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Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

An Author Correction to this article was published on 12 September 2018

Abstract

Transcription factors and chromatin modifiers are important in the programming and reprogramming of cellular states during development1,2. Transcription factors bind to enhancer elements and recruit coactivators and chromatin-modifying enzymes to facilitate transcription initiation3,4. During differentiation a subset of these enhancers must be silenced, but the mechanisms underlying enhancer silencing are poorly understood. Here we show that the histone demethylase lysine-specific demethylase 1 (LSD1; ref. 5), which demethylates histone H3 on Lys 4 or Lys 9 (H3K4/K9), is essential in decommissioning enhancers during the differentiation of mouse embryonic stem cells (ESCs). LSD1 occupies enhancers of active genes that are critical for control of the state of ESCs. However, LSD1 is not essential for the maintenance of ESC identity. Instead, ESCs lacking LSD1 activity fail to differentiate fully, and ESC-specific enhancers fail to undergo the histone demethylation events associated with differentiation. At active enhancers, LSD1 is a component of the NuRD (nucleosome remodelling and histone deacetylase) complex, which contains additional subunits that are necessary for ESC differentiation. We propose that the LSD1–NuRD complex decommissions enhancers of the pluripotency program during differentiation, which is essential for the complete shutdown of the ESC gene expression program and the transition to new cell states.

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Figure 1: LSD1 is associated with enhancer and core promoter regions of active genes in ESCs.
Figure 2: LSD1 inhibition results in incomplete silencing of ESC genes during differentiation.
Figure 3: LSD1 is associated with a NuRD complex at active enhancers in ESCs.
Figure 4: LSD1 is required for H3K4me1 removal at ESC enhancers.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

ChIP-Seq and GeneChip expression data are deposited in the Gene Expression Omnibus under accession number GSE27844.

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Acknowledgements

We thank J. Lovén, M. H. Kagey, J. Dowen, A. C. Mullen, A. Sigova, P. B. Rahl, T. Lee and members of Y. Shi’s laboratory for experimental assistance, reagents and helpful discussions; and J.-A. Kwon, V. Dhanapal, J. Love, S. Gupta, T. Volkert, W. Salmon and N. Watson for assistance with ChIP-Seq, expression arrays and immunofluorescence imaging acquisition. This work was supported by a Canadian Institutes of Health Research Fellowship (S.B.), a Career Development Award from the Medical Research Council (S.M.C.), and by National Institutes of Health grants HG002668 and NS055923 (R.Y.).

Author information

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Authors

Contributions

W.A.W., S.B., H.A.H., C.T.F., S.M.C and R.A.Y. designed, conducted and interpreted the ChIP-Seq, immunofluorescence and expression experiments. W.A.W., D.A.O. and G.M.F. performed data analysis. The manuscript was written by S.B., W.A.W. D.A.O., H.A.H., G.M.F. and R.A.Y.

Corresponding author

Correspondence to Richard A. Young.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-13 with legends. (PDF 2530 kb)

Supplementary Information

This file contains a Supplementary Discussion, Supplementary Experimental Procedures (see Contents for more information) and Supplementary References. (PDF 307 kb)

Supplementary Tables 1-5

This zipped file contains the following: Supplementary Table 1- Summary of occupied genes and regions; Supplementary Table 2 - Summary of LSD1 occupancy at active and poised enhancers; Supplementary Table 3 - Gene expression changes 48 hours after Oct4 repression in ZHBTc4 DMSO (control)- and TCP-treated cells; Supplementary Table 4 Genes co-occupied by LSD1 and REST; Supplementary Table 5 - Enhancer decommissioning 48 hours after Oct4 depletion in ZHBTc4 DMSO (control)- and TCP-treated cells. (ZIP 27599 kb)

Supplementary Data 1

This file contains compressed ChIP-Seq data in WIG format for upload into the UCSC genome browser. This file contains data for: mES_CoREST_min1.0.WIG; mES_HDAC1_combn_min1.0.WIG; mES_HDAC2_combn_min1.0.WIG; mES_LSD1_min1.0.WIG; mES_Med1_min1.0.WIG; mES_Mi2(combined)_min1.0.WIG; mES_Nanog_min1.0.WIG; mES_Oct4_min1.0.WIG; mES_p300_min1.0.WIG; mES_Pol2_min1.0.WIG; mES_REST_min1.0.WIG; mES_Sox2_min1.0.WIG; mES_Suz12_min1.0.WIG; mES_TBP_min1.0.WIG; mES_WCE_min1.0.WIG. The first track for each data set contains the ChIP-Seq density across the genome in 25bp bins. The minimum ChIP-Seq density shown in these files is 1.0 reads per million total reads. Subsequent tracks identify genomic regions identified as enriched at a p-value threshold of 10-9. (ZIP 13280 kb)

Supplementary Data 2

This file contains compressed ChIP-Seq data in WIG format for upload into the UCSC genome browser. This file contains data for: mES_H3K36me3_min1.0.WIG; mES_H3K4me1_min1.0.WIG; mES_H3K4me3_min1.0.WIG; mES_H3K79me2_min1.0.WIG. The first track for each data set contains the ChIP-Seq density across the genome in 25bp bins. The minimum ChIP-Seq density shown in these files is 1.0 reads per million total reads. Subsequent tracks identify genomic regions identified as enriched at a p-value threshold of 10-9. (ZIP 16300 kb)

Supplementary Data 3

This file contains compressed ChIP-Seq data in WIG format for upload into the UCSC genome browser. This file contains data for: DMSO_0HR_H3K4me1.WIG; WCE_DMSO_48HR_min1.0.WIG; DMSO_48HR_H3K4me1.WIG; TCP_48HR_H3K4me1.WIG; WCE_TCP_48HR_min1.0.WIG. The first track for each data set contains the ChIP-Seq density across the genome in 25bp bins. The minimum ChIP-Seq density shown in these files is 1.0 normalized read per million total reads. Subsequent tracks identify genomic regions identified as enriched at a p-value threshold of 10-9. (ZIP 13821 kb)

Supplementary Data 4

This file contains compressed ChIP-Seq data in WIG format for upload into the UCSC genome browser. This file contains data for: WCE_DMSO_min1.0.WIG; mES_DMSO_H3K27ac.WIG; mES_DMSO_H3K4me1.WIG; mES_C646_H3K27ac.WIG; mES_C646_H3K4me1.WIG. The first track for each data set contains the ChIP-Seq density across the genome in 25bp bins. The minimum ChIP-Seq density shown in these files is 1.0 reads per million total reads. Subsequent tracks identify genomic regions identified as enriched at a p-value threshold of 10-9. (ZIP 20243 kb)

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Whyte, W., Bilodeau, S., Orlando, D. et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 482, 221–225 (2012). https://doi.org/10.1038/nature10805

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