Gene expression networks in the Drosophila Genetic Reference Panel.

Genome Research
Logan J EverettTrudy F C Mackay

Abstract

A major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. This question is best addressed in a genetic mapping population in which all molecular polymorphisms are known and for which molecular endophenotypes and complex traits are assessed on the same genotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and for which phenotypes of many quantitative traits have been evaluated. We mapped expression quantitative trait loci for annotated genes, novel transcribed regions, transposable elements, and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, as well as genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic vari...Continue Reading

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Citations

Nov 7, 2019·Genome Research·Shanshan ZhouTrudy F C Mackay
Oct 28, 2020·G3 : Genes - Genomes - Genetics·Fabio MorganteTrudy F C Mackay
Dec 5, 2020·Journal of Biological Rhythms·Shailesh KumarSusan T Harbison
Dec 15, 2020·ELife·Dana M TalsnessClement Y Chow
Dec 10, 2020·Journal of Animal Science and Biotechnology·Shaopan YeZhe Zhang
Oct 30, 2020·Nature Communications·Wen HuangTrudy F C Mackay
Apr 1, 2021·Genetics·Krisna Van DykeFrank W Albert
Feb 18, 2021·Genome Biology and Evolution·Daniel K FabianJanet M Thornton
May 27, 2021·Genome Research·Brandon M BakerRobert R H Anholt

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