REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit monoclonal anti-β-tubulin	Cell Signaling Technology	Cat. #2128, RRID:AB_823664
Rabbit monoclonal anti-SIRT5	Cell Signaling Technology	Cat. #8782, RRID:AB_2716763
Rabbit monoclonal anti-acetyl-lysine	Cell Signaling Technology	Cat. #9814, RRID:AB_10544700
Rabbit monoclonal anti-malonyl-lysine	PTM Biolabs	Cat. #PTM-901
Rabbit monoclonal anti-succinyl-lysine	PTM Biolabs	Cat. #PTM-401
Rabbit monoclonal anti-glutaryl-lysine	PTM Biolabs	Cat. #PTM-1151
Rabbit monoclonal anti-ACC	Cell Signaling Technology	Cat. #3676, RRID:AB_2219397
Rabbit polyclonal anti-phospho-ACC (Ser79)	Cell Signaling Technology	Cat. #3661, RRID:AB_330337
Rabbit monoclonal anti-H2B	Cell Signaling Technology	Cat. #12364, RRID:AB_2714167
Rabbit monoclonal anti-KAT2A	Cell Signaling Technology	Cat. #3305, RRID:AB_2128281
Mouse monoclonal anti-HSP60	Abcam	Cat. #ab59457, RRID:AB_2121285
Rabbit polyclonal anti-Lamin A/C	Cell Signaling Technology	Cat. #2032, RRID:AB_2136278
Rabbit monoclonal anti-COX IV	Abcam	Cat. #ab16056
Rabbit monoclonal anti-GAPDH	Cell Signaling Technology	Cat. #5174, RRID:AB_10622025
Mouse monoclonal anti-Fibrillarin	Abcam	Cat. #ab4566, RRID:AB_304523
Goat anti-rabbit IgG, Alexa Fluor 555	Invitrogen	Cat. #A-21428
Goat anti-mouse IgG, Alexa Fluor 488	Invitrogen	Cat. #A-11001
Rabbit monoclonal anti-Tri-Methyl-Histone H3 (Lys4) (C42D8)	Cell Signaling Technology	Cat. #9751, RRID:AB_2616028
Rabbit (DA1E) isotype control mAb IgG	Cell Signaling Technology	Cat. #66362, RRID:AB_2924329
Chemicals, peptides, and recombinant proteins
Orlistat	Selleck	Cat. #1629
AICAR	Selleck	Cat. #S1802
Trichostatin A	Cayman Chem	Cat. #89730
Nicotinamide	Sigma-Aldrich	Cat. #72340
Recombinant KAT domain of human KAT2A	Enzo	Cat. #BML-SE272
Human N-terminal (a.a. 1–20) histone peptides	This study, see Table S3	N/A
7-diethylamino-3-(4′-maleimidylphenyl)-4-methylcoumarin (CPM)	Invitrogen	Cat. #D346
Critical commercial assays
Lipofectamine 3000	Invitrogen	Cat. #L3000
Histone extraction kit	EpiGentek	Cat. #OP-0006
nuclear extraction kit	Epigentek	Cat. #OP-0002
CUT&RUN assay kit	Cell Signaling Technology	Cat. #86652
Deposited data
Raw data and complete mouse brain malonylation proteome MS datasets	This paper	MassIVE ID number: MSV000089318; ProteomeXchange ID: PXD033458http://massive.ucsd.edu/ProteoSAFe/status.jsp?task=a23d5ddef1b54e89b858221ce57863ab
Raw data and complete mouse liver malonylation proteome MS datasets	Nishida et al., 20154	MassIVE ftp://MSV000079116:a@massive.ucsd.edu.
Experimental models: Cell lines
Human: K562	ATCC	CRL-3343
Human: K562-dCas9-KRAB	Gilbert et al., 201419	N/A
Human: HEK293T	ATCC	CRL-3216
Human: HeLa	ATCC	CCL-2
Experimental models: Organisms/strains
Mouse: B6;129-Sirt5tm1Fwa/J	The Jackson Laboratory	Strain #:012757; RRID:IMSR_JAX:012757
Mouse: C57BL/6J	The Jackson Laboratory	Strain #:000664; RRID:IMSR_JAX:000664
Oligonucleotides
Primers for qPCR	This study, see Table S2	N/A
Recombinant DNA
pEBB-Flag-GCN5	Addgene	RRID:Addgene_74784
pU6-sgRNA-EF1Alpha-puro-T2A-BFP	Addgene	RRID:Addgene_60955
pCMV-VSV-G envelope vector	Cell Biolabs	Cat. # RV-110
pCMV-dR8.91 packaging vector	Creative Biogen	Cat. #OVT2971
Software and algorithms
GraphPad Prism 6	GraphPad	https://graphpad.com/
ImageJ	Schindelin et al., 201252	https://imagej.nih.gov/ij/
U-NET	Ronneberger et al., 201548	https://lmb.informatik.uni-freiburg.de/resources/opensource/unet/
Skyline-daily (version 21.1.1.223)	MacLean et al., 201051	https://skyline.ms