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Cited by 388Genomics and Chromatin DynamicsChromosomal and Genetic VariationsNuclear Structure and Function

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

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Ulianov, Sergey V., Khrameeva, Ekaterina E., Gavrilov, Alexey A., Flyamer, Ilya M., Kos, Pavel, Mikhaleva, Elena A., Penin, Aleksey A., Logacheva, Maria D. +5 more·2016·Genome Research
DOI 10.1101/gr.196006.115PMC PMC4691752
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Abstract

Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster , we performed Hi-C and poly(A) + RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin.

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  • It has been proposed that Drosophila TADs are formed by condensation of nucleosomes and thus should be rather called 'compartmental domains'.

    “It has been proposed that Drosophila TADs are formed by condensation of nucleosomes [123] and thus should be rather called “compartmental domains” [124].”

    From Enhancer Function in the 3D Genome (2023) · cites this paper as [123]

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Authors
Ulianov, S. V., Khrameeva, E. E., Gavrilov, A. A., Flyamer, I. M., Kos, P., Mikhaleva, E. A., Penin, A. A., Logacheva, M. D., Imakaev, M. V., Chertovich, A., Gelfand, M. S., Shevelyov, Y. Y., & Razin, S. V.
Affiliations
  • Lomonosov Moscow State University (RU)
  • Skolkovo Institute of Science and Technology (RU)
  • Russian Academy of Sciences (RU)
  • Institute of Molecular Genetics (RU)
  • Massachusetts Institute of Technology (US)
Corresponding author
Razin, Sergey V.
ORCID
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2015-10-30
Volume
26
Issue
1
Pages
70-84
ISSN
  • 1088-9051 (ISSN-L)
  • 1549-5469
DOI
10.1101/gr.196006.115
PMC
PMC4691752
OpenAlex
W2172400873
Cited by
388
References
12
Citations by year
2026: 12 · 2025: 20 · 2024: 31 · 2023: 25 · 2022: 34 · 2021: 50 · 2020: 50 · 2019: 38 · 2018: 55 · 2017: 42 · 2016: 28 · 2015: 3
Type
posted content
Language
en
Open access
Locations
  • Genome Research (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
  • HighWire Press Open Archive (submittedVersion)
Funders
  • Russian Foundation for Basic Research (13-00-40086-K, 14-04-91331, 14-04-00010, 14-03-00825)
  • Presidium of the Russian Academy of Sciences
  • Russian Science Foundation (14-14-01088, 14-24-00155)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords
topologically associating domains, chromosome segregation, chromatin folding, insulator proteins, Su(Hw), active chromatin, TAD boundaries, polytene chromosomes, nucleosome compaction, chromatin acetylation, Drosophila melanogaster, gene expression regulation
MeSH terms
Animals, Cell Line, Chromatin, Chromosome Mapping, Computer Simulation, Drosophila melanogaster, Models, Molecular, Nucleosomes, Transcription, Genetic, Sequence Analysis, RNA, Chromatin Assembly and Disassembly, Genome, Insect, Polytene Chromosomes

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