The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Transcription factor binding dynamics during human ES cell differentiation
Open accessAbstract
Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome-wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers. We describe core regulatory dynamics and show the lineage-specific behaviour of selected factors. In addition to the orchestrated remodelling of the chromatin landscape, we find that the binding of several transcription factors is strongly associated with specific loss of DNA methylation in one germ layer, and in many cases a reciprocal gain in the other layers. Taken together, our work shows context-dependent rewiring of transcription factor binding, downstream signalling effectors, and the epigenome during human embryonic stem cell differentiation. Lineage-specific transcription factors and signalling pathways cooperate with pluripotency regulators to control the transcriptional networks that drive cell specification and exit from an embryonic stem cell state; here, we report genome-wide binding data for 38 transcription factors combined with analysis of epigenomic and gene expression data during the differentiation of human embryonic stem cells into the three germ layers. Lineage-specific transcription factors and signalling pathways cooperate with pluripotency regulators when cells exit the embryonic stem cell state and activate the transcriptional networks that control cell specification. Here, as part of the Epigenome Roadmap project, Meissner and colleagues report genome-wide binding data for 38 transcription factors — combined with analysis of epigenomic and gene expression data — during the differentiation of human embryonic stem cells into the three germ layers. They reveal the orchestrated changes in transcription factor binding during differentiation, such as key roles for GATA4 and OTX2 in the transition to mesoderm and ectoderm, respectively.
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Cites
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368
Self-citationSuper-enhancers in the control of cell identity and disease
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Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling
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DNA methylation: roles in mammalian development
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Self-citationGenome-scale DNA methylation maps of pluripotent and differentiated cells
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Self-citationA unique chromatin signature uncovers early developmental enhancers in humans
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DNA-binding factors shape the mouse methylome at distal regulatory regions
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Charting a dynamic DNA methylation landscape of the human genome
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Self-citationDensely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
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Cited by
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368
Self-citationPeak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling
Meers, M. P., Tenenbaum, D., & Henikoff, S. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0287-4 · Cited by 556
Non-redundant functions of EMT transcription factors
Stemmler, M. P., Eccles, R. L., Brabletz, S., & Brabletz, T. (2019) · Nature Cell Biology · doi:10.1038/s41556-018-0196-y · Cited by 524
Sensitivity of transcription factors to DNA methylation
Héberlé, É., & Bardet, A. F. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190033 · Cited by 347
AP-1 imprints a reversible transcriptional programme of senescent cells.
Martínez-Zamudio, R. I., Roux, P.-F., de Freitas, J. A. N. L. F., Robinson, L., Doré, G., Sun, B., Belenki, D., Milanovic, M., Herbig, U., Schmitt, C. A., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0529-5 · Cited by 236
Metadata
- Authors
- Tsankov, A. M., Gu, H., Akopian, V., Ziller, M. J., Donaghey, J., Amit, I., Gnirke, A., & Meissner, A.
- Venue
- Nature
- Published
- 2015-02-18
- Volume
- 518
- Issue
- 7539
- Pages
- 344-349
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2102663142
- Cited by
- 360
- References
- 12
- FWCI
- 15.57
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Tsankov, A. M., Gu, H., Akopian, V., Ziller, M. J., Donaghey, J., Amit, I., Gnirke, A., & Meissner, A. (2015). Transcription factor binding dynamics during human ES cell differentiation. Nature. https://doi.org/10.1038/nature14233
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