Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Recombinant DNA reagent | pGBT-RP2.1 |
Clark et al., 2011; Ichino et al., 2020 |
Addgene: 31828; GenBank: HQ335170.1 |
Figure 1 |
| Genetic reagent (Danio rerio) | Tg(−2.8fabp10:Cre; −0.8cryaa:Venus)S955 | Ni et al., 2012 | Provided by Dr. Wenbiao Chen, Vanderbilt University |
Figure 7(C–F) and 8(A-D), Figure 7—figure supplement 1 |
| Genetic reagent (Danio rerio) | Tg(MLS: EGFP) | Kim et al., 2008 | Kind gift provided by Dr. Sridhar Sivasubbu (CSIR-IGIB) provided to him by Dr. Seok-Yong Choi, Chonnam National University |
Figure 3C–D, Figure 3—figure supplement 1 |
| Software, algorithm | RoseTTAFold |
Baek et al., 2021; https://github.com/RosettaCommons/RoseTTAFold |
https://github.com/RosettaCommons/RoseTTAFold | Figure 2A–C |
| Software, algorithm | PyMOL (The PyMOL Molecular Graphics System, Version 2.5.2 Schrödinger, LLC) | https://pymol.org/2/ | Figure 2A–C | |
| Software, algorithm | CLUSTAL Omega v.1.2.4 |
Sievers et al., 2011
http://www.clustal.org/omega/ |
Figure 2—figure supplement 3 | |
| Software, algorithm | Jalview v.2.11.1.7 |
Waterhouse et al., 2009
https://www.jalview.org/ |
Figure 2—figure supplement 3 | |
| Software, algorithm | Pfam HMM database | https://pfam.xfam.org/ | Figure 2—figure supplement 3 | |
| Software, algorithm | TPRpred |
Karpenahalli et al., 2007
https://toolkit.tuebingen.mpg.de/tools/tprpred |
||
| Software, algorithm | FIMO motif scanning program in the MEME Suite |
Grant et al., 2011
https://meme-suite.org/meme/tools/fimo |
Supplementary file 1B and Supplementary file 1C | |
| Other | Human reference mitochondrial genome (NC_012920.1) |
https://www.ncbi.nlm.nih.gov/nuccore/251831106 | Supplementary file 1B | |
| Other | Zebrafish reference mitochondrial genome (NC_002333.2) | https://www.ncbi.nlm.nih.gov/nuccore/NC_002333.2 | Supplementary file 1C | |
| Instrument | Zebrafish embryonic genotyper |
Lambert et al., 2018
https://www.wfluidx.com/ |
||
| Commercial assay or kit | MyTaq Red polymerase | Meridian Bioscience | Catalog no: BIO-21105 | |
| Chemical compound, drug | Agarose | VWR Life Science | Catalog no: 0710 | |
| Chemical compound, drug | Tween-20 | Bio-Rad | Catalog no: 170–6531 | |
| Chemical compound, drug | Sodium hydroxide anhydrous | MP Biomedicals | Catalog no: 153495 | |
| Chemical compound, drug | Tris base | Millipore-Sigma | Catalog no: 11814273001 | |
| Chemical compound, drug | Phenylthiocarbamide | Millipore-Sigma | Catalog no: P7629 | |
| Chemical compound, drug | Tricaine | Millipore-Sigma | Catalog no: A5040 | |
| Chemical compound, drug | Low-melting agarose | Fisher Scientific | Catalog no: BP1360 | |
| Recombinant DNA reagent | pT3TS-NLS-BFP | This paper | ||
| Commercial assay or kit | T3 mMessage mMachine transcription kit |
Thermo Scientific | Catalog no: AM1348 | |
| Commercial assay or kit | NEB Monarch RNA cleanup kit | New England Biolabs | Catalog no: T2040L | |
| Chemical compound, drug | PstI (restriction enzyme) | New England Biolabs | Catalog no: R0140S | |
| Chemical compound, drug | N,O,-bis-(trimethylsilyl) trifluoroacetamide with 1% trimethylchlorosilane (BSTFA +TMCS) |
Thermo Scientific | Catalog no: TS-38834 | |
| Chemical compound, drug | Ethyl acetate | EMD-Millipore | Catalog no: EX0245-1 | |
| Chemical compound, drug | Sodium Chloride | Fisher Scientific | Catalog no: S271 | |
| Chemical compound, drug | 6 N Hydrochloric acid | EMD-Millipore | Catalog no: HX0603-75 | |
| Chemical compound, drug | O-(2,3,4,5,6-Pentafluorobenzyl)hydroxylamine Hydrochloride | TCI America | Catalog no: P0822 | |
| Chemical compound, drug | TRIzol | Thermo Scientific | Catalog no: 15596026 | |
| Chemical compound, drug | Chloroform | Millipore-Sigma | Catalog no: C2432 | |
| Chemical compound, drug | Ethanol | Millipore-Sigma | Catalog no: E7023 | |
| Chemical compound, drug | Ethylenediaminetetraacetic acid disodium salt dihydrate (EDTA) |
Millipore-Sigma | Catalog no: E5134 | |
| Chemical compound, drug | Potassium chloride | Millipore-Sigma | Catalog no: P5405 | |
| Chemical compound, drug | NP-40 permeating solution | Alfa Aesar | Catalog no: J60838 | |
| Chemical compound, drug | Proteinase K | Qiagen | Catalog no: 19133 | |
| Chemical compound, drug | Dnase I | Qiagen | Catalog no: 79254 | |
| Commercial assay or kit | RNeasy Mini Kit | Qiagen | Catalog no: 74104 | |
| Commercial assay or kit | SuperScript III Reverse Transcriptase | Thermo Scientific | Catalog no: 18080093 | |
| Commercial assay or kit | SensiFAST SYBR Lo-ROX kit | Meridian Bioscience | Catalog no: BIO-94005 | |
| Chemical compound, drug | Acridine orange | Millipore-Sigma | Catalog no: A8097 | |
| Software, algorithm | FIJI | https://imagej.net/software/fiji/ | ||
| Software, algorithm | GraphPad Prism 8 | https://www.graphpad.com/ | ||
| Commercial assay or kit | NEBNext Ultra RNA Library Prep Kit |
New England BioLabs | Catalog no: E7530 | Library preparation performed at GENEWIZ, LLC (USA) |
| Software, algorithm | Trimmomatic | Bolger et al., 2014 | RNA sequencing analysis | |
| Software, algorithm | Kallisto | Bray et al., 2016 | RNA sequencing analysis | |
| Software, algorithm | Tximport | Soneson et al., 2015 | RNA sequencing analysis | |
| Software, algorithm | DESeq2 |
Love et al., 2014 Differential gene expression analysis |
RNA sequencing analysis | |
| Software, algorithm | Zebrafish Information Network (ZFIN) |
https://zfin.org/ | ||
| Software, algorithm | Ensembl | http://useast.ensembl.org/Danio_rerio/Info/Index | ||
| Software, algorithm | PANTHER |
Mi et al., 2019
http://www.pantherdb.org/geneListAnalysis.do |
||
| Software, algorithm | GeneTrail |
Stöckel et al., 2016
https://genetrail2.bioinf.uni-sb.de/ |
||
| Chemical compound, drug | Oil red o stain | Millipore-Sigma | Catalog no: O1391 | |
| Chemical compound, drug | 4% Paraformaldehyde | Alfa Aesar | Catalog no: J61899 | |
| Chemical compound, drug | Phosphate buffer saline | Millipore-Sigma | Catalog no: | |
| Chemical compound, drug | BODIPY FL C12 | Thermo Scientific | Catalog no: D3822 | |
| Chemical compound, drug | TopFluor Cholesterol | Avanti Polar Lipids | Catalog no: 810255 | |
| Software, algorithm | R | https://www.r-project.org/ |