Enhancer decommissioning by lsd1 during embryonic stem cell differentiation

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. Access through your institution Buy or subscribe This

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DEMETHYLASE-INDEPENDENT ROLES OF LSD1 IN REGULATING ENHANCERS AND CELL FATE TRANSITION Article Open access 22 August 2023 HISTONE H3.3 LYSINE 9 AND 27 CONTROL REPRESSIVE CHROMATIN AT CRYPTIC

ENHANCERS AND BIVALENT PROMOTERS Article Open access 30 August 2024 COOPERATIVE ROLE OF LSD1 AND CHD7 IN REGULATING DIFFERENTIATION OF MOUSE EMBRYONIC STEM CELLS Article Open access 18

November 2024 ACCESSION CODES PRIMARY ACCESSIONS GENE EXPRESSION OMNIBUS * GSE27844 DATA DEPOSITS ChIP-Seq and GeneChip expression data are deposited in the Gene Expression Omnibus under

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Download references 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 Author notes * Warren A. Whyte and Steve Bilodeau: These authors contributed equally to this work.

AUTHORS AND AFFILIATIONS * Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, 02142, Massachusetts, USA Warren A. Whyte, Steve Bilodeau, David A. Orlando, Heather A.

Hoke, Garrett M. Frampton & Richard A. Young * Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA Warren A. Whyte, Heather A. Hoke, 

Garrett M. Frampton & Richard A. Young * Department of Molecular Biology, Adolf-Butenandt Institut, Ludwig-Maximilians-Universität München, 80336 Munich, Germany, Charles T. Foster *

Department of Biochemistry, University of Leicester, Leicester LE1 9HN, UK, Charles T. Foster & Shaun M. Cowley Authors * Warren A. Whyte View author publications You can also search for

this author inPubMed Google Scholar * Steve Bilodeau View author publications You can also search for this author inPubMed Google Scholar * David A. Orlando View author publications You can

also search for this author inPubMed Google Scholar * Heather A. Hoke View author publications You can also search for this author inPubMed Google Scholar * Garrett M. Frampton View author

publications You can also search for this author inPubMed Google Scholar * Charles T. Foster View author publications You can also search for this author inPubMed Google Scholar * Shaun M.

Cowley View author publications You can also search for this author inPubMed Google Scholar * Richard A. Young View author publications You can also search for this author inPubMed Google

Scholar 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. ETHICS DECLARATIONS

COMPETING INTERESTS 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) POWERPOINT SLIDES POWERPOINT SLIDE FOR FIG. 1 POWERPOINT SLIDE FOR FIG. 2 POWERPOINT SLIDE FOR FIG. 3 POWERPOINT SLIDE FOR FIG. 4 RIGHTS AND PERMISSIONS

Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE 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 Download citation * Received: 14 October 2010 * Accepted: 16 December 2011 * Published: 01 February 2012 * Issue Date: 09

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