Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster

Abstract

Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies of the left arm of chromosome 2 and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of gene regulation due to altered nuclear architecture are rare. These rare cases include trans de-repression when deficiencies delete chromatin characterized as repressive in other studies. Generally, effects of breakpoints on expression are promoter proximal (~100bp) or in the gene body. Effects of deficiencies genome-wide are in genes with regulatory relationships to genes within the deleted segments, highlighting the subtle expression network defects in these sensitized genetic backgrounds.

Dynamic Sex Chromosome Expression in Drosophila Male Germ Cells

“…We extracted total RNA from gonad samples using RNeasy 96 kit following the manufacturer's protocol. We quantified RNA using the Quant-iT RiboGreen quantification kit and used 200 ng of total RNA for library preparation (76). We spiked in External RNA Control Consortium (ERCC) spike-ins pools 78A and 78B (transcribed from a certified standard reference) prior to fragmentation.…”

3D genome evolution and reorganization in the Drosophila melanogaster species group

“…Previous research has yielded conflicting results on the conservation of TAD domains. While the overarching opinion is that TADs are highly conserved due to their role in restricting gene-enhancer interactions and therefore, gene expression, more current research suggests that TADs may actually diverge quickly and that TAD reorganization is not necessarily associated with divergence in gene expression [13,18,29,34,6]. Given the high degree of evolutionary conservation despite extensive chromosomal rearrangement between D. melanogaster and D. triauraria (Figure 2c), we expected that entire TAD contact domains including boundary regions would be conserved (i.e.…”

“…Slightly (∼2%) more of the genes in non-orthologous domains are differentially expressed, however this difference is not significant (Fishers Exact Test p-value = 0.151). One possibility that would explain the lack of association between TAD reorganization and gene expression divergence is that, in the relatively compact Drosophila genome, most gene regulatory sequences are directly adjacent to the genes they regulate and are therefore rarely separated by chromosomal rearrangements or TAD reorganization [29].…”

“…The extensive changes in chromosome topology caused by the rearrangements found on Drosophila balancer chromosomes is not associated with differences in gene expression [18]. Also in Drosophila, studies involving deletion mutations [29] and experimentally-induced inversions [34] found that these mutations, which should disrupt TAD organization, had little effect on gene expression.…”

Drosophila small ovaryencodes a zinc-finger repressor required for ovarian differentiation

“…Stranded PolyA+ RNA-seq libraries from sov and control ovaries (Table S5) were created (H. Lee, Cho, et al 2016) and are available at GEO (GSE113977).…”