Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development
Open accessPublished version of a preprint
Abstract
Acquisition of cell fate is thought to rely on the specific interaction of remote cis-regulatory modules (CRMs), for example, enhancers and target promoters. However, the precise interplay between chromatin structure and gene expression is still unclear, particularly within multicellular developing organisms. In the present study, we employ Hi-M, a single-cell spatial genomics approach, to detect CRM-promoter looping interactions within topologically associating domains (TADs) during early Drosophila development. By comparing cis-regulatory loops in alternate cell types, we show that physical proximity does not necessarily instruct transcriptional states. Moreover, multi-way analyses reveal that multiple CRMs spatially coalesce to form hubs. Loops and CRM hubs are established early during development, before the emergence of TADs. Moreover, CRM hubs are formed, in part, via the action of the pioneer transcription factor Zelda and precede transcriptional activation. Our approach provides insight into the role of CRM-promoter interactions in defining transcriptional states, as well as distinct cell types.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the developing Drosophila embryo, enhancer-promoter loops are formed before TADs, and likely also precede the onset of zygotic transcription.
“in the developing Drosophila embryo, enhancer–promoter loops are formed before TADs, and likely also precede the onset of zygotic transcription [453, 454].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [453]
In “Cis-regulatory networks emerge before TADs and gene expression” (page unavailable), the paper reports promoter–CRM loops at nc11, before TAD formation and expression of the studied doc genes. It places TAD emergence at nc14 during the major wave of zygotic gene activation, but does not establish that the loops precede the onset of zygotic transcription generally. (LLM, conf=0.85)
Experimental — accuracy not yet measuredHi-M was employed in the developing Drosophila embryo to show that cis-regulatory elements cooperate to form hubs early in development prior to transcription, facilitated by the pioneer factor Zelda.
“Hi-M was recently employed in the developing Drosophila embryo to show that cis-regulatory elements cooperate to form hubs early in development prior to transcription, facilitated by the pioneer factor Zelda [453].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [453]
Hubs detected by these techniques sometimes contain multiple promoters, corroborating evidence for promoter-promoter contacts from conventional 3C-derived methods.
“in addition to multiple enhancers, hubs detected by these techniques sometimes contain multiple promoters, corroborating the evidence for promoter-promoter contacts from the conventional 3C-derived methods [453, 498].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [453]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
Lupiáñez, D. G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J. M., Laxova, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.004 · Cited by 2,132 · see citing works
The long-range interaction landscape of gene promoters
Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works
Deng, W., Lee, J., Wang, H., Miller, J., Reik, A., Gregory, P. D., Dean, A., & Blobel, G. A. (2012) · Cell · doi:10.1016/j.cell.2012.03.051 · Cited by 734 · see citing works
Enhancer loops appear stable during development and are associated with paused polymerase
Ghavi-Helm, Y., Klein, F. A., Pakozdi, T., Ciglar, L., Noordermeer, D., Huber, W., & Furlong, E. E. M. (2014) · Nature · doi:10.1038/nature13417 · Cited by 536 · see citing works
Topology of mammalian developmental enhancers and their regulatory landscapes
de Laat, W., & Duboule, D. (2013) · Nature · doi:10.1038/nature12753 · Cited by 521 · see citing works
Visualizing DNA folding and RNA in embryos at single-cell resolution
Mateo, L. J., Murphy, S. E., Hafner, A., Cinquini, I. S., Walker, C. A., & Boettiger, A. N. (2019) · Nature · doi:10.1038/s41586-019-1035-4 · Cited by 446 · see citing works
Functional implications of genome topology
Cavalli, G., & Misteli, T. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2474 · Cited by 415 · see citing works
The Spatial Organization of the Human Genome
Bickmore, W. A. (2013) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091212-153515 · Cited by 391 · see citing works
Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
Ghavi-Helm, Y., Jankowski, A., Meiers, S., Viales, R. R., Korbel, J. O., & Furlong, E. E. M. (2019) · Nature Genetics · doi:10.1038/s41588-019-0462-3 · Cited by 354 · see citing works
Harrison, M. M., Li, X.-Y., Kaplan, T., Botchan, M. R., & Eisen, M. B. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002266 · Cited by 338 · see citing works
Rubin, A. J., Barajas, B. C., Furlan-Magaril, M., Lopez-Pajares, V., Mumbach, M. R., Howard, I., Kim, D. S., Boxer, L. D., Cairns, J., Spivakov, M., et al. (2017) · Nature Genetics · doi:10.1038/ng.3935 · Cited by 293 · see citing works
Chromatin structure dynamics during the mitosis-to-G1 phase transition
Zhang, H., Emerson, D. J., Gilgenast, T. G., Titus, K. R., Lan, Y., Huang, P., Zhang, D., Wang, H., Keller, C. A., Giardine, B., et al. (2019) · Nature · doi:10.1038/s41586-019-1778-y · Cited by 271 · see citing works
Cardozo Gizzi, A. M., Cattoni, D. I., Fiche, J.-B., Espinola, S. M., Gurgo, J., Messina, O., Houbron, C., Ogiyama, Y., Papadopoulos, G. L., Cavalli, G., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.01.011 · Cited by 258 · see citing works
Self-citationSingle-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains
Oudelaar, A. M., Davies, J. O. J., Hanssen, L. L. P., Telenius, J. M., Schwessinger, R., Liu, Y., Brown, J. M., Downes, D. J., Chiariello, A. M., Bianco, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0253-2 · Cited by 196 · see citing works
Flagged first, then by citations
Research works printed but not linked: 22
- Alberts, B. et al. Molecular Biology of the Cell. (2017) doi:10.1201/9781315735368. · DOI
- Ron, G., Globerson, Y., Moran, D. & Kaplan, T. Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains. Nat. Commun. 8, 2237 (2017).
- Morgan, S. L. et al. Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping. Nat. Commun. 8, 15993 (2017).
- Oudelaar, A. M. et al. A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus. Nat. Commun. 10, 5412 (2019).
- Dufourt, J. et al. Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs. Nat. Commun. 9, 5194 (2018).
- Beliveau, B. J. et al. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc. Natl. Acad. Sci. U. S. A. 109, 21301-21306 (2012).
- Hamm, D. C. et al. A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis in Drosophila melanogaster. PLoS Genet. 13, e1007120 (2017).
- Koenecke, N., Johnston, J., Gaertner, B., Natarajan, M. & Zeitlinger, J. Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis. Genome Biol. 17, 196 (2016).
- Nien, C.-Y. et al. Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PLoS Genet. 7, e1002339 (2011).
- Hao, N., Shearwin, K. E. & Dodd, I. B. Positive and Negative Control of Enhancer- Promoter Interactions by Other DNA Loops Generates Specificity and Tunability. Cell Reports vol. 26 2419-2433.e3 (2019).
- Stein, D. S. & Stevens, L. M. Maternal control of the Drosophila dorsal-ventral body axis. Wiley Interdiscip. Rev. Dev. Biol. 3, 301-330 (2014).
- Deignan, L. et al. Regulation of the BMP Signaling-Responsive Transcriptional Network in the Drosophila Embryo. PLoS Genet. 12, e1006164 (2016).
- Chopra, V. S., Kong, N. & Levine, M. Transcriptional repression via antilooping in the Drosophila embryo. Proc. Natl. Acad. Sci. U. S. A. 109, 9460-9464 (2012).
- Paliou, C. et al. Preformed chromatin topology assists transcriptional robustness of during limb development. Proc. Natl. Acad. Sci. U. S. A. 116, 12390-12399 (2019).
- Cattoni, D. I. et al. Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions. Nat. Commun. 8, 1753 (2017).
- Eagen, K. P., Aiden, E. L. & Kornberg, R. D. Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map. Proc. Natl. Acad. Sci.
- U. S. A. (2017) doi:10.1073/pnas.1701291114. · DOI
- Saunders, A., Core, L. J., Sutcliffe, C., Lis, J. T. & Ashe, H. L. Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. Genes Dev. 27, 1146-1158 (2013).
- Boettiger, A. N. et al. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature (2016) doi:10.1038/nature16496. · DOI
- The Astropy Collaboration et al. The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package. AJS 156, 123 (2018).
- Morlot, J.-B., Mozziconacci, J. & Lesne, A. Network concepts for analyzing 3D genome structure from chromosomal contact maps. EPJ Nonlinear Biomedical Physics vol. 4 (2016).
- Chen, K. et al. A global change in RNA polymerase II pausing during the Drosophila midblastula transition. Elife 2, e00861 (2013).
Cited by
Sorted by citations
Transcriptional enhancers and their communication with gene promoters
Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works
Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging
Sabaté, T., Lelandais, B., Bertrand, E., & Zimmer, C. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad034 · Cited by 13 · see citing works
- Authors
- Espinola, S. M., Götz, M., Bellec, M., Messina, O., Fiche, J.-B., Houbron, C., Dejean, M., Reim, I., Cardozo Gizzi, A. M., Lagha, M., & Nollmann, M.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Friedrich-Alexander-Universität Erlangen-Nürnberg (DE)
- Corresponding author
- Lagha, Mounia
- ORCID
- Venue
- Nature Genetics
- Published
- 2021-04
- Volume
- 53
- Issue
- 4
- Pages
- 477-486
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W3144036649
- Cited by
- 174
- References
- 14
- Citations by year
- 2026: 19 · 2025: 24 · 2024: 33 · 2023: 26 · 2022: 42 · 2021: 28 · 2020: 2
- FWCI
- 10.59
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Conicet (submittedVersion, cc-by-nc-sa)
- Funders
- European Commission (HORIZON2020, 724429)
- Deutsche Forschungsgemeinschaft (431471305)
- Agence Nationale de la Recherche (10-INBS-04, ANR‐10_INBS‐04, ANR-10, ANR-10-LABX-0012, ANR-10-INBS-0004)
- Institut National de la Santé et de la Recherche Médicale (ANR-10-INBS-04)
- Centre National de la Recherche Scientifique (ANR-10-INBS-04)
- Université de Montpellier
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- cis-regulatory modules, chromatin looping, topologically associating domains, enhancer-promoter looping, Zelda, pioneer transcription factors, transcriptional activation, cell fate specification
- MeSH terms
- Animals, Cell Differentiation, Chromatin, Drosophila melanogaster, Embryo, Nonmammalian, Enhancer Elements, Genetic, Nuclear Proteins, Promoter Regions, Genetic, Transcription Factors, Transcription, Genetic, Gene Expression Regulation, Developmental, Cell Lineage, Gene Expression Profiling, Genomics, Drosophila Proteins, Single-Cell Analysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
