Cited by 376Genomics and Chromatin DynamicsChromosomal and Genetic VariationsChromatin Remodeling and Cancer

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Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

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Ghavi-Helm, Yad, Jankowski, Aleksander, Meiers, Sascha, Viales, Rebecca R., Korbel, Jan O., Furlong, Eileen E. M.·2019·Nature Genetics

DOI 10.1038/s41588-019-0462-3PMC PMC7116017

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Abstract

Chromatin topology is intricately linked to gene expression, yet its functional requirement remains unclear. Here, we comprehensively assessed the interplay between genome topology and gene expression using highly rearranged chromosomes (balancers) spanning ~75% of the Drosophila genome. Using transheterozyte (balancer/wild-type) embryos, we measured allele-specific changes in topology and gene expression in cis, while minimizing trans effects. Through genome sequencing, we resolved eight large nested inversions, smaller inversions, duplications and thousands of deletions. These extensive rearrangements caused many changes to chromatin topology, disrupting long-range loops, topologically associating domains (TADs) and promoter interactions, yet these are not predictive of changes in expression. Gene expression is generally not altered around inversion breakpoints, indicating that mis-appropriate enhancer-promoter activation is a rare event. Similarly, shuffling or fusing TADs, changing intra-TAD connections and disrupting long-range inter-TAD loops does not alter expression for the majority of genes. Our results suggest that properties other than chromatin topology ensure productive enhancer-promoter interactions.

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Authors: Ghavi-Helm, Y., Jankowski, A., Meiers, S., Viales, R. R., Korbel, J. O., & Furlong, E. E. M.
Affiliations: Lyon 1 Université (FR)
European Molecular Biology Laboratory (DE)
Corresponding author: Ghavi-Helm, Yad
Korbel, Jan O.
Furlong, Eileen E. M.
ORCID: Ghavi-Helm, Yad
Jankowski, Aleksander
Meiers, Sascha
Viales, Rebecca R.
Korbel, Jan O.
Furlong, Eileen E. M.
Venue: Nature Genetics
Publisher: Springer Science and Business Media LLC
Published: 2019-07-15
Volume: 51
Issue: 8
Pages: 1272-1282
ISSN: 1061-4036 (ISSN-L)
1546-1718
DOI: 10.1038/s41588-019-0462-3
PMC: PMC7116017
OpenAlex: W2958578938
Cited by: 354
References: 57
Citations by year: 2026: 16 · 2025: 33 · 2024: 41 · 2023: 54 · 2022: 60 · 2021: 74 · 2020: 56 · 2019: 19
FWCI: 17.94
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature Genetics (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
HAL (submittedVersion)
Funders: Nature
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords: chromatin topology, gene expression, balancer chromosomes, chromosomal inversions, topologically associating domains, enhancer-promoter interactions, cis effect, Drosophila, chromosomal duplication, chromosomal deletion
MeSH terms: Animals, Chromatin, Chromosome Mapping, Drosophila melanogaster, Enhancer Elements, Genetic, Female, Gene Expression Regulation, Male, Promoter Regions, Genetic, Gene Rearrangement, Genome, Insect, Chromosomes, Insect

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Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

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