Transcription factors and 3D genome conformation in cell-fate decisions

doi:10.1038/s41586-019-1182-7

Review

. 2019 May;569(7756):345-354.

doi: 10.1038/s41586-019-1182-7. Epub 2019 May 15.

Transcription factors and 3D genome conformation in cell-fate decisions

Ralph Stadhouders^{1

2}, Guillaume J Filion^{3

4}, Thomas Graf^{5

6}

Affiliations

¹ Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands. r.stadhouders@erasmusmc.nl.
² Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands. r.stadhouders@erasmusmc.nl.
³ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
⁴ Universitat Pompeu Fabra (UPF), Barcelona, Spain.
⁵ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. thomas.graf@crg.eu.
⁶ Universitat Pompeu Fabra (UPF), Barcelona, Spain. thomas.graf@crg.eu.

PMID: 31092938
DOI: 10.1038/s41586-019-1182-7

Review

Transcription factors and 3D genome conformation in cell-fate decisions

Ralph Stadhouders et al. Nature. 2019 May.

. 2019 May;569(7756):345-354.

doi: 10.1038/s41586-019-1182-7. Epub 2019 May 15.

Authors

Ralph Stadhouders^{1

2}, Guillaume J Filion^{3

4}, Thomas Graf^{5

6}

Affiliations

¹ Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands. r.stadhouders@erasmusmc.nl.
² Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands. r.stadhouders@erasmusmc.nl.
³ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
⁴ Universitat Pompeu Fabra (UPF), Barcelona, Spain.
⁵ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. thomas.graf@crg.eu.
⁶ Universitat Pompeu Fabra (UPF), Barcelona, Spain. thomas.graf@crg.eu.

PMID: 31092938
DOI: 10.1038/s41586-019-1182-7

Abstract

How cells adopt different identities has long fascinated biologists. Signal transduction in response to environmental cues results in the activation of transcription factors that determine the gene-expression program characteristic of each cell type. Technological advances in the study of 3D chromatin folding are bringing the role of genome conformation in transcriptional regulation to the fore. Characterizing this role of genome architecture has profound implications, not only for differentiation and development but also for diseases including developmental malformations and cancer. Here we review recent studies indicating that the interplay between transcription and genome conformation is a driving force for cell-fate decisions.

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References

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[1] Davidson, E. H. Emerging properties of animal gene regulatory networks. Nature 468, 911–920 (2010). - PubMed - PMC - DOI

[2] Davidson, E. H. Emerging properties of animal gene regulatory networks. Nature 468, 911–920 (2010). - PubMed - PMC - DOI

[3] Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A. & Luscombe, N. M. A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet. 10, 252–263 (2009). - PubMed - DOI

[4] Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A. & Luscombe, N. M. A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet. 10, 252–263 (2009). - PubMed - DOI

[5] Lambert, S. A. et al. The human transcription factors. Cell 172, 650–665 (2018). - PubMed - DOI

[6] Lambert, S. A. et al. The human transcription factors. Cell 172, 650–665 (2018). - PubMed - DOI

[7] Kundaje, A. et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317–330 (2015). - PubMed - PMC - DOI

[8] Kundaje, A. et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317–330 (2015). - PubMed - PMC - DOI

[9] de Laat, W. & Duboule, D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 502, 499–506 (2013). - PubMed - DOI

[10] de Laat, W. & Duboule, D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 502, 499–506 (2013). - PubMed - DOI

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Transcription factors and 3D genome conformation in cell-fate decisions

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Transcription factors and 3D genome conformation in cell-fate decisions

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