2020 journal article
Gene expression networks in the Drosophila Genetic Reference Panel
GENOME RESEARCH, 30(3), 485–496.
MeSH headings : Animals; DNA Transposable Elements; Drosophila melanogaster / genetics; Drosophila melanogaster / metabolism; Drosophila melanogaster / microbiology; Female; Gene Expression Regulation; Gene Regulatory Networks; Genetic Variation; High-Throughput Nucleotide Sequencing; Male; Microbiota / genetics; Quantitative Trait Loci; Sequence Analysis, RNA
TL;DR:
This study performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and mapped expression quantitative trait loci for annotated genes, novel transcribed regions, transposable elements and microbial species, providing new insights regarding the role of natural genetic variation in regulating gene expression.
(via Semantic Scholar)
genome.cshlp.org (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: April 14, 2020
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 variation in regulating gene expression and generates testable hypotheses for future functional analyses.