The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
Open accessAbstract
The generation of distinctive cell types that form different tissues and organs requires precise, temporal and spatial control of gene expression. This depends on specific cis-regulatory elements distributed in the noncoding DNA surrounding their target genes. Studies performed on mammalian embryonic stem cells and Drosophila embryos suggest that active enhancers form part of a defined chromatin landscape marked by histone H3 lysine 4 mono-methylation (H3K4me1) and histone H3 lysine 27 acetylation (H3K27ac). Nevertheless, little is known about the dynamics and the potential roles of these marks during vertebrate embryogenesis. Here, we provide genomic maps of H3K4me1/me3 and H3K27ac at four developmental time-points of zebrafish embryogenesis and analyze embryonic enhancer activity. We find that (1) changes in H3K27ac enrichment at enhancers accompany the shift from pluripotency to tissue-specific gene expression, (2) in early embryos, the peaks of H3K27ac enrichment are bound by pluripotent factors such as Nanog, and (3) the degree of evolutionary conservation is higher for enhancers that become marked by H3K27ac at the end of gastrulation, suggesting their implication in the establishment of the most conserved (phylotypic) transcriptome that is known to occur later at the pharyngula stage.
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Cites
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 2×
“To that end, we have calculated average conservation scores (phastCons) (Siepel et al. 2005) for each DAR present in each cluster and plotted their cumulative frequencies (Fig.”
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“1B; Heintzman et al. 2007; Creyghton et al. 2010; Hawkins et al. 2011; Rada-Iglesias et al. 2011).”
InfluentialMapping and analysis of chromatin state dynamics in nine human cell types
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Histone modifications at human enhancers reflect global cell-type-specific gene expression
Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533
Widespread transcription at neuronal activity-regulated enhancers
Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450
A unique chromatin signature uncovers early developmental enhancers in humans
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233
Active Genes Are Tri-Methylated at K4 of Histone H3
Santos-Rosa, H., Schneider, R., Bannister, A. J., Sherriff, J., Bernstein, B. E., Emre, N. C. T., Schreiber, S. L., Mellor, J., & Kouzarides, T. (2002) · Nature · doi:10.1038/nature01080 · Cited by 2,138
Enhancer function: new insights into the regulation of tissue-specific gene expression
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Heterozygous deletion of the linked genes ZIC1 and ZIC4 is involved in Dandy-Walker malformation
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Cited by
Modification of Enhancer Chromatin: What, How, and Why?
Calo, E., & Wysocka, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.038 · Cited by 1,457
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
Genomic Perspectives of Transcriptional Regulation in Forebrain Development
Nord, A. S., Pattabiraman, K., Visel, A., & Rubenstein, J. L. R. (2015) · Neuron · doi:10.1016/j.neuron.2014.11.011 · Cited by 152
Extensive conservation of ancient microsynteny across metazoans due to cis -regulatory constraints
Irimia, M., Tena, J. J., Alexis, M. S., Fernandez-Miñan, A., Maeso, I., Bogdanović, O., de la Calle-Mustienes, E., Roy, S. W., Gómez-Skarmeta, J. L., & Fraser, H. B. (2012) · Genome Research · doi:10.1101/gr.139725.112 · Cited by 146
Self-citationBaranasic, D., Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01089-w · Cited by 101
Metadata
- Authors
- Bogdanović, O., Fernandez-Miñán, A., Tena, J. J., de la Calle-Mustienes, E., Hidalgo, C., van Kruysbergen, I., van Heeringen, S. J., Veenstra, G. J. C., & Gómez-Skarmeta, J. L.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2012-05-16
- Volume
- 22
- Issue
- 10
- Pages
- 2043-2053
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2163811581
- Cited by
- 233
- References
- 9
- Type
- posted content
- Language
- en
- Open access
- hybrid
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- Bogdanović, O., Fernandez-Miñán, A., Tena, J. J., de la Calle-Mustienes, E., Hidalgo, C., van Kruysbergen, I., van Heeringen, S. J., Veenstra, G. J. C., & Gómez-Skarmeta, J. L. (2012). Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Research. https://doi.org/10.1101/gr.134833.111
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