KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-Histone H3 (acetyl K27) - ChIP Grade	Abcam	ab4729, Lot: GR3374555-1
Anti-Histone H3 (mono methyl K4)	Abcam	ab8895, Lot: GR3407156-1
Anti-OTX2 (D7Y3J)	Cell Signaling Technology	mAb #11943, Lot#1
Anti-Nanog (A-11)	Santa Cruz Biotechnology	sc-374001, Lot#E0521
Anti-PAX7	DSHB	N/A
β-Actin (N-21)	Santa Cruz Biotechnology	sc-130656, Lot #C2515
MyoD (4H207)	Santa Cruz Biotechnology	sc-71629, Lot #G2012
MyoG (F5D)	Santa Cruz Biotechnology	sc-12732, Lot #A0620
Goat Anti Rabbit IgG-HRP	Azure biosystem	AC2114, Lot 210812-57
Goat Anti mouse IgG-HRP	Azure biosystem	AC2115, Lot 210204-50
Bacterial and virus strains
NEB® 5-alpha Competent E. coli (High Efficiency)	NEB	C2987H
One Shot™ TOP10 Chemically Competent E. coli	ThermoFisher scientific	C404010
Chemicals, peptides, and recombinant proteins
Knock-Out™ Serum Replacement	ThermoFisher	10828028
Recombinant Protein-Rspo3	R&D Biosystems	4120-RS-025
Leukemia inhibitory factor-LIF	Millipore	ESG1106
Recombinant Murine BMP4	Peprotech	315–27
BSA solution	Gibco	101020–021
LDN193189	Stemgent	04–0074
CHIRON99021	Stemgent	04-0004-02
Recombinant Murine FGF	Peprotech	450-33
Recombinant Murine IGF	Peprotech	250-19
Recombinant Mouse HGF	R&D Biosystems	2207-HG-2-025
Dynabeads Protein G	ThermoFisher Scientific	10004D
TRIzol Reagent	Thermo Fisher Scientific	15596018
Polybrene	Sigma	TR-1003-G
Protease Inhibitor	Roche	11836170001
Phase Lock Gel Heavy	5 PRIME	2302810
Chloroform	Sigma	67-66-3
10% SDS	Invitrogen	15553-027
Neurobasal Medium	Gibco	21103-049
DMEM/F12 (1:1)	Gibco	11320-033
Dimethyl sulfoxide	Sigma	276855
2-Mercaptoethanol	Sigma	M6250
Dulbecco’s Modified Eagle Medium (DMEM)	Gibco	12439-054
Pen Strep Glutamine (100x)	Gibco	10378-016
GlutaMAX (100x)	Gibco	35050-061
MEM NEAA	Gibco	11140-050
Sodium Pyruvate (100mM)	Gibco	11360-070
BSA Fraction V (7.5%)	Gibco	15260-037
Critical commercial assays
DNeasy Blood & Tissue Kits	Qiagen	69504
QIAprep Spin Miniprep Kit	Qiagen	27106
Lenti-X™ Concentrator	Clontech	631231
Lipofectamine 2000	Invitrogen	11668-019
Power SYBR Green PCR Master Mix	Thermo Fisher Scientific	4368708
PCR purification kit	Qiagen	28106
qScript™ cDNA Synthesis Kit	Quantabio	95047-100
Arima HiC kit	Arima	A510008GFP
Accel-NGSO 2S Plus DNA	SWIFT Bioscience	A160140 v00
NEBNext Ultra II DNA library prep kit	NEB	#E7645
NEBNext Ultra II RNA library preparation kit for Illumina	NEB	#E7490
Chromium Single Cell 3’ Library & Gel Bead Kit v3.1	10x Genomics	P/N 1000121
Deposited data
RNA-seq, ATAC-seq, H327ac and H3K4me1 ChIP-seq, HiC, Single cell RNA-seq, Single cell ATAC-seq, Multiome single nuclei ATAC and gene expression	This paper	GSE198730
Experimental models: Cell lines
HEK 293T cells	ATCC	CRL-1573
C2C12 cells	ATCC	GSC-6001G
ESC Pax3-GFP	Chal et al., 2015	N/A
ESC Pax3-GFP Del −3.5kb	This paper	N/A
ESC Pax3-GFP Del −3.5kb and −25kb	This paper	N/A
ESC Pax3-GFP Del En7	This paper	N/A
Oligonucleotides
sgRNA sequences	Table S4	N/A
RT q-PCR oligos	Table S4	N/A
PCR oligos	Table S4	N/A
Recombinant DNA
pSpCas9(BB)-2A-GFP (PX458)	Addgene	Plasmid #48138
pSpCas9(BB)-2A-GFP-gRNA1_−3.5kb	This paper	N/A
pSpCas9(BB)-2A-GFP-gRNA4_−3.5kb	This paper	N/A
pSpCas9(BB)-2A-GFP-gRNA1_−25kb	This paper	N/A
pSpCas9(BB)-2A-GFP-gRNA4_−25 kb	This paper	N/A
pSpCas9(BB)-2A-GFP-gRNA2_En7	This paper	N/A
pSpCas9(BB)-2A-GFP-gRNA4_En7	This paper	N/A
pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFP	Addgene	Plasmid #71237
pLV hU6-sgRNA_Pax7_promoter_ hUbC-dCas9-KRAB-T2a-GFP	This paper	N/A
pLV hU6-sgRNA_Pax7_−3.5kb_ hUbC-dCas9-KRAB-T2a-GFP	This paper	N/A
pLV hU6-sgRNA_Pax7_−25kb_ hUbC-dCas9-KRAB-T2a-GFP	This paper	N/A
pLV hU6-sgRNA_Pax7_ En7_ hUbC-dCas9-KRAB-T2a-GFP	This paper	N/A
psPAX2	Addgene	Plasmid ##12260
pMD2.G	Addgene	Plasmid #12259
pGL4.26[luc2/minP/Hygro]	Promega	#E8441
pGL4.26-Ctrl	This paper	N/A
pGL4.26-En7	This paper	N/A
Software and algorithms
BioRender		biorender.com
Prism Software, version 8	Graphpad Software	https://www.Graphpad.com
Metascape	Zhou et al. (2019)	https://metascape.org/gp/index.html#/main/step1
CellRanger ver. 3.1.0	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation
Cell Ranger ATAC v1.1.0	10x Genomics	https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
R	The R Project for Statistical Computing	https://www.r-project.org/
Seurat v4.1.0	Stuart et al., 2019	https://cran.r-project.org/web/packages/Seurat/index.html
Signac v1.5.0	Stuart et al., 2021	https://satijalab.org/signac
Harmony	Korsunsky et al., 2019	https://github.com/immunogenomics/harmony
Monocle3	Cao et al., 2019	https://cole-trapnell-lab.github.io/monocle3/
JASPAR 2020	Fornes et al. (2020)	https://bioconductor.org/packages/release/data/annotation/html/JASPAR2020.html
FBSTools	Tan and Lenhard (2016)	https://bioconductor.org/packages/release/bioc/html/TFBSTools.html
cellranger-arc version 2.0.0	10x Genomics	https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
Seurat ver. 4.1.0	Hao et al., 2021	https://satijalab.org/seurat/
Signac ver.1.5.0	Stuart et al., 2021	https://satijalab.org/signac/news/index.html
MACS 1.4.2	Zhang et al., 2008	https://libraries.io/pypi/MACS
Bowtie/1.1.1	Langmead et al., 2009	http://bowtie-bio.sourceforge.net/index.shtml
BedGraphToBigWig	Kent et al., 2010	https://www.encodeproject.org/software/bedgraphtobigwig/
Bedtools/2.29.2	Quinlan and Hall, 2010	https://bedtools.readthedocs.io/en/latest/content/installation.html
HOMER/4.11.1	Heinz et al., 2010	http://homer.ucsd.edu/homer/
Partek Genomics Suite 7.18	Partek Inc.	https://www.partek.com/partek-genomics-suite/
TopHat 2.1.1	Trapnell et al., 2009	https://ccb.jhu.edu/software/tophat/index.shtml
Trim Galore (version 0.6.6)	N/A	https://github.com/FelixKrueger/TrimGalore
Bcl2fastq/2.20.0	Illumina	https://emea.support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html
Juicer 1.6	Durand et al., 2016	https://github.com/aidenlab/juicer/releases
HiCExplorer3.6	Wolff et al., 2020	https://hicexplorer.readthedocs.io/en/latest/
HOMER	Heinz et al., 2010	http://homer.ucsd.edu/homer/
Custom scripts	This paper	https://doi.org/10.5281/zenodo.6889278