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Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development

Nature Chemical Biology volume 8, pages 270–276 (2012)Cite this article

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Abstract

Transcription factors have diverse roles during embryonic development, combinatorially controlling cellular states in a spatially and temporally defined manner. Resolving the dynamic transcriptional profiles that underlie these patterning processes is essential for understanding embryogenesis at the molecular level. Here we show how temporal, tissue-specific changes in embryonic transcription factor function can be discerned by integrating caged morpholino oligonucleotides with photoactivatable fluorophores, fluorescence-activated cell sorting and microarray technologies. As a proof of principle, we have dynamically profiled No tail a (Ntla)-dependent genes at different stages of axial mesoderm development in zebrafish, discovering discrete sets of transcripts that are coincident with either notochord cell fate commitment or differentiation. Our studies reveal new regulators of notochord development and the sequential activation of distinct transcriptomes within a cell lineage by a single transcriptional factor and demonstrate how optically controlled chemical tools can dissect developmental processes with spatiotemporal precision.

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Figure 1: Notochord development is promoted by distinct Ntla transcriptomes.
Figure 2: Embryonic expression of Ntla-dependent genes.
Figure 3: Embryonic function of Ntla-dependent genes.
Figure 4: Temporal dynamics of Ntla-dependent mesoderm development.

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Acknowledgements

We thank S. Amacher and A. Garnett for helpful discussions, M. Halpern (Carnegie Institution) for providing ntla and flh cDNA, W. Talbot (Stanford University) for pax2a cDNA, J. Mich and X. Ouyang (both from Stanford University) for sharing in situ hybridization probes and C. Crumpton for technical assistance with FACS. This work was supported by funding from the US National Institutes of Health (R01 GM072600, R01 GM087292 and DP1 OD003792) and the March of Dimes Foundation (1-FY-08-433).

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  1. Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA

    Ilya A Shestopalov, Cameron L W Pitt & James K Chen

Authors
  1. Ilya A Shestopalov
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  2. Cameron L W Pitt
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Contributions

J.K.C. and I.A.S. conceived the study; J.K.C. directed its execution; I.A.S. and C.L.W.P. designed, conducted and interpreted the experiments; and J.K.C. and I.A.S. wrote the manuscript with contributions from C.L.W.P.

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Correspondence to James K Chen.

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The authors declare no competing financial interests.

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Shestopalov, I., Pitt, C. & Chen, J. Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development. Nat Chem Biol 8, 270–276 (2012). https://doi.org/10.1038/nchembio.772

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