KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal MYOD	Santa Cruz	M-318
Rabbit polyclonal H3K27Ac	Active Motif
Mouse monoclonal MYOD	BD Bioscience	554130
Mouse monoclonal MyHC	DSHB	MF20
Goat anti-mouse IgG, Fc subclass 1 specific	Jackson Immuno	NC0469362
Goat anti-mouse IgG, Fc subclass 2b specific	Jackson Immuno	NC0266980
Mouse monoclonal GAPDH	Abcam	ab9485
Anti-bActin-HRP	Abcam	ab20272
Anti-human TNNT2	Abcam	ab10214
Bacterial and Virus Strains
Biological Samples
Chemicals, Peptides, and Recombinant Proteins
Doxycycline	Sigma-Aldrich	D3072–1 ML
Puromycin dihydrochloride	MP Biomedicals	ICN10055210
ITS	Sigma-Aldrich	I2146
Hoechst 33258	Life Technologies	H3569
PMSF	Sigma-Aldrich	93482
Protease inhibitors	Roche	11697498001
DpnII	NEB	R0543
T4 DNA Ligase	NEB	M0202L
Proteinase K	NEB	P8107
BSA	NEB	B9000
biotin-14-dATP	Life Technology	19524–016
Critical Commercial Assays
Neon Transfection System	Invitrogen	MPK5000, MPK10025
BCA Protein Assay Kit	Invitrogen	23235
TruSeq Stranded mRNA Library Prep Kit set A	Illumina	RS-122–2101
Deposited Data
RNA-seq, ChIP-seq, Hi-C	This paper	GEO: GSE98530
Other ChIP-seq data	(Consortium, 2012; Jin et al., 2013; Sala et al., 2019; Yue et al., 2014)	GEO: GSM935404, GSM733762, GSM733783, GSM1055818, GSM915188, GSM733666, GSM733755, GSM915165, GSE128527
Other RNA-seq data	(Chronis et al., 2017)	GEO: GSM2417196, GSM2417197, GSM2417198, GSM2417204, GSM2417203
Experimental Models: Cell Lines
IMR90	Coriell	I90–83
C2C12	ATCC	CRL-1772
Experimental Models: Organisms/Strains
Oligonucleotides
PCR primers - see list at the end of STAR Methods	This paper	N/A
siScr	Dharmacon	D-001210-01-05
siMyod	Ambion	s232596
Recombinant DNA
Helper plasmid	Provided by Dr. Alessandro Rosa	N/A
epB-Puro-TT plasmid EMPTY	Provided by Dr. Alessandro Rosa	N/A
epB-Puro-TT plasmid EMPTY mouse Myod1 cDNA	Provided by Dr. Alessandro Rosa	N/A
Software and Algorithms
TopHat2.1.1	(Kim et al., 2013)	https://ccb.ihu.edu/software/tophat/index.shtml
HTSeq-0.6.1	(Anders et al., 2015)	https://htseq.readthedocs.io/en/release0.11.1/
DESeq2	(Love et al., 2014)	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Ingenuity Pathway Analysis	Qiagen	https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/
Bowtie2–2.0.5/bowtie2	(Langmead and Salzberg, 2012)	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Samtools1.3	(Li et al., 2009)	http://samtools.sourceforge.net/
Macs2v2.1.1	(Zhang et al., 2008)	http://liulab.dfci.harvard.edu/MACS/
Bedtoolsv2.26.0	(Quinlan and Hall, 2010)	http://bedtools.readthedocs.io/en/latest/
HiCPro-v2.7.7	(Servant et al., 2015)	https://github.com/nservant/HiC-Pro
HiTC	(Servant et al., 2012)	https://bioconductor.org/packages/release/bioc/html/HiTC.html
HiCPlotter	(Akdemir and Chin, 2015)	https://github.com/kcakdemir/HiCPlotter
Armatus	(Filippova et al., 2014)	https://www.cs.cmu.edu/~ckingsf/software/armatus/
DiffHic	(Lun and Smyth, 2015)	https://bioconductor.org/packages/release/bioc/html/diffHic.html
Jaspar	(Mathelier et al., 2014)	http://jaspar.genereg.net/
MEME	(Bailey et al., 2009)	http://meme-suite.org/tools/meme-chip
HOMER	(Heinz et al., 2010)	http://homer.ucsd.edu/homer/
DNA FISH analysis	This paper	DOI: http://dx.doi.org/10.17632/tvb7yvpr4s.1#file-b6ac28c9-29d2-48ae-9658-ecf953457b98 DOI: http://dx.doi.org/10.17632/tvb7yvpr4s.1#file-01a31ffd-8040-41cc-9b0e-98d9a4ac9c88
Circular permutation	This paper	DOI: http://dx.doi.org/10.17632/rvzzpsh6vg.2#file-96dfb6d0-d6e3-4a42-ac13-a78fb2346b27
Other
Olympus IX71 microscope
RPI spinning disk microscope