|
Antibodies
|
| Anti-PGC-1α |
Novus |
NBP1-04676 |
| Anti-PGC-1α1/-a |
Santa Cruz Biotechnology |
sc-518025 |
| Anti-FLAG-HRP |
Sigma |
A8592 |
| Anti-FLAG |
Sigma-Aldrich |
F1804 |
| Anti-CBP80 |
Bethyl Laboratories or gift from Yoon Ki Kim |
A301-793A N/A |
| Anti-CBP20 |
Santa Cruz Biotechnology |
sc-48793 |
| Anti-MED1 |
Santa Cruz Biotechnology |
sc-5334 |
| Anti-MED4 |
Abcam |
ab129170 |
| Anti-MED14 |
Invitrogen |
PA5-44864 |
| Anti-CDK9 |
Santa Cruz Biotechnology |
sc-484 or sc-13130 |
| Anti-Cyclin T1 |
Cell Signaling |
81464 |
| Anti-MEF2 (MEF2A + MEF2C) |
Abcam |
ab64644 |
| Anti-ERRα |
Cell Signaling |
13826 |
| Anti-ERα |
Proteintech |
21244-1-AP |
| Anti-RNAPII (total) |
Millipore |
05-623 |
| Anti-RNAPII(pS5) |
Abcam |
ab5131 |
| Anti-RNAPII(pS2) |
Abcam |
ab5095 |
| Anti-eIF4AIII |
Bethyl Laboratories or Santa Cruz Biotechnology |
A302-981A sc-33632 |
| Anti-MAGOH |
Santa Cruz Biotechnology |
sc-56724 |
| Anti-INTS3 |
Proteintech |
16620-1-AP |
| Anti-INTS10 |
Proteintech |
15271-1-AP |
| Anti-INTS11 |
Sigma-Aldrich |
HPA029025 |
| Anti-PABPC1 |
Abcam |
ab21060 |
| Anti-β-Actin |
Sigma-Aldrich |
A2228 |
| Anti-α-Tubulin |
Santa Cruz Biotechnology |
sc-58666 |
| Anti-GAPDH |
Cell Signaling |
2118 |
| Anti-Calnexin |
Enzo |
ADI-SPA-865 |
| Anti-NONO |
Bethyl or Santa Cruz Biotechnology |
A300-582A sc-46220 |
| Anti-Histone H3 |
Abcam |
ab1791 |
| Goat anti-Mouse IgG (H+L) Poly-HRP Secondary Antibody, HRP |
Invitrogen |
32230 |
| Goat anti-Rabbit IgG (H+L) Secondary Antibody [HRP] (Pre-adsorbed) |
Novus |
NBP1-75318 |
| Peroxidase IgG Fraction Monoclonal Mouse Anti-Rabbit IgG, light chain specific |
Jackson ImmunoResearch |
211-032-171 |
| Clean-Blot™ IP Detection Reagent (HRP) |
Thermo Fisher Scientific |
21230 |
| Anti-PAX7 |
Developmental Studies Hybridoma Bank |
AB_528428 |
| Anti-MyoD |
BD Biosciences |
554130 |
| Anti-Ki67(Alexa 488) |
Cell Signaling |
11882S |
| Anti-MyoG |
Abcam |
ab124800 |
| Anti-Skeletal muscle myosin |
Sigma Aldrich |
HPA1239 |
| Anti-eMHC |
Developmental Studies Hybridoma Bank |
BF-45 and F1.652 |
| Anti-Myosin heavy chain Type I |
Developmental Studies Hybridoma Bank |
BA-D5 |
| Anti-Myosin heavy chain Type IIA |
Developmental Studies Hybridoma Bank |
SC-71 |
| Myosin heavy chain Type IIB |
Developmental Studies Hybridoma Bank |
BF-F3 |
| Anti-Laminin |
Sigma-Aldrich |
L0663 |
| Goat anti-Mouse IgG2b Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 568 |
Invitrogen |
A-21144 |
| Goat anti-Mouse IgG1 Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 633 |
Invitrogen |
A-21126 |
| Goat anti-Mouse IgG, IgM (H+L) Secondary Antibody, Alexa Fluor™ 488 |
Invitrogen |
A-10680 |
|
Bacterial and virus strains
|
| One Shot™ MAX Efficiency™ DH5α-T1R Competent Cells |
Invitrogen |
12297016 |
|
Biological samples
|
| N/A |
|
|
|
Chemicals, peptides, and recombinant proteins
|
| DMEM, high glucose, pyruvate |
Gibco |
11995-065 |
| Ham’s F-10 Nutrient Mix |
Gibco |
11550-043 |
| Trypsin-EDTA (0.25%), phenol red |
Gibco |
25200-056 |
| Avantor Seradigm Premium Grade Fetal Bovine Serum (FBS) |
VWR |
97068-085 |
| Horse Serum, New Zealand origin |
Gibco |
16050-114 |
| Penicillin-Streptomycin (10,000 U/mL) |
Gibco |
15140-122 |
| Hexadimethrine bromide (Polybrene) |
Santa Cruz Biotechnology |
SC134220 |
| Puromycin |
Gibco |
A11138-03 |
| Hepes |
Gibco |
15630-106 |
| Collagenase Type II |
Gibco |
17101-015 |
| Dispase |
Gibco |
17105-041 |
| GlutaMAX™ Supplement |
Gibco |
35050-061 |
| Primocin |
InvivoGen |
ant-pm-1 |
| Basic Fibroblast Growth Factors (bFGF), Human Recombinant |
Corning |
354060 |
| Matrigel® Basement Membrane Matrix |
Coming |
354234 |
| α-amanitin |
Santa Cruz Biotechnology |
CAS 23109-05-9 |
| THZ1 |
APExBIO |
A8882 |
| 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) |
Sigma-Aldrich |
D1916 |
| Trypan Blue Stain (0.4%) |
Gibco |
15250-061 |
| Lipofectamine™ 2000 |
Invitrogen |
11668019 |
| Lipofectamine™ RNAiMAX |
Invitrogen |
13778075 |
| Opti-MEM™ I Reduced Serum Medium |
Gibco |
31985070 |
| PBS, pH 7.4 |
Gibco |
10010023 |
| Halt™ Protease and Phosphatase Inhibitor Cocktail |
Thermo Fisher Scientific |
78442 |
| N-ethylmaleimide |
Alpha Aesar |
40526 |
| Protein A-Agarose |
Roche |
10037256 |
| Dynabeads™ Protein A |
Invitrogen |
10002D |
| ANTI-FLAG® M2 Affinity Gel |
Sigma-Aldrich |
A2220 |
| Anti-FLAG® M2 Magnetic Beads |
Millipore |
M8823 |
| Mouse IgG–Agarose |
Sigma-Aldrich |
A0919 |
| Ambion™ RNase I, cloned, 100 U/μL |
Ambion |
AM2295 |
| RNase A, DNase and protease-free |
Thermo Fisher Scientific |
EN0531 |
| TURBO™ DNase |
Invitrogen |
AM2238 |
| Micrococcal Nuclease (MNase) |
Cell Signaling |
10011 |
| 3×FLAG® peptide |
Sigma-Aldrich |
F4799 |
| Heparin sodium salt from porcine intestinal mucosa |
Sigma-Aldrich |
H3393 |
| TRIzol™ Reagent |
Invitrogen |
15596018 |
| Maxima™ H Minus cDNA Synthesis Master Mix |
Thermo Fisher Scientific |
M1662 |
| Superscript™ III Reverse Transcriptase |
Invitrogen |
18080093 |
| dNTP Mixture |
Omega |
S123315 |
| Random Primers |
Invitrogen |
58875 |
| RNase OUT™ Recombinant Ribonuclease Inhibitor |
Invitrogen |
10777019 |
| SUPERase·In™ RNase Inhibitor |
Invitrogen |
AM2696 |
| PerfeCTa SYBR Green SuperMix, ROX™
|
Quantabio |
95055-02K |
| PerfeCTa SYBR Green SuperMix, Low ROX™
|
Quantabio |
95056-02K |
| T4 RNA ligase 2, truncated KQ |
New England Biolabs |
M0373 |
| RNA 5′ pyrophosphohydrolase (RppH) |
New England Biolabs |
M0356S |
| T4 polynucleotide kinase (T4 PNK) |
New England Biolabs |
M0201L |
| NEBNext® Ultra™ II Q5® Master Mix |
New England Biolabs |
M0544 |
| SYBR™ Gold Nucleic Acid Gel Stain |
Thermo Fisher Scientific |
S11494 |
| RQ1 RNase-free DNase |
Promega |
M6101 |
| Shrimp Alkaline Phosphatase (rSAP) |
New England Biolabs |
M0371L |
| Cas9 2NLS Nuclease |
Synthego |
N/A |
| AccuStart II GelTrack PCR SuperMix |
Quantabio |
95136 |
| Cas9 2NLS Nuclease |
Synthego |
N/A |
| Recombinant Murine IFN-ɣ |
Prepotech |
50-813-665 |
|
Critical commercial assays
|
| Satellite Cell Isolation Kit, mouse |
Miltenyi Biotec |
130-104-268 |
| Anti-Integrin α-7 MicroBeads, mouse |
Miltenyi Biotec |
130-104-261 |
| miRNeasy Mini Kit |
Qiagen |
217004 |
| RNase-Free DNase Set |
Qiagen |
79254 |
| RiboMinus™ Eukaryote Kit v2 |
Thermo Fisher Scientific |
A15020 |
| 5′ DNA Adenylation Kit |
New England Biolabs |
E2610 |
| Monarch® RNA Cleanup |
New England Biolabs |
T2040 |
| Gel Cassettes, Pippin HT, 2% agarose |
Sage Science |
HTC2010 |
| NEBNext® Multiplex Small RNA Library Prep Set for Illumina®
|
New England Biolabs |
E7560 |
| TruSeq RNA Library Prep Kit v2 |
Illumina |
RS-122-2001/2 |
| CUTANA™ ChIC/CUT&RUN Kit |
EpiCypher |
14-1048 |
| NucleoBond® Xtra Maxi EF |
Macherey-Nagel |
740424.50 |
|
Deposited data
|
| PRO-seq, RNA-seq, native RIP-seq, and RIP-seq footprinting from C2C12 MBs |
This paper |
GSE197312 |
| Original imaging data |
This paper |
doi:10.17632/39mxxdfkdn.1
|
|
Experimental models: Cell lines
|
| C2C12 MBs |
ATCC |
CRL-1772™
|
| HEK293T cells |
ATCC |
CRL-3216™
|
| CTL C2C12 MBs |
This paper |
N/A |
| PGC-1α-KD C2C12 MBs |
This paper |
N/A |
|
Experimental models: Organisms/strains
|
| C57BL/6J mice |
The Jackson Laboratory |
000664 |
|
PGC-1α(CBM)5mut/5mut C57BL/6J mice |
This paper |
N/A |
|
Oligonucleotides
|
| PCR primers for the generation of constructs: see Table S4
|
This paper |
see Table S4
|
| Gene-specific shRNA and siRNA sequences: see Table S4
|
This paper |
see Table S4
|
| SilencerTM Negative Control No.1 siRNA |
Ambion |
N/A |
| RT-qPCR primers: see Table S4
|
This paper |
see Table S4
|
| CUT&RUN-qPCR primers: see Table S4
|
This paper |
see Table S4
|
| CUT&RUN Spike-in DNA sequence: see Table S4
|
This paper |
see Table S4
|
| Protospacer sequence used to generate CBM sgRNA: see Table S4
|
This paper |
see Table S4
|
| Single-stranded oligodeoxynucleotide repair template to introduce 5 point mutations in the CBM of the mouse Ppargc1a gene: see Table S4
|
This paper |
see Table S4
|
|
Recombinant DNA
|
| pcDNA3×FLAG |
Cho et al., 2018
|
N/A |
| pcDNA3×FLAG-PGC-1α(WT) |
Cho et al., 2018
|
N/A |
| pcDNA3×FLAG-PGC-1α(NR1mut) |
This paper |
N/A |
| pcDNA3×FLAG-PGC-1α(NR2mut) |
This paper |
N/A |
| pcDNA3×FLAG-PGC-1α(NR3mut) |
This paper |
N/A |
| pcDNA3×FLAG-PGC-1α(NR1-3mut) |
This paper |
N/A |
| pcDNA3×FLAG-PGC-1α(ΔRS) |
Cho et al., 2018
|
N/A |
| pcDNA3×FLAG-PGC-1α(ΔCBM) |
Cho et al., 2018
|
N/A |
| pcDNA3×FLAG-PGC-1α(CBM5mut) |
Cho et al., 2018
|
N/A |
| VSV-G plasmid |
Addgene |
8454 |
| pCG-gag-pol plasmid |
Cho et al., 2018
|
N/A |
| MISSION shRNA pLKO.1-puro plasmid |
Cho et al., 2018
|
N/A |
| pRetroSuper-GFP-shRNA plasmid |
Cho et al., 2018
|
N/A |
|
Software and algorithms
|
| CRISPOR |
Haeussler et al., 2016
|
N/A |
| ImageJ |
Schneider et al., 2012
|
N/A |
| Integrative Genomics Viewer (v2.9.2) |
Robinson et al., 2017
|
N/A |
| Prism9 |
GraphPad |
N/A |
| Custom PRO-seq analysis scripts |
AdelmanLab GitHub |
DOI 10.5281/zenodo.5519915
|
| fastP (v0.20.0) |
Chen et al., 2018
|
N/A |
| STAR (v2.7.2c) |
Dobin et al., 2013
|
N/A |
| featureCounts (v2.0.3) |
Liao et al., 2014
|
N/A |
| DESeq2 |
Love et al., 2014
|
N/A |
|
Other
|
| N/A |
|
|
