Mechanisms of trichostatin A inhibiting AGS proliferation and identification of lysine-acetylated proteins

Table 1 Oligonucleotide sequences used in real-time polymerase chain reaction

Gene	Primer (5' to 3')	Length (bp)
β-actin	F: 5'TGGAGAAAATCTGGCACCA3'	189
	R: 5'CAGGCGTACAGGGATAGCAC3'
p21	F: 5'TCCAAGAGGAAGCCCTAATCC3'	101
	R: 5'ACAAACTGAGACTAAGGCAGAAGATG3'
p53	F: 5'TCAGTCTACCTCCCGCCATAA3'	231
	R: 5'GTGCAGGCCAACTTGTTCAGT3'
Bcl-2	F: 5'CCTTTTCTACTTTGCCAGCAAAC3'	149
	R: 5'GAGGCCGTCCCAACCAC3'
CDK2	F: 5'GCTAGCAGACTTTGGACTAGCCAG3'	85
	R: 5'AGCTCGGTACCACAGGGTCA3'
CyclinD1	F: 5'AACAGAAGTGCGAGGAGGAG3'	299
	R: 5'CTGGCATTTTGGAGAGGAAG3'
Bax	F: 5'CCAGGGTGGTTGGGTGAGACT3'	231
	R: 5'TGGGAGGTCAGCAGGGTAGAT3'

Bcl-2: B cell lymphoma-2; CDK2: Cyclin-dependent kinase 2; Bax: Bcl-associated X protein.

Table 2 Proteomic identification of acetylated proteins in AGS cells

Reference	Sequence
Filamin A, alpha	K.TGVAVNKPAEFTVDAK*HGGK.A
Heat shock cognate 71 kDa protein	R.RFDDAVVQSDMK*HWPFMVVNDAGRPK.H
Heat shock protein HSP 90-alpha	R.MKENQK*HIYYITGETK.D
	R.MK*ENQKHIYYITGETK.D
Histone H2B type 1-C/E/F/G/I	M.PEPAK*SAPAPK*K*GSK*K*AVTK*AQK.K
	R.LLLPGELAK*HAVSEGTK.A
Histone H2B type 1-D	K.SAPAPK*K*GSK*K*AVTK*AQK*K.D
Histone H2B type 1-H	K.#KGSK*K*AVTK*AQK*K.D
Histone H2B type 2	K.SAPAPK*K*GSK*K*AVTK*VQK.K
Ezrin	R.QAVDQIK*SQEQLAAELAEYTAK.I
Histone H4	M.SGRGK*GGK*GLGK*GGAK*R.H
Fructose-bisphosphate aldolase A	K.DGADFAK*WR.C
Histone H2B type 1-B	K.K*GSK*K*AITK*AQK*K.D
	K.SAPAPK*K*GSK*K*AITK*AQK.K
	R.LLLPGELAK*HAVSEGTK.A
Tubulin beta chain	R.ISVYYNEATGGK*YVPR.A
Histone H2B type 1-M	K.K*GSK*K*AINK*AQK.K
T-complex protein 1 subunit theta	K.EGAK*HFSGLEEAVYR.N
Tubulin beta-4B chain	R.INVYYNEATGGK*YVPR.A
Uncharacterized protein	K.HELQANCYEEVK*DR.C
Histone H3	R.K*QLATK*AAR.K
	R.K*STGGK*APR.K
Glyceraldehyde-3-phosphate dehydrogenase	R.VIISAPSADAPMFVMGVNHEK*YDNSLK.I
Heterogeneous nuclear ribonucleoprotein Q	K.SAFLCGVMK*TYR.Q
Phosphoglycerate kinase 1	R.FHVEEEGK*GK.D
Histone H3.1	R.EIAQDFK*TDLR.F
T-complex protein 1 subunit alpha	K.DDK*HGSYEDAVHSGALND.-
Phosphoglycerate mutase 1	K.AETAAK*HGEAQVK.I
Nucleophosmin	K.VEAK*FINYVK.N
60S ribosomal protein L3	K.FIDTTSK*FGHGR.F
ADP/ATP translocase 3	K.QIFLGGVDK*HTQFWR.Y
U1 small nuclear ribonucleoprotein 70 kDa	R.VNYDTTESK*LR.R
ATP5O ATP synthase subunit O, mitochondrial	GEVPCTVTSASPLEEATLSELK*TVLK
CREB-binding protein	K.#KK*NNK*K*TNK*NK*SSISR.A
	K.SHAHK*MVK*WGLGLDDEGSSQGEPQSK*SPQESR.R
	R.KKEESTAASETTEGSQGDSK*NAK*K.K
HUMAN Histone H2A.Z	M.AGGK*AGK*DSGK*AK*TK.A
Uncharacterized protein	K.FK*YDDAER.R
Uncharacterized protein	K.SAFLCGVMK*TYR.Q
Heat shock protein beta-1	K.DGVVEITGK*HEER.Q
T-complex protein 1 subunit beta	R.EALLSSAVDHGSDEVK*FR.Q
Galectin-1	K.LPDGYEFK*FPNR.L
Histone H2A type 1-H	R.GK*QGGK*AR.A
Asparagine synthetase	K.VASVEMVK*YHHCR.D
Retinoblastoma binding protein 7	K.IECEIK*INHEGEVNR.A
Glucose-6-phosphate isomerase	R.SGDWK*GYTGK.T
Uncharacterized protein	R.EQCCYNCGK*PGHLAR.D
Uncharacterized protein	K.IASK*YDHQAEEDLR.N
Actin-related protein 3	K.EFNK*YDTDGSK.W
Histone H2A type 2-B	R.GK*QGGK*AR.A
Uncharacterized protein	K.ITIMPK*.H
Programmed cell death protein 5	K.HGDPGDAAQQEAK*HR.E
Fumarate hydratase, mitochondrial	K.VPNDK*YYGAQTVR.S
Lamin-B receptor	K.YGVAWEK*YCQR.V
Uncharacterized protein	K.VTGTLETK*YK.W
PC4 and SFRS1-interacting protein	K.TKDQGK*K*GPNK*K*.L
26S protease regulatory subunit 10B	K.VVSSSIVDK*YIGESAR.L
Hematological and neurological expressed 1 protein	R.RNPPGGK*SSLVLG.-
Uncharacterized protein	R.LNQVIFPVSYNDK*FYK.D
Acyl-CoA-binding protein	K.TK*PSDEEM@LFIYGHYK.Q
Probable global transcription activator SNF2L2	K.K*GK*GGAK.T
Chromodomain-helicase-DNA-binding protein 4	R.NLGK*GK.R
Biorientation of chromosomes in cell division protein 1-like	K.SLLEEK*LVLK*SK*.S
Aspartate aminotransferase	R.DVFLPK*PTWGNHTPIFR.D
Histone-lysine N-methyltransferase MLL3	K.TLVLSDK*HSPQK*K.S
Bromodomain-containing protein 1	R.HPSSPCSVK*HSPTR.E
LINE-1 type transposase domain-containing protein 1	R.KFQK*LKNKEEVLK*.A
B-cell CLL/lymphoma 9-like protein	R.GHCPPAPAK*PMHPENK*LTNHGK.T
WD repeat-containing protein 46	M.ETAPK*PGK.D
Metastasis-associated protein MTA2	R.VGCK*YQAEIPDR.L
Cyclin-dependent kinase 11B	R.SHSAEGGK*HAR.V
Homeobox protein Hox-C8	R.YQTLELEK*.E
Ubiquitin carboxyl-terminal hydrolase 8	R.KEEQEQK*AKK*K.Q
28S ribosomal protein S9, mitochondrial	K.AEAIVYK*HGSGR.I
GDNF family receptor alpha-like	K.K*CINKSDNVK*EDK*FK.W
Solute carrier organic anion transporter family member 4C1	K.FGK*SIK.D
Ovochymase-1	R.#GAFGISYIDLK*VLGPK.D
Coiled-coil domain-containing protein 13	K.KKIEEDRFAFTGTAGVAGDVVATK*.I
Threonine synthase-like 1	K.LSCGEWK*SLVGATYVER.A
Secreted frizzled-related protein 1	K.K*K*DLKKLVLYLK*.N
Dynein heavy chain 3, axonemal	R.LREAEGKLAAQMQK*.L
Histone acetyltransferase KAT6B	R.#QSPAKVQSK*NK*YLHSPESR.P !
Polycomb protein SCMH1	R.KPGK*K*R.G
Zinc finger protein 512B	K.#EK*K*K*NLAGGK*K*.R
Dedicator of cytokinesis protein 7	R.AHGELHEQFK*R.K
Remodeling and spacing factor 1	R.GK*DISTITGHR.G
HIRA-interacting protein 3	R.#TQLKGGK*R.L
Ubiquitin-fold modifier-conjugating enzyme 1	K.ICLTDHFK*PLWAR.N
Uncharacterized protein	K.QNKTK*R.Q
Chromosome 1 open reading frame 149	R.YLTNQK*NSNSK*NDR.R
Uncharacterized protein	K.#EK*GDK*K*EGKDVK*.V
Uncharacterized protein	K.NLACEESK*R.K
Ubiquitin carboxyl-terminal hydrolase	R.DLLQFFK*PR.Q
Uncharacterized protein	R.YLVASK*.E