REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-β-Tubulin	Sigma-Aldrich	Cat# T0198; RRID:AB_477556
Mouse monoclonal anti-Actin	Sigma-Aldrich	Cat# A1978; RRID:AB_476692
Histone H3	Abcam	Cat# ab1791; RRID:AB_302613
Rabbit monoclonal anti-CTCF	Abcam	Cat# ab188408; RRID:AB_2819212
Rabbit monoclonal anti-CTCF	Cell Signalling Technology	Cat# 3418; RRID:AB_2086791
Rabbit polyclonal anti-HA	Abcam	Cat# ab9110; RRID:AB_307019
Rabbit monoclonal anti-CREB	Cell Signalling Technology	Cat# 9197; RRID:AB_331277
Rabbit monoclonal anti-Phospho-CREB (Ser133)	Cell Signalling Technology	Cat# 9196; RRID:AB_331275
Anti-Rabbit IgG- Peroxidase	Sigma-Aldrich	Cat# A0545; RRID:AB_257896
Anti-Mouse IgG- Peroxidase	Sigma-Aldrich	Cat# A9044; RRID:AB_258431
IgG from rabbit serum	Sigma-Aldrich	Cat# I8140; RRID:AB_1163661
Alexa Fluor 647-conjugated anti-rabbit antibody	Thermo Fisher Scientific	Cat# A-21244; RRID:AB_2535812
Rabbit polyclonal anti-CTCF	Diagenode	Cat# C15410210; RRID:AB_2753160
Rabbit IgG	Diagenode	Cat# C15410206; RRID:AB_2722554
Bacterial and virus strains
Ad-CMV-HA-CTCF	This paper	N/A
Ad-CMV-Control	This paper	N/A
Chemicals, peptides and recombinant proteins
RNaseOUT™ Recombinant Ribonuclease Inhibitor	Invitrogen	10777019
Random Hexamer (50uM)	Invitrogen	N8080127
TriZol	Invitrogen	15596018
DEPC treated water	Invitrogen	AM9915G
UltraPure Distilled Water	Invitrogen	10977015
dNTP Mix	Genei	652400021730
DAPI	Roche	10236276001
Glucose Solution	Gibco™	A2494001
L- Glutamine	Sigma-Aldrich	59202C
Sodium Pyruvate	Sigma-Aldrich	S8636
Oligomycin	MP Biomedicals	215178605
FCCP	Sigma-Aldrich	C2920
Rotenone	Sigma-Aldrich	R8875
Collagenase	Sigma-Aldrich	C5138
Rat tail collagen	Sigma-Aldrich	C3867
High Glucose DMEM	Sigma-Aldrich	D7777
Low Glucose DMEM	Sigma-Aldrich	D5523
DMEM without glucose	Sigma-Aldrich	D5030
Fetal Bovine Serum	Gibco™	10270106
Antibiotic Antimycotic Solution	Sigma-Aldrich	A5955
Sodium pyruvate	Sigma-Aldrich	P225
EGTA	Sigma-Aldrich	E3889
EDTA	Sigma-Aldrich	E9884
Bovine serum albumin	MP Biomedicals	160069
DTT	Sigma-Aldrich	578517
Tris Base	Himedia	MB029
Glucagon	Sigma-Aldrich	G2044
Forskolin	Sigma-Aldrich	F3917
WY-14643	Sigma-Aldrich	C7081
HEPES	USB	16926
20% SDS	Himedia	ML007
Formaldehyde	SDFCL	38421-L05
Magnetic Protein A beads	Biorad	#1614013
Ribonucleases A	Sigma-Aldrich	R4875
Proteinase K	Roche	REF03115879001
Lipofectamine™ RNAiMAX Transfection Reagent	Invitrogen™	13778150
IGEPAL® CA-630	Sigma-Aldrich	I3021
Triton X-100	Sigma-Aldrich	T8787
Lithium chloride	Sigma-Aldrich	L9650
Sodium deoxycholate	Sigma-Aldrich	SRE0046
Sodium Bicarbonate	Himedia	TC230
Sodium Bicarbonate	Sigma-Aldrich	S6014
Sodium Chloride	MPTM	194848
cOmplete™, EDTA-free Protease Inhibitor Cocktail	Roche	COEDTAF-RO
PhosSTOP™	Roche	PHOSS-RO
Phenylmethanesylfonyl fluoride (PMSF)	Sigma-Aldrich	P7626
Bicinchoninic Acid solution	Sigma-Aldrich	B9643
Tween 20	Himedia	TC287
PVDF Membrane	Millipore	IPVH00010
Skim milk powder	Himedia	GRM1254
Paraformaldehyde	Sigma-Aldrich	158127
Oil Red O	Sigma-Aldrich	O0625
Critical commercial assays
Seahorse XFe24 FluxPaks	SeaHorse Bioscience	102340-100
Chemiluminescence detection kit	Thermo Scietific	34095, 34080
SuperScript-IV RT kit	Invitrogen	18090200
KAPA SYBR® FAST Universal 2X qPCR Master Mix	Roche	SFUKB
iDeal ChIP-seq kit for Transcription Factors	Diagenode	C01010170
High Sensitivity NGS Fragment Analysis Kit	Agilent	DNF-474
Agencourt AMPure XP	Beckman Coulter	N/A
MicroPlex Library Preparation Kit v2 (12 indexes)	Diagenode	C05010012
Qubit™ dsDNA HS and BR Assay Kits	Invitrogen	Q32854
Deposited data
CTCF ChIP-seq fed and fasted mice liver	This Paper	GEO: GSE207692
RNA-seq and DHS-seq from ad-lib fed and 24 hrs starved liver, CEBPb, CREB, GR, H3K27ac (Fed and 24 hrs Fasted) ChIP-seq	Goldstein et al.54	GEO: GSE72087
PPARα and PPARδ ChIP-seq	Sommars et al.57	GEO: GSE118789
RXR (Bexarotene treated) and LXR (T0901317 treated) ChIP-seq	Boergesen and Mandrup80	GEO: GSE35262
HNF4α (ZT16) ChIP-seq	Qu et al.81	GEO: GSE118007
ERRα ChIP-seq	Chaveroux et al.82	GEO: GSE43638
FOXO1 (unfed) ChIP-seq	Kalvisa et al.83	GEO: GSE119713
THRb (T3 treated) ChIP-seq	Ramadoss et al.58	GEO: GSE52613
SREBP2 ChIP-seq	Seo et al.59	GEO: GSE28082
SREBP1 (ZT14) ChIP-seq	Gilardi et al.84	GEO: GSE48375
REV-ERBα and REV-ERBβ (ZT8)-	Cho et al.85	GEO: GSE34020
BMAL, PER1, PER2, CLOCK, NPAS2, CRY1, CRY2, RNA POL-II Ser5-P, RNA POL-II 8WG16, CBP, p300 ChIP-seq	Koike et al.86	GEO: GSE39860
RAD21, SMC3 ChIP-seq	Schwarzer et al.87	GEO: GSE93431
RNA-seq from liver collected at different ZTs in ad-libitum condition-	Guan et al.88	GEO: GSE143528
Experimental models: cell lines
Human: HEK293	ATCC	CRL-1573; RRID:CVCL_0045
Human: HEK293T	ATCC	CRL-11268; RRID:CVCL_1926
Experimental models: organisms/strains
Mouse: C57BL/6NCrl	CRL	Strain No: 027; RRID:IMSR_CRL:027
Fly: w1118	Bloomington Drosophila Stock Center (BDSC)	Strain No.: 5905; RRID:BDSC_5905
Fly: UAS-CTCF-RNAi	Bloomington Drosophila Stock Center (BDSC)	Strain No.: 40850; RRID:BDSC_40850
Fly: Actingal4 (w∗; PAct5C-GAL425FO1/CyO)	Gift from Maithreyi Narasimha lab at TIFR Mumbai	N/A
Oligonucleotides
Control and CTCF KD GapmeRs	Qiagen	339518 LG00240087-EFA, 339518 LG00240081-EFA, 339516 LG00000002-EFA
Control and Jpx siRNA	Dharmacon, ON-TARGETplus	R-174220-00-0005, D-001810-10-05
Recombinant DNA
pAdTrack-Control	He et al.89	pAdTrack-CMV (Plasmid #16405)
pAdTrack-HA-CTCF	This Paper	N/A
Software and algorithms
ImageJ	ImageJ	https://imagej.nih.gov/ij/ ; RRID:SCR_003070
Galaxy	Afgan et al.90	https://usegalaxy.org/ ; RRID:SCR_006281
DAVID	Huang et al.91,92	https://david.ncifcrf.gov/ ; RRID:SCR_001881
HOMER (v4.11, 10-24-2019)	Heinz et al.93	http://homer.ucsd.edu/homer/ ; RRID:SCR_010881
Ensembl BioMart	Cunningham et al.94	https://nov2020.archive.ensembl.org/biomart/martview ; RRID:SCR_010714
Lift Genome Annotations	N/A	https://genome.ucsc.edu/cgi-bin/hgLiftOver
CircadiOmics	Agostinelli et al.,95 Ceglia et al.,96 Patel et al.97	http://circadiomics.ics.uci.edu/
bedtools v2.30.0	Quinlan and Hall98	https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html; RRID:SCR_006646