REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-MOTS-c	This paper	N/A
Anti-ATF1 Polyclonal	Thermo Fisher Scientific	Cat# PA5–24788; RRID: AB_2542288
Anti-NFE2L1 Polyclonal Antibody	Thermo Fisher Scientific	Cat# PA5–34837; RRID: AB_2552189
Anti-NFE2L2-human (IP)	Abeam	Cat# ab62352 ; RRID: AB_944418
Anti-NRF2 (D1Z9C) XP Rabbit monoclonal	Cell Signaling Technology	Cat# PA5–24788; RRID: AB_2542288
phospho-AMPKα antibody	Cell Signaling Technology	Cat#2535S; RRID: AB_331250
AMPKα antibody	Cell Signaling Technology	Cat#2532S; RRID: AB_330331
Anti-Lamin B1 (D4Q4Z) Rabbit mAb	Cell Signaling Technology	Cat#12586S; RRID: AB_2650517
Anti-Histone H2B (D2H6) Rabbit mAb	Cell Signaling Technology	Cat# 12364; RRID: AB_2714167
Histone H4 antibody	Abeam	Cat#ab10158; RRID: AB_296888
MT-COII antibody	Abeam	Cat#ab79393; RRID: AB_1603751
VDAC antibody	Cell Signaling Technology	Cat#4661S; RRID: AB_10557420
Anti-GAPDH (D16H11) XP Rabbit mAb	Cell Signaling Technology	Cat#5174S; RRID: AB_10622025
Anti-GFP (D5.1) XP Rabbit mAb	Cell Signaling Technology	Cat#2956S; RRID: AB_1196615
Anti-GFP (FL)	Santa Cruz Biotechnology	Cat#sc-8334; RRID: AB_641123
Anti-Myc	Cell Signaling Technology	Cat#5605S; RRID: AB_1903938
Anti-Normal Rabbit IgG	Cell Signaling Technology	Cat#2729S; RRID: ABJ031062
Anti-Rabbit IgG, HRP-linked	Cell Signaling Technology	Cat#7074S; RRID: AB_2099233
Alexa Fluor 488 AffiniPure Goat Anti-Rabbit IgG (H+L)	Thermo Fisher Sceintific	Cat#A-11034; RRID:AB_2576217
Bacterial and Virus Strains
DH5α Competent Cells	Thermo Fisher Scientific	Cat#18258012
Chemicals, Peptides, and Recombinant Proteins
Actinonin	Enzo Life Sciences	Cat#ALX-260–128
DL-Sulforaphane	Sigma-Aldrich	Cat#S4441
tert-Butyl hydroperoxide solution	Sigma-Aldrich	Cat#458139
Methyl viologen dichloride hydrate	Sigma-Aldrich	Cat#856177
Metformin	Sigma-Aldrich	Cat#317240
AICAR	AdipoGen	Cat#AGCR 10061
MitoTracker Deep Red FM	Thermo Fisher Scientific	Cat#M22426
MOTS-c peptide	GenScript	N/A
DAPI	Sigma	Cat#D9542
N-Acetyl Cysteine	Sigma	Cat#A9165
tert-Butyl Hydroperoxide	Sigma	Cat#B2633
Rotenone	Sigma	Cat#8875
Dimethyl Sulfoxide	Sigma	Cat#D8418
Clarity ECL Substrate	Bio-Rad	Cat#1705060
Proteinase K	Thermo Fisher Scientific	Cat#26160
SYBR Green Master Mix	Thermo Fisher Scientific	Cat#4309155
Lipofectamine 3000	Thermo Fisher Scientific	Cat#L3000015
MitoSOX Red	Thermo Fisher Scientific	Cat#M36008
Critical Commercial Assays
SMARTer Stranded RNA-Seq Kit	Takara/Clontech	Cat#634839
Quant-iT dsDNA HS Kit	Thermo Fisher Scientific	Cat#Q33120
ChIP DNA Clean & Concentrator Kits	Zymo	Cat#D5205
LightShift Chemiluminescent EMSA Kit	Thermo Fisher Scientific	Cat#20148
Dual-Luciferase Reporter Assay System	Promega Corporation	Cat#E1910
NEBNext rRNA Depletion Kit	New England Biolabs	Cat#E6310L
Deposited Data
MOTS-c overexpression RNA-seq	This paper	SRA:SRP136364
Human transcript sequence data	Biomart	Ensv91
ATF1 ChlP-seq in HepG2 cells (and Input controls)	ENCODE DCC; Biswas and Chan, 2010; Brunmair et al., 2004	SRR2184485; SRR2184486; SRR2184487; SRR2184488; SRR2184489; SRR2184490; SRR2184491; SRR2184492; ENCFF190EPQO; ENCFF950AXC
ATF1 ChlP-seq in K562 cells (and Input controls)	ENCODE DCC; Brunmair et al., 2004	ENCFF000YFC; ENCFF000YFE; SRR351543; SRR351542; SRR351541; SRR351540
ATF1 ChlP-seq in LoVo cells (and Input controls)	Stephenne et al., 2011	SRR952507; SRR952608
JUND ChlP-seq in HCT-116 cells (and Input controls)	Brunmair et al., 2004	SRR577903; SRR577904
JUND ChlP-seq in HepG2 cells (and Input controls)	Brunmair et al., 2004	SRR351817;SRR351818
JUND ChlP-seq in SK-N-SH cells (and Input controls)	Brunmair et al., 2004	SRR578017;SRR578018
JUND ChlP-seq in MCF-7 cells (and Input controls)	Brunmair et al., 2004	SRR577997; SRR577998
JUND ChlP-seq in T-47D cells (and Input controls)	Brunmair et al., 2004	SRR577650; SRR577651
NRF2 ChlP-seq in A549 cells (and Input controls)	ENCODE DCC; Brunmair et al., 2004	ENCFF003TGD; ENCFF004JMG
NRF2 ChlP-seq in HepG2 cells (and Input controls)	ENCODE DCC; Brunmair et al., 2004	ENCFF063AFU; ENCFF421XBU
NRF2 ChlP-seq in Hel_a-S3 cells (and Input controls)	ENCODE DCC; Brunmair et al., 2004	ENCFF686TXK; ENCFF068LXE
NRF2 ChlP-seq in IMR-90 cells (and Input controls)	ENCODE DCC; Brunmair et al., 2004	ENCFF461GBT; ENCFF467POD
NRF2 ChlP-seq in Lymphoblastoid cells cells (and Input controls)	Chepelev et al., 2013	SRR491140; SRR491141; SRR491142; SRR491143
Experimental Models: Cell Lines
HEK293	American Type Culture Collection	CRL-1573
HepG2	American Type Culture Collection	HB-8065
C2C12	American Type Culture Collection	CRL-1772
Oligonucleotides
NFE2L2 Human siRNA Oligo Duplex	Origene	Cat#SR321100
AMPKα2siRNAII	Cell Signaling Technology	Cat# 6630S
Please refer to Table S1 for oligonucleotide information	N/A	N/A
Recombinant DNA
pcDNA3.1/NT-eGFP	Gen Script	N/A
pcDNA3.1	Thermo Fisher Scientific	Cat# V79520
Renilla luciferase	Promega Corporation	Cat#E2231
pGL4.37[luc2P/ARE/Hygm])	Promega Corporation	Cat#E3641
Software and Algorithms
kallisto 0.43.0	Bray et al., 2016	https://pachterlab.github.io/kallisto/download
DESeq2 1.16.1	Corton et al., 1995	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Pheatmap 1.0.8	Kim et al., 2016	https://cran.r-project.org/web/packages/pheatmap/index.html
HOMER software suite (v4.9.1)	Heinz et al., 2010	http://homer.ucsd.edu/homer/
GOrilla enrichment tool	Eden et al., 2007, 2009	http://cbl-gorilla.cs.technion.ac.il/
bowtie 0.12.7	Langmead et al., 2009	N/A
MACS2 V2.0.8	Zhang et al., 2008	N/A
bedtools V2.26.0	Rabinovitch et al., 2017	https://github.com/arq5x/bedtools2/releases
QuantStudio 6 Flex Real-Time PCR software	Thermo Fisher Scientific	N/A
GraphPad Prism v6	GraphPad Software	N/A
Other
In house scripts	This paper	https://github.com/Benayounl_aboratory/MOTSC_nuclear_project