Abstract
Topologically associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. However, recent studies suggest that the insulating complexes, CTCF/cohesin, present at TAD borders in mammals are absent from those in Drosophila melanogaster, raising the possibility that border elements are not conserved among metazoans. Using in situ Hi-C with sub-kb resolution, here we show that the D. melanogaster genome is almost completely partitioned into >4000 TADs, nearly sevenfold more than previously identified. The overwhelming majority of these TADs are demarcated by the insulator complexes, BEAF-32/CP190, or BEAF-32/Chromator, indicating that these proteins may play an analogous role in flies as that of CTCF/cohesin in mammals. Moreover, extended regions previously thought to be unstructured are shown to consist of small contiguous TADs, a property also observed in mammals upon re-examination. Altogether, our work demonstrates that fundamental features associated with the higher-order folding of the genome are conserved from insects to mammals.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Animals
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Biological Evolution
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CCCTC-Binding Factor / genetics
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CCCTC-Binding Factor / metabolism
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Cell Cycle Proteins / genetics
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Cell Cycle Proteins / metabolism
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Chromatin / chemistry
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Chromatin / ultrastructure*
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Chromatin Assembly and Disassembly
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Chromosomal Proteins, Non-Histone / genetics
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Chromosomal Proteins, Non-Histone / metabolism
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Chromosome Mapping / instrumentation
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Chromosome Mapping / methods*
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Chromosomes, Insect / chemistry
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Chromosomes, Insect / ultrastructure*
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Cohesins
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DNA-Binding Proteins / genetics
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DNA-Binding Proteins / metabolism
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Drosophila Proteins / genetics
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Drosophila Proteins / metabolism
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Drosophila melanogaster / genetics*
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Drosophila melanogaster / ultrastructure
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Eye Proteins / genetics
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Eye Proteins / metabolism
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Gene Expression
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Genome, Insect*
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Humans
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Mammals / genetics*
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Microtubule-Associated Proteins / genetics
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Microtubule-Associated Proteins / metabolism
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Molecular Conformation
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Nuclear Matrix-Associated Proteins / genetics
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Nuclear Matrix-Associated Proteins / metabolism
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Nuclear Proteins / genetics
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Nuclear Proteins / metabolism
Substances
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BEAF-32 protein, Drosophila
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CCCTC-Binding Factor
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CP190 protein, Drosophila
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CTCF protein, human
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Cell Cycle Proteins
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Chro protein, Drosophila
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Chromatin
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Chromosomal Proteins, Non-Histone
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DNA-Binding Proteins
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Drosophila Proteins
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Eye Proteins
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Microtubule-Associated Proteins
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Nuclear Matrix-Associated Proteins
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Nuclear Proteins