REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
YY1	Santa Cruz	Cat# sc-1703X
YY1	Abcam	Cat# ab109237
CTCF	EMD-Millipore	Cat# 07-729
YY1	Abcam	Cat# ab199998
Beta-Actin	Sigma	Cat# A5441
HA-HRP	Cell Signaling	Cat# 2999
HA	Abcam	Cat# ab9110
FLAG	Sigma	Cat# F7425
FLAG-HRP	Sigma	Cat# A8592
Rabbit IgG	Millipore	Cat# 12-370
H3K27ac	Abcam	Cat# ab4729
H3K27ac	Active Motif	Cat# 39133
OCT3/4	Santa Cruz	Cat# sc-5279
Cas9	Cell Signaling	Cat# 14697
TUJI	BioLegend	Cat# 801201
GFAP	Dako	Cat# Z0344
GATA4	Abcam	Cat# ab84593
Bacterial and Virus Strains
BL21-CodonPlus (DE3)-RIL cells	Stratagene	Cat# 230245
Chemicals, Peptides, and Recombinant Proteins
Human Recombinant YY1	This study	N/A
dTAG-47 compound	This study	N/A
Critical Commercial Assays
LightShift Chemiluminescent EMSA Kit	Thermo Scientific	Cat# 20148
TruSeq DNA Sample Preparation v2 Kit	Illumina	Cat# RS-122-2001
Nextera DNA Library Preparation Kit	Illumina	Cat# FC-121-1030
Expand Long Template Polymerase	Roche	Cat# 11759060001
TruSeq Stranded mRNA Library Prep Kit	Illumina	Cat# RS-122-2101
Pierce BCA Assay	Thermo Scientific	Cat# 23225
Lipofectamine 3000 Transfection Reagent	Life Technologies	Cat# L3000001
Power SYBR Green Master Mix	Applied Biosystems	Cat# 4368577
TaqMan Universal PCR Master Mix	Applied Biosystems	Cat# 4304437
Deposited Data
Raw and analyzed data	This study	GEO: GSE99521
See Table S4 for deposited genomics datasets	N/A	N/A
mES ChIP-MS data	Ji et al., 2015	http://www.pnas.org/content/suppl/2015/03/06/1502971112.DCSupplemental/pnas.1502971112.st01.xls
CRISPR cell essentiality screen	Wang et al., 2015	http://science.sciencemag.org/content/sci/suppl/2015/10/14/science.aac7041.DC1/aac7041_SM_Table_S3.xlsx
GTEx gene expression values	Genotype-Tissue Expression Project	https://www.gtexportal.org/home/
Mouse reference genome, NCBI build 37, NCBI37/mm9	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/grc/mouse
Human reference genome, NCBI build 37, GRCh37/hg19	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/grc/human
Super-enhancer and typical enhancer constituents	Whyte et al., 2013	http://www.cell.com/cms/attachment/2031389007/2048455341/mmc1.zip
Experimental Models: Cell Lines
V6.5 Murine Embryonic Stem Cells	R. Jaenisch	N/A
V6.5 mESC YY1-dTAG knock-in line	This study	N/A
HCT116	ATCC	Cat# CCL-247
Jurkat	ATCC	Cat# TIB-152
K562	ATCC	Cat# CCL-243
HEK293T	ATCC	Cat# CRL-3216
Oligonucleotides
See Table S5	N/A	N/A
Recombinant DNA
His6-YY1	Shi Y.	N/A
Cas9-GFP	Jaenisch R.	N/A
pAW62.YY1.FKBP.knock-in.mCherry	This study	Deposited to Addgene Cat# 104370
pAW63.YY1.FKBP.knock-in.BFP	This study	Deposited to Addgene Cat# 104371
pAW91.dCas9	This study	Deposited to Addgene Cat# 104372
pAW90.dCas9-YY1	This study	Deposited to Addgene Cat# 104373
pAW12.lentiguide.GFP	This study	Deposited to Addgene Cat# 104374
pAW13.lentiguide.mCherry	This study	Deposited to Addgene Cat# 104375
pAW49.pUC19.YY1	This study	Deposited to Addgene Cat# 104376
pAW79.pUC19.noYY1	This study	Deposited to Addgene Cat# 104377
Software and Algorithms
Bowtie	Langmead et al., 2009	http://bowtie-bio.sourceforge.net/index.shtml
Samtools	Li et al., 2009	http://samtools.sourceforge.net
MACS	Zhang et al., 2008	http://liulab.dfci.harvard.edu/MACS/index.html
BEDTools	Quinlan and Hall, 2010	http://bedtools.readthedocs.io/en/latest/
bamToGFF	Bradner Lab	https://github.com/BradnerLab/pipeline
UCSC Genome Browser	Kent et al., 2002	http://genome.ucsc.edu/cgi-bin/hgGateway
Kallisto	Bray et al., 2016	https://pachterlab.github.io/kallisto/
Deseq2	Love et al., 2014	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
PANTHER GO	Mi et al., 2013, 2017	http://pantherdb.org
Origami	This study	https://github.com/younglab/origami
Cell Ranger	10X Genomics	https://www.10xgenomics.com
Loupe Cell Browser	10X Genomics	https://www.10xgenomics.com
Other
Processed insulated neighborhood calls in mouse and human stem cells.	Hnisz et al., 2016a	http://younglab/wi.mit.edu/insulatedneighborhoods.html