The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development
Open accessAbstract
The spatial organization of chromosomes is critical in establishing gene expression programs. We generated in situ Hi-C maps throughout zebrafish development to gain insight into higher-order chromatin organization and dynamics. Zebrafish chromosomes segregate in active and inactive chromatin (A/B compartments), which are further organized into topologically associating domains (TADs). Zebrafish A/B compartments and TADs have genomic features similar to those of their mammalian counterparts, including evolutionary conservation and enrichment of CTCF binding sites at TAD borders. At the earliest time point, when there is no zygotic transcription, the genome is highly structured. After zygotic genome activation (ZGA), the genome loses structural features, which are re-established throughout early development. Despite the absence of structural features, we see clustering of super-enhancers in the 3D genome. Our results provide insight into vertebrate genome organization and demonstrate that the developing zebrafish embryo is a powerful model system to study the dynamics of nuclear organization.
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Topological domains in mammalian genomes identified by analysis of chromatin interactions
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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
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Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
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Cohesin Loss Eliminates All Loop Domains
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Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
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Cited by
Organizational principles of 3D genome architecture
Rowley, M. J., & Corces, V. G. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0060-8 · Cited by 1,171
Mechanisms regulating zygotic genome activation
Schulz, K. N., & Harrison, M. M. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0087-x · Cited by 555
The maternal-to-zygotic transition revisited
Vastenhouw, N. L., Cao, W. X., & Lipshitz, H. D. (2019) · Development · doi:10.1242/dev.161471 · Cited by 445
The role of transcription in shaping the spatial organization of the genome
van Steensel, B., & Furlong, E. E. M. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0114-6 · Cited by 247
Hi-C analyses with GENOVA: a case study with cohesin variants
van der Weide, R. H., van den Brand, T., Haarhuis, J. H. I., Teunissen, H., Rowland, B. D., & de Wit, E. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqab040 · Cited by 161
Metadata
- Authors
- Kaaij, L. J. T., van der Weide, R. H., Ketting, R. F., & de Wit, E.
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2018-07
- Volume
- 24
- Issue
- 1
- Pages
- 1-10.e4
- ISSN
- 2211-1247 (ISSN-L)
- OpenAlex
- W2810823898
- Cited by
- 160
- References
- 23
- FWCI
- 6.91
- Type
- journal article
- Language
- en
- Open access
- gold
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- Kaaij, L. J. T., van der Weide, R. H., Ketting, R. F., & de Wit, E. (2018). Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development. Cell Reports. https://doi.org/10.1016/j.celrep.2018.06.003
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