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Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

ABSTRACT: Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

PROVIDER: PRJNA494393 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7952600_1.fastq.gz	Fastqsanger.gz
	SRR7952600_2.fastq.gz	Fastqsanger.gz
	SRR7952610_1.fastq.gz	Fastqsanger.gz
	SRR7952610_2.fastq.gz	Fastqsanger.gz
	SRR7952601_1.fastq.gz	Fastqsanger.gz

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Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [ChIP-seq]

Project description:Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [ChIP-seq]

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Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling.

Project description:Genome rearrangements that occur during evolution impose major challenges on regulatory mechanisms that rely on three-dimensional genome architecture. Here, we developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly related Drosophila species. We observe extensive genome shuffling between these species with one synteny breakpoint after approximately every six genes. A/B compartments, a set of large gene-dense topologically associating domains (TADs), and spatial contacts between high-affinity sites (HAS) located on the X chromosome are maintained over 40 million years, indicating architectural conservation at various hierarchies. Evolutionary conserved genes cluster in the vicinity of HAS, while HAS locations appear evolutionarily flexible, thus uncoupling functional requirement of dosage compensation from individual positions on the linear X chromosome. Therefore, 3D architecture is preserved even in scenarios of thousands of rearrangements highlighting its relevance for essential processes such as dosage compensation of the X chromosome.

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Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-10-14 | GSE120752 | GEO

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [HiC]

Project description:We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism.

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Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [ChIP-seq]

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