![]() 2016 Samata and Akhtar 2018), and this appears to be conserved in other drosophilids ( Russo et al. melanogaster, the Male-specific lethal (MSL) complex mediates approximately twofold up-regulation of X-linked genes in males ( Kuroda et al. Which balances the transcriptional output from sex chromosomes between males and females. One example of such a chromosome-wide process is dosage compensation, Regulation at genome-wide or chromosome-wide scales. The observation of genomic rearrangements throughout evolution can raise the question of how they impact mechanisms of transcriptional Apart from being cost-effective, such assemblies at the same time provide additional information about genome conformation. 2013 Kaplan and Dekker 2013 Korbel and Lee 2013 Marie-Nelly et al. Prime examples of such Hi-C-assisted genome assemblies are the mosquitoĪedes aegypti, the domestic goat Capra hircus, or the barley Hordeum vulgare L. Hi-C-derived informationĬan aid for such questions, because contacts between pairs of loci in the whole genome provide linking information to orderĪnd orient genome scaffolds into entire chromosomes. Rearrangements and their impact on 3D genome architecture requires chromosome-length genome assemblies. 2007 Wiegmann and Richards 2018) are typically composed of thousands of scaffolds, which hinder comparisons related to genome organization. melanogaster, current Drosophila genome assemblies ( Drosophila 12 Genomes Consortium et al. It remains unclear whether genome architecture is maintained in highly rearranged, yet related, genomes within a givenĮxcept for D. 2012) whose genome is more than 10-times smaller, more gene-dense, and exposed to faster rates of molecular evolution compared TADs have also been described in non-mammalian species (e.g., Drosophila) ( Sexton et al. ![]() Mammals revealed few selected examples in which contiguous orthologous genes inserted at different genomic positions in aĭifferent species maintain TAD integrity ( Vietri Rudan et al. TADs and their boundaries tend to correlate with genomic rearrangements during evolution as interspecies comparisons in Within them referred to as topologically associating domains (TADs) ( Dixon et al. Those techniques revealed several regulatory layers of genome organization, including regions that show preferential contacts Processes such as dosage compensation of the X chromosome.Ĭhromosome conformation capture techniques such as Hi-C provide genome-wide contact maps between loci within chromosomes ( Lieberman-Aiden et al. Therefore, 3D architecture is preserved even in scenarios of thousands of rearrangements highlighting its relevance for essential Evolutionary conserved genes cluster in the vicinity of HAS, while HAS locations appear evolutionarilyįlexible, thus uncoupling functional requirement of dosage compensation from individual positions on the linear X chromosome. High-affinity sites (HAS) located on the X chromosome are maintained over 40 million years, indicating architectural conservationĪt various hierarchies. ![]() A/B compartments, a set of large gene-dense topologically associating domains (TADs), and spatial contacts between We observe extensive genome shuffling between these species with one synteny breakpoint after approximately every Here, we developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C dataįor studying genome topology in three distantly related Drosophila species. Genome rearrangements that occur during evolution impose major challenges on regulatory mechanisms that rely on three-dimensional ![]()
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