Open Access Open Badges Research

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

Shaun Mahony1, Esteban O Mazzoni2, Scott McCuine3, Richard A Young3, Hynek Wichterle2 and David K Gifford1*

  • * Corresponding author: David K Gifford

  • † Equal contributors

Author Affiliations

1 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA

2 Departments of Pathology, Neurology, and Neuroscience, Center for Motor Neuron Biology and Disease, Columbia University Medical Center, 630 West 168th St, New York, NY 10032, USA

3 Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA

For all author emails, please log on.

Genome Biology 2011, 12:R2  doi:10.1186/gb-2011-12-1-r2

Published: 13 January 2011



Among its many roles in development, retinoic acid determines the anterior-posterior identity of differentiating motor neurons by activating retinoic acid receptor (RAR)-mediated transcription. RAR is thought to bind the genome constitutively, and only induce transcription in the presence of the retinoid ligand. However, little is known about where RAR binds to the genome or how it selects target sites.


We tested the constitutive RAR binding model using the retinoic acid-driven differentiation of mouse embryonic stem cells into differentiated motor neurons. We find that retinoic acid treatment results in widespread changes in RAR genomic binding, including novel binding to genes directly responsible for anterior-posterior specification, as well as the subsequent recruitment of the basal polymerase machinery. Finally, we discovered that the binding of transcription factors at the embryonic stem cell stage can accurately predict where in the genome RAR binds after initial differentiation.


We have characterized a ligand-dependent shift in RAR genomic occupancy at the initiation of neurogenesis. Our data also suggest that enhancers active in pluripotent embryonic stem cells may be preselecting regions that will be activated by RAR during neuronal differentiation.