEO | 2009-08-05

SECONDARY ACCESSION(S): PRJNA118723

REPOSITORIES: GEO

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Publications

Allele-specific expression assays using Solexa.

Main Bradley J BJ   Bickel Ryan D RD   McIntyre Lauren M LM   Graze Rita M RM   Calabrese Peter P PP   Nuzhdin Sergey V SV  

BMC Genomics 20090909


Allele-specific expression (ASE) assays can be used to identify cis, trans, and cis-by-trans regulatory variation. Understanding the source of expression variation has important implications for disease susceptibility, phenotypic diversity, and adaptation. While ASE is commonly measured via relative fluorescence at a SNP, next generation sequencing provides an opportunity to measure ASE in an accurate and high-throughput manner using read counts.We introduce a Solexa-based method to perform larg  ...[more]

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