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esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function

Abstract

Signalling by the cytokine LIF and its downstream transcription factor, STAT3, prevents differentiation of pluripotent embryonic stem cells (ESCs). This contrasts with most cell types where STAT3 signalling induces differentiation. We find that STAT3 binding across the pluripotent genome is dependent on Brg1, the ATPase subunit of a specialized chromatin remodelling complex (esBAF) found in ESCs. Brg1 is required to establish chromatin accessibility at STAT3 binding targets, preparing these sites to respond to LIF signalling. Brg1 deletion leads to rapid polycomb (PcG) binding and H3K27me3-mediated silencing of many Brg1-activated targets genome wide, including the target genes of the LIF signalling pathway. Hence, one crucial role of Brg1 in ESCs involves its ability to potentiate LIF signalling by opposing PcG. Contrary to expectations, Brg1 also facilitates PcG function at classical PcG targets, including all four Hox loci, reinforcing their repression in ESCs. Therefore, esBAF does not simply antagonize PcG. Rather, the two chromatin regulators act both antagonistically and synergistically with the common goal of supporting pluripotency.

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Figure 1: esBAF is dedicated to the LIF/STAT3 signalling pathway.
Figure 2: STAT3 binding genome wide is Brg1 dependent.
Figure 3: Brg1 is essential to enhance accessibility at STAT3 target genes.
Figure 4: Brg1-deletion leads to genome-wide increased H3K27me3 at Brg1-activated genes and reduced H3K27me3 at Brg1-repressed genes.
Figure 5: Synergistic interaction between Brg1 and PRC2 at Hox genes.
Figure 6: Increased levels of H3K27me3 at Brg1 and STAT3 co-activated genes in Brg1-knockout ESCs.
Figure 7: Opposing activity and localization of esBAF and PRC2 complexes.
Figure 8: esBAF both antagonizes and synergizes with PRC2 to promote pluripotency.

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Acknowledgements

We thank G. Bejerano, A. Wenger, D. Bristor and C. McLean for their computational expertise and assistance, NIEHS (NIH) core facility for their advice and expertise in carrying out ChIP-seq, and P. Wade and G. Hu for providing useful comments. We thank J. Wu and L. Chen for assistance in the derivation of Brg1cond ESCs. This work was financially supported by grants from the HHMI and NIH grants R01NS46789, R01AI60037 and R01HD55391 to G.R.C., and the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences (1ZIAES102625-02) to R.J. L.H. and W.Q.H. are financially supported by A*STAR (Singapore); E.L.M. and J.L.R. are financially supported by the National Science Foundation.

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L.H., R.J. and G.R.C. contributed to experimental design, execution and data analysis. R.J. carried out ChIP-seq and all related data analysis. J.L.R. and W.Q.H. contributed to experimental execution. E.L.M. carried out data analysis. L.H. and G.R.C. wrote the manuscript.

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Correspondence to Raja Jothi or Gerald R. Crabtree.

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Ho, L., Miller, E., Ronan, J. et al. esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. Nat Cell Biol 13, 903–913 (2011). https://doi.org/10.1038/ncb2285

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