Retinoic acid receptors recognize the mouse genome through binding elements with diverse spacing and topology.
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.
Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, 1 Rue Laurent Fries, 67404 Illkirch Cédex, France.
Emmanuel
E
Moutier
Tao
T
Ye
Mohamed-Amin
MA
Choukrallah
Sylvia
S
Urban
Judit
J
Osz
Amandine
A
Chatagnon
Laurence
L
Delacroix
Diana
D
Langer
Natacha
N
Rochel
Dino
D
Moras
Gerard
G
Benoit
Irwin
I
Davidson
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation; D018920:Coculture Techniques; D016384:Consensus Sequence; D024202:Electrophoretic Mobility Shift Assay; D058732:Embryoid Bodies / Q000378:metabolism; D016678:Genome; D051379:Mice; D011485:Protein Binding; D018168:Receptors, Retinoic Acid / Q000737:chemistry / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid; D020218:Response Elements; D047488:Retinoid X Receptors / Q000737:chemistry / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D017186:Titrimetry; D014158:Transcription, Genetic
D018168:Receptors, Retinoic Acid; D047488:Retinoid X Receptors