Biology subjects

Steven Russell

Publications and source records attributed to Steven Russell.

4 recordsLinked to original sources

bioRxiv2016

Regions of very low H3K27me3 partition the Drosophila genome into topological domains

BackgroundIt is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood.\n\nResultsWe have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing mid-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4/Putzig. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the transcription start sites of housekeeping genes than with the H3K27me3 domain boundaries.\n\nConclusionsWe suggest that the D domain chromatin state, characterised by very low H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome.

Genomics↗

bioRxiv2016

Interplay between copy number, dosage compensation and expression noise in Drosophila

Gene copy number variations are associated with many disorders characterized by high phenotypic heterogeneity. Disease penetrance differs even in genetically identical twins. Can such heterogeneity arise, in part, from increased expression variability of one dose genes? While increased variability in the context of single cell gene expression is well recognized, our computational simulations indicated that in a multicellular organism intrinsic single cell level noise should cancel out and thus the impact of gene copy reduction on organismal level expression variability must be due to something else. To systematically examine the impact of gene dose reduction on expression variability in a multi-cellular organism, we performed experimental gene expression measurements in Drosophila DrosDel autosomal deficiency lines. Genome-wide analysis revealed that autosomal one dose genes have higher gene expression variability relative to two dose genes. In flies, gene dose reduction is often accompanied by dosage compensation at the gene expression level. Surprisingly, expression noise was increased by compensation. This increased compensation-dependent variability was found to be a property of one dose autosomal genes but not X-liked genes in males despite the fact that they too are dosage compensated, suggesting that sex chromosome dosage compensation also results in noise reduction. Previous studies attributed autosomal dosage compensation to feedback loops in interaction networks. Our results suggest that these feedback loops are not optimized to deliver consistent responses to gene deletion events and thus gene deletions can lead to heterogeneous responses even in the context of an identical genetic background. Additionally, we show that expression variation associated with reduced dose of transcription factors propagate through the gene interaction network, impacting a large number of downstream genes. These properties of gene deletions could contribute to the phenotypic heterogeneity of diseases associated with haploinsufficiency.\n\nAuthor SummaryGene copy number variations are associated with many human disorders characterized by high phenotypic heterogeneity and understanding the effects of gene copy alterations is essential if we wish to understand factors influencing disease heterogeneity. While heterogeneous responses to reductions in gene dosage can be attributed in part to genetic background differences, we found that responses to dosage reduction vary, even in identical genetic backgrounds. Heterogeneities are not restricted to reduced dosage genes, but propagate through gene networks to affect downstream genes with normal copy number. We also found that reduction in gene dosage is associated with the introduction of expression variation or noise. Expression noise was also observed to propagate across the gene network, further contributing to the heterogeneous response to gene deletion. Through the use of computational simulation, we showed that the majority of the increased noise we observed is most likely due to extrinsic rather than intrinsic sources. Irrespective of the source of the observed noise, we propose that the presence of expression noise and its propagation through gene networks is likely to contribute to the heterogeneity of disease phenotypes observed in humans.

Genomics↗

bioRxiv2015

Genome-wide expression profiling Drosophila melanogaster deficiency heterozygotes reveals diverse genomic responses.

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 on 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 changes in 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 (~100 bp) or within the gene body. Genome-wide effects of deficiencies are observed at genes with regulatory relationships to genes within the deleted segments, highlighting the subtle expression network defects in these sensitized genetic backgrounds.\n\nAuthor summaryDeletions alter gene dose in heterozygotes and bring distant regions of the genome into juxtaposition. We find that the transcriptional dose response is generally varied, gene-specific, and coherently propagates into gene expression regulatory networks. Analysis of deletion heterozygote expression profiles indicates that distinct genetic pathways are weakened in adult flies bearing different deletions even though they show minimal or no overt phenotypes. While there are exceptions, breakpoints have a minimal effect on the expression of flanking genes, despite the fact that different regions of the genome are brought into contact and that important elements such as insulators are deleted. These data suggest that there is little effect of nuclear architecture and long-range enhancer and/or silencer promoter contact on gene expression in the compact Drosophila genome.

Genetics↗

bioRxiv2014

Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila

BackgroundGroup B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. In Drosophila melanogaster, the two group B Sox proteins Dichaete and SoxNeuro show widespread common binding across the genome. While some instances of functional compensation have been observed in Drosophila, the function of common binding and the extent of its evolutionary conservation is not known.\n\nResultsWe used DamID-seq to examine the genome-wide binding patterns of Dichaete and SoxNeuro in four species of Drosophila. Through a quantitative comparison of Dichaete binding, we evaluated the rate of binding site turnover across the genome as well as at specific functional sites. We also examined the presence of Sox motifs within binding intervals and the correlation between sequence conservation and binding conservation. To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species.\n\nConclusionWe find that, while the regulatory networks driven by Dichaete and SoxNeuro are largely conserved across the drosophilids studied, binding site turnover is widespread and correlated with phylogenetic distance. Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites. We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important. Our analysis provides insights into the evolution of group B Sox function, highlighting the specific conservation of shared binding sites and suggesting alternative sources of neofunctionalisation between paralogous family members.

Genomics↗