Retinoic Acid Receptors Recognize the Mouse Genome through Binding Elements with Diverse Spacing and Topology
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Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) and bind to RA response elements (RAREs) in the regulatory regions of their target genes. Although previous studies on limited sets of RA-regulated genes have defined canonical RAREs as direct repeats of the consensus RGKTCA separated by 1, 2, or 5 nucleotides (DR1, DR2, DR5), we show that in mouse embryoid bodies or F9 embryonal carcinoma cells, RARs occupy a large repertoire of sites with DR0, DR8, and IR0 (inverted repeat 0) elements. Recombinant RAR-RXR binds these non-canonical spacings in vitro with comparable affinities to DR2 and DR5. Most DR8 elements comprise three half-sites with DR2 and DR0 spacings. This specific half-site organization constitutes a previously unrecognized but frequent signature of RAR binding elements. In functional assays, DR8 and IR0 elements act as independent RAREs, whereas DR0 does not. Our results reveal an unexpected diversity in the spacing and topology of binding elements for the RAR-RXR heterodimer. The differential ability of RAR-RXR bound to DR0 compared to DR2, DR5, and DR8 to mediate RA-dependent transcriptional activation indicates that half-site spacing allosterically regulates RAR function.
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Recent genome-wide ChIP-seq technology allowed the identification of new RAR-binding loci and expanded the repertoire of potential high-affinity response elements.
“Most interestingly, the recent genome wide ChIP-seq (chromatin immunoprecipitation coupled with deep sequencing) technology allowed the identifi cation of new RAR-binding loci and expanded the repertoire of potential high-affi nity response elements (80)(81)(82).”
From Vitamin A and retinoid signaling: genomic and nongenomic effects (2013) · cites this paper as [81]
RARs can occupy a larger repertoire of sites with noncanonical IR0, DR0, and DR8 spacing, most DR8 elements comprising three half-sites with DR2 and DR0 spacing.
“They also revealed that RARs can occupy a larger repertoire of sites with noncanonical IR0 (inverted repeats), DR0, and DR8 spacing, most DR8 elements comprising three half-sites with DR2 and DR0 spacing ( 81 ) ( Fig. 3B ).”
From Vitamin A and retinoid signaling: genomic and nongenomic effects (2013) · cites this paper as [81]
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- Authors
- Moutier, E., Ye, T., Choukrallah, M.-A., Urban, S., Osz, J., Chatagnon, A., Delacroix, L., Langer, D., Rochel, N., Moras, D., Benoit, G., & Davidson, I.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Friedrich Miescher Institute (CH)
- Lyon 1 Université (FR)
- University of Liège (BE)
- Corresponding author
- Davidson, Irwin
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2012-07
- Volume
- 287
- Issue
- 31
- Pages
- 26328-26341
- ISSN
- 0021-9258 (ISSN-L)
- PMC
- PMC3406717
- OpenAlex
- W2149216452
- Cited by
- 163
- References
- 51
- Citations by year
- 2026: 7 · 2025: 5 · 2024: 9 · 2023: 6 · 2022: 13 · 2021: 15 · 2020: 14 · 2019: 11 · 2018: 9 · 2017: 10 · 2016: 14 · 2015: 21 · 2014: 18 · 2013: 10 · 2012: 1
- FWCI
- 6.43
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by)
- ORBi (University of Liège) (submittedVersion, other-oa)
- univOAK (4 institutions : Université de Strasbourg, Université de Haute Alsace, INSA Strasbourg, Bibliothèque Nationale et Universitaire de Strasbourg) (submittedVersion)
- Funders
- European Commission
- Agence Nationale de la Recherche
- Institut National de la Santé et de la Recherche Médicale
- Université de Strasbourg
- Centre National de la Recherche Scientifique
- Institut National Du Cancer
- Institute of Genetics
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Retinoids in leukemia and cellular processes
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Peroxisome Proliferator-Activated Receptors
- Keywords
- retinoic acid receptor, retinoid X receptor, retinoic acid response element, inverted repeats, RAR/RXR heterodimers, transcriptional activation, allosteric regulation, mouse genome, embryonal carcinoma cells, embryoid bodies
- MeSH terms
- Animals, Base Sequence, Binding Sites, Binding, Competitive, Cells, Cultured, Protein Binding, Repetitive Sequences, Nucleic Acid, Transcription, Genetic, Consensus Sequence, Genome, Titrimetry, Sequence Analysis, DNA, Receptors, Retinoic Acid, Coculture Techniques, Response Elements, Electrophoretic Mobility Shift Assay, Chromatin Immunoprecipitation, Retinoid X Receptors, Mice, Embryoid Bodies
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