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

Mahony S, Mazzoni EO, McCuine S, Young RA, Wichterle H, Gifford DK - Genome Biol. (2011)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

ABSTRACT

Background: 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.

Results: 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.

Conclusions: 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.

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ChIP-seq data improves motif specificity. The true positive and additional prediction rates are shown when predicting post-RA RAR binding sites by ranking sites according to motif similarity or when combining motif information with various other data sources (see Materials and methods).
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Figure 6: ChIP-seq data improves motif specificity. The true positive and additional prediction rates are shown when predicting post-RA RAR binding sites by ranking sites according to motif similarity or when combining motif information with various other data sources (see Materials and methods).

Mentions: The observed relationships between RAR binding and earlier binding events suggest that TF binding information from ES cells can be used to predict where signaling TFs will bind in a proximal developmental state. Predicting if a motif sequence will be bound based on motif similarity alone leads to high rates of additional predictions (Figure 6) [44]; for a motif similarity threshold with which we can correctly predict 500 post-RA bound RAREs, we also predict that approximately 65,000 additional sites should be bound. Recent reports demonstrate the use of co-temporal histone modification ChIP-seq data for predicting TF binding to motif sequences [14,16,45]. We can similarly combine the motif-similarity score with a score based on the sum of normalized read counts from ES cell TF ChIP-seq experiments in 500-bp windows around the sites (see Materials and methods). As shown in Figure 6, this combined score significantly decreases the rate of additional predictions for a given true-positive rate. Using the combined motif and ES cell TF score, we reduce the number of additional predictions 85% (to approximately 9,600) while correctly predicting 500 bound RAREs. We find that ES cell TF binding data outperforms conservation, ES cell p300 ChIP-seq data, and ES cell H3K4 methylation data in predicting which RARE motifs will be bound (Figure 6).


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

Mahony S, Mazzoni EO, McCuine S, Young RA, Wichterle H, Gifford DK - Genome Biol. (2011)

ChIP-seq data improves motif specificity. The true positive and additional prediction rates are shown when predicting post-RA RAR binding sites by ranking sites according to motif similarity or when combining motif information with various other data sources (see Materials and methods).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091300&req=5

Figure 6: ChIP-seq data improves motif specificity. The true positive and additional prediction rates are shown when predicting post-RA RAR binding sites by ranking sites according to motif similarity or when combining motif information with various other data sources (see Materials and methods).
Mentions: The observed relationships between RAR binding and earlier binding events suggest that TF binding information from ES cells can be used to predict where signaling TFs will bind in a proximal developmental state. Predicting if a motif sequence will be bound based on motif similarity alone leads to high rates of additional predictions (Figure 6) [44]; for a motif similarity threshold with which we can correctly predict 500 post-RA bound RAREs, we also predict that approximately 65,000 additional sites should be bound. Recent reports demonstrate the use of co-temporal histone modification ChIP-seq data for predicting TF binding to motif sequences [14,16,45]. We can similarly combine the motif-similarity score with a score based on the sum of normalized read counts from ES cell TF ChIP-seq experiments in 500-bp windows around the sites (see Materials and methods). As shown in Figure 6, this combined score significantly decreases the rate of additional predictions for a given true-positive rate. Using the combined motif and ES cell TF score, we reduce the number of additional predictions 85% (to approximately 9,600) while correctly predicting 500 bound RAREs. We find that ES cell TF binding data outperforms conservation, ES cell p300 ChIP-seq data, and ES cell H3K4 methylation data in predicting which RARE motifs will be bound (Figure 6).

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

ABSTRACT

Background: 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.

Results: 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.

Conclusions: 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.

Show MeSH