Abstract
Topologically associating domains (TADs), CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP, we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C. elegans and A. thaliana. Architectural proteins insulate compartmental domains by reducing interaction frequencies between neighboring regions in Drosophila, but CTCF loops do not play a distinct role in this organism. In mammals, compartmental domains exist alongside CTCF loop domains to form topological domains. The results suggest that compartmental domains are responsible for domain structure in all eukaryotes, with CTCF playing an important role in domain formation in mammals.
Keywords:
CTCF; Hi-C; TAD; compartment; epigenetics; insulator; loop; transcription.
Copyright © 2017 Elsevier Inc. All rights reserved.
MeSH terms
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Animals
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Arabidopsis / genetics
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Arabidopsis / metabolism
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Arabidopsis Proteins / chemistry
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Arabidopsis Proteins / genetics
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Arabidopsis Proteins / metabolism
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Caenorhabditis elegans / genetics
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Caenorhabditis elegans / metabolism
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Caenorhabditis elegans Proteins / chemistry
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Caenorhabditis elegans Proteins / genetics
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Caenorhabditis elegans Proteins / metabolism
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Chromatin / chemistry
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Chromatin / genetics
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Chromatin / metabolism*
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Chromatin Assembly and Disassembly*
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Chromosomal Proteins, Non-Histone / chemistry
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Chromosomal Proteins, Non-Histone / genetics
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Chromosomal Proteins, Non-Histone / metabolism*
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Computer Simulation
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DNA / chemistry
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DNA / genetics
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DNA / metabolism*
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DNA, Plant / chemistry
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DNA, Plant / genetics
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DNA, Plant / metabolism
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Drosophila Proteins / chemistry
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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 / metabolism*
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Histones / chemistry
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Histones / genetics
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Histones / metabolism*
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Humans
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Models, Biological
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Nucleic Acid Conformation
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Protein Conformation
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Structure-Activity Relationship
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Transcription, Genetic
Substances
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Arabidopsis Proteins
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Caenorhabditis elegans Proteins
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Chromatin
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Chromosomal Proteins, Non-Histone
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DNA, Plant
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Drosophila Proteins
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Histones
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DNA