The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation
Open accessAbstract
The Drosophila genome activator Vielfaltig (Vfl), also known as Zelda (Zld), is thought to prime enhancers for activation by patterning transcription factors (TFs). Such priming is accompanied by increased chromatin accessibility, but the mechanisms by which this occurs are poorly understood. Here, we analyze the effect of Zld on genome-wide nucleosome occupancy and binding of the patterning TF Dorsal (Dl). Our results show that early enhancers are characterized by an intrinsically high nucleosome barrier. Zld tackles this nucleosome barrier through local depletion of nucleosomes with the effect being dependent on the number and position of Zld motifs. Without Zld, Dl binding decreases at enhancers and redistributes to open regions devoid of enhancer activity. We propose that Zld primes enhancers by lowering the high nucleosome barrier just enough to assist TFs in accessing their binding motifs and promoting spatially controlled enhancer activation if the right patterning TFs are present. We envision that genome activators in general will utilize this mechanism to activate the zygotic genome in a robust and precise manner.
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Cites
Transcription factors: from enhancer binding to developmental control
Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227
Pioneer transcription factors: establishing competence for gene expression
Zaret, K. S., & Carroll, J. S. (2011) · Genes & Development · doi:10.1101/gad.176826.111 · Cited by 1,589
Transcriptional enhancers: from properties to genome-wide predictions
Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356
The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila
Liang, H.-L., Nien, C.-Y., Liu, H.-Y., Metzstein, M. M., Kirov, N., & Rushlow, C. (2008) · Nature · doi:10.1038/nature07388 · Cited by 478
Self-citationShadow enhancers as a source of evolutionary novelty
Hong, J.-W., Hendrix, D. A., & Levine, M. S. (2008) · Science · doi:10.1126/science.1160631 · Cited by 474
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
Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?
Arnosti, D. N., & Kulkarni, M. M. (2005) · Journal of Cellular Biochemistry · doi:10.1002/jcb.20352 · Cited by 309
Cited by
Hendrickson, P. G., Doráis, J. A., Grow, E. J., Whiddon, J. L., Lim, J.-W., Wike, C. L., Weaver, B. D., Pflueger, C., Emery, B. R., Wilcox, A. L., et al. (2017) · Nature Genetics · doi:10.1038/ng.3844 · Cited by 734
Base-resolution models of transcription-factor binding reveal soft motif syntax
Avsec, Ž., Weilert, M., Shrikumar, A., Krueger, S., Alexandari, A., Dalal, K., Fropf, R., McAnany, C., Gagneur, J., Kundaje, A., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00782-6 · Cited by 610
Self-citationMechanisms regulating zygotic genome activation
Schulz, K. N., & Harrison, M. M. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0087-x · Cited by 555
Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription
Hug, C. B., Grimaldi, A. G., Kruse, K., & Vaquerizas, J. M. (2017) · Cell · doi:10.1016/j.cell.2017.03.024 · Cited by 466
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
Metadata
- Authors
- Sun, Y., Nien, C.-Y., Chen, K., Liu, H.-Y., Johnston, J., Zeitlinger, J., & Rushlow, C.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2015-09-02
- Volume
- 25
- Issue
- 11
- Pages
- 1703-1714
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2171675401
- Cited by
- 176
- References
- 7
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Sun, Y., Nien, C.-Y., Chen, K., Liu, H.-Y., Johnston, J., Zeitlinger, J., & Rushlow, C. (2015). Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. Genome Research. https://doi.org/10.1101/gr.192542.115
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