RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements.
Bottom Line: We show here that this dual regulation is associated with RAR/RXR genomic redistribution during the differentiation process.In-depth analysis of RAR/RXR binding sites occupancy dynamics and composition show that in undifferentiated cells, RAR/RXR interact with genomic regions characterized by binding of pluripotency-associated factors and high prevalence of the non-canonical DR0-containing RA response element.Our data offer an unprecedentedly detailed view on the action of RA in triggering pluripotent cell differentiation and demonstrate that RAR/RXR action is mediated via two different sets of regulatory regions tightly associated with cell differentiation status.
Affiliation: Université de Lyon, Université Claude Bernard Lyon1, CGphiMC UMR CNRS 5534, 69622 Villeurbanne, France.Show MeSH
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Mentions: We next investigated whether the RAR/RXR occupancy profiles identified by clustering (Figure 2D) were specifically associated with molecular features such as the presence of RARE motifs or transcription factor binding sites experimentally identified in F9 and ES cells. To this end, we performed Fisher's exact tests to detect features whose prevalence varied significantly in one cluster compared to all other RAR/RXR binding regions. The results are presented in Figure 5A and Supplementary Figure S8, where red (resp. green) bars indicate features that are significantly enriched (resp. depleted) in the cluster. First we observe that each binding pattern is characterized by a unique combination of molecular features. For instance, the regions assigned to clusters exhibiting high average occupancy in untreated F9 cells are characterized by their association with ESRRB and POU5F1 binding events (clusters B, D and F in Figure 2D and Supplementary Figure S3 panel A). Also, all clusters exhibiting a maximum occupancy in the early phase of the RA-induced PrE differentiation process, namely clusters A–D, are associated with a higher prevalence of DR0 type motif. Among these four clusters, subtle binding pattern variations appear coupled with specific core pluripotency factor binding sites layouts and are independent or negatively associated with PrE differentiation-associated transcription factor like SOX17. Cluster A, which exhibits only a transient occupancy at 2 h after RA stimulation, is only associated with DR0 enrichment while clusters B, C and D are also associated with NR5A2 and SMAD1 binding but differ in their association with SOX2, NANOG, POU5F1, TCF3 and PRDM14 binding events and the presence of DR2 motif.
Affiliation: Université de Lyon, Université Claude Bernard Lyon1, CGphiMC UMR CNRS 5534, 69622 Villeurbanne, France.