Table II. The Nuclear p32-associated proteins that are not involved in ribosome biogenesis. The nuclear p32-associated proteins are indicated. Proteins are classified into functional groups based on SwissProt classification. Proteins were identified by LC-MS/MS (LTQ-Orbitrap XL or Q-Tof2) and/or immunoblot analysis (IB), as described in Supplementary Tables I and II, and Figs. 1C and 1D. Proteins detected in mock are not listed in this table. Uniprot KB accession numbers, entry names, protein names as well as gene symbols are shown.

	Uniprot KB accession	Uniprot KB Entry name	Protein name	Gene symbol	ID method
					LTQ-Orbitrap XL	Q-Tof2	IB
	Chromatin remodeling
1	Q969G3	SMCE1_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1	SMARCE1	○
2	Q12824	SNF5_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1	SMARCB1	○
3	O60264	SMCA5_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5	SMARCA5	○
4	Q8TAQ2	SMRC2_HUMAN	SWI/SNF complex subunit SMARCC2	SMARCC2	○	○
5	Q92922	SMRC1_HUMAN	SWI/SNF complex subunit SMARCC1	SMARCC1	○
6	Q86U86	PB1_HUMAN	Protein polybromo-1	PBRM1	○
7	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	PHF10	○
8	P51610	HCFC1_HUMAN	Host cell factor 1	HCFC1	○
9	Q6ZRS2	SRCAP_HUMAN	Helicase SRCAP	SRCAP	○
10	Q9P2D1	CHD7_HUMAN	Chromodomain-helicase-DNA-binding protein 7	CHD7	○
11	Q14839	CHD4_HUMAN	Chromodomain-helicase-DNA-binding protein 4	CHD4	○
12	Q9NPI1	BRD7_HUMAN	Bromodomain-containing protein 7	BRD7	○
13	Q68CP9	ARID2_HUMAN	AT-rich interactive domain-containing protein 2	ARID2	○
	RNA polymerase III transcription
14	Q12789	TF3C1_HUMAN	General transcription factor 3C polypeptide 1 (TFIIIC220)	GTF3C1	○	○	○
15	Q8WUA4	TF3C2_HUMAN	General transcription factor 3C polypeptide 2	GTF3C2	○	○
16	Q9Y5Q9	TF3C3_HUMAN	General transcription factor 3C polypeptide 3 (TFIIIC102)	GTF3C3	○	○	○
17	Q9UKN8	TF3C4_HUMAN	General transcription factor 3C polypeptide 4	GTF3C4	○	○
18	Q9Y5Q8	TF3C5_HUMAN	General transcription factor 3C polypeptide 5	GTF3C5	○	○
19	O15318	RPC7_HUMAN	DNA-directed RNA polymerase III subunit RPC7	POLR3G			○
	Transcription
20	Q9H869	YYAP1_HUMAN	YY1-associated protein 1	YY1AP1	○
21	Q8WXI9	P66B_HUMAN	Transcriptional repressor p66-beta	GATAD2B	○
22	Q13263	TIF1B_HUMAN	Transcription intermediary factor 1-beta	TRIM28	○
23	P05412	JUN_HUMAN	Transcription factor AP-1	JUN	○
24	P51532	SMCA4_HUMAN	Transcription activator BRG1	SMARCA4	○
25	Q14498	RBM39_HUMAN	RNA-binding protein 39	RBM39	○
26	Q8N7H5	PAF1_HUMAN	RNA polymerase II-associated factor 1 homolog	PAF1	○
27	P30876	RPB2_HUMAN	DNA-directed RNA polymerase II subunit RPB2	POLR2B	○
28	P15336	ATF2_HUMAN	Cyclic AMP-dependent transcription factor ATF-2	ATF2	○
29	Q7RTS1	BHA15_HUMAN	Class A basic helix-loop-helix protein 15	BHLHA15	○
	DNA binding/replication/repair
30	Q14683	SMC1A_HUMAN	Structural maintenance of chromosomes protein 1A	SMC1A	○
31	P12004	PCNA_HUMAN	Proliferating cell nuclear antigen	PCNA	○
32	Q9Y2S7	PDIP2_HUMAN	Polymerase delta-interacting protein 2	POLDIP2	○
33	Q9UBB5	MBD2_HUMAN	Methyl-CpG-binding domain protein 2	MBD2	○
34	O00255	MEN1_HUMAN	Menin	MEN1	○
35	P78527	PRKDC_HUMAN	DNA-dependent protein kinase catalytic subunit	PRKDC	○
36	P26358	DNMT1_HUMAN	DNA (cytosine-5)-methyltransferase 1	DNMT1	○
37	Q7Z7K6	CENPV_HUMAN	Centromere protein V	CENPV	○
38	Q53HL2	BOREA_HUMAN	Borealin	CDCA8	○
	mRNA splicing/stabilization
39	Q07955	SRSF1_HUMAN	Serine/arginine-rich splicing factor 1 (ASF/SF2)a	SRSF1			○
40	O95104	SFR15_HUMAN	Splicing factor, arginine/serine-rich 15	SFRS15	○
41	Q99590	SFRIP_HUMAN	SFRS2-interacting protein	SRSF2IP	○
42	Q86U06	RBM23_HUMAN	Probable RNA-binding protein 23	RBM23	○
43	P09651	ROA1_HUMAN	Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1)a	HNRNPA1		○	○
44	P48634	BAT2_HUMAN	Large proline-rich protein BAT2a	BAT2	○	○
45	Q14004	CDK13_HUMAN	Cell division protein kinase 13a	CDK13	○
	RNA binding protein
46	Q9NQ29	LUC7L_HUMAN	Putative RNA-binding protein Luc7-like 1	LUC7L	○
47	Q9UHX1	PUF60_HUMAN	Poly(U)-binding-splicing factor PUF60	PUF60	○
48	P51116	FXR2_HUMAN	Fragile X mental retardation syndrome-related protein 2	FXR2	○
49	Q06787	FMR1_HUMAN	Fragile X mental retardation 1 protein	FMR1	○
	Telomere
50	Q9NYB0	TE2IP_HUMAN	Telomeric repeat-binding factor 2-interacting protein 1	TERF2IP	○
51	Q15554	TERF2_HUMAN	Telomeric repeat-binding factor 2	TERF2	○
	Nuclear envelop/pore/lamina
52	Q5SNT2	TM201_HUMAN	Transmembrane protein 201	TMEM201	○
53	O94901	SUN1_HUMAN	SUN domain-containing protein 1	SUN1	○
54	Q8N1F7	NUP93_HUMAN	Nuclear pore complex protein Nup93	NUP93	○
55	Q92621	NU205_HUMAN	Nuclear pore complex protein Nup205	NUP205	○
56	Q12769	NU160_HUMAN	Nuclear pore complex protein Nup160	NUP160	○
57	Q8WUM0	NU133_HUMAN	Nuclear pore complex protein Nup133	NUP133	○
58	P57740	NU107_HUMAN	Nuclear pore complex protein Nup107	NUP107	○
59	Q96HA1	P121A_HUMAN	Nuclear envelope pore membrane protein POM 121	POM121	○
60	Q14739	LBR_HUMAN	Lamin-B receptora	LBR	○
	Protein glycosylation
61	P39656	OST48_HUMAN	Dolichyl-diphosphooligosaccharide-protein glycosyltransferase 48 kDa subunit	DDOST	○
62	P04843	RPN1_HUMAN	Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 1	RPN1	○
	Importin
63	P52292	IMA2_HUMAN	Importin subunit alpha-2	KPNA2	○
64	P52294	IMA1_HUMAN	Importin subunit alpha-1	KPNA1	○
	Mitochondorial protein
	OXPHOS complex
65	P21912	DHSB_HUMAN	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial	SDHB	○
66	P31040	DHSA_HUMAN	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	SDHA	○
67	O75306	NDUS2_HUMAN	NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial	NDUFS2	○
68	P36542	ATPG_HUMAN	ATP synthase subunit gamma, mitochondrial	ATP5C1	○
	Mitochondrial membrane protein
69	Q9Y277	VDAC3_HUMAN	Voltage-dependent anion-selective channel protein 3	VDAC3	○
70	P45880	VDAC2_HUMAN	Voltage-dependent anion-selective channel protein 2	VDAC2	○
71	P21796	VDAC1_HUMAN	Voltage-dependent anion-selective channel protein 1	VDAC1	○	○
72	Q9H9B4	SFXN1_HUMAN	Sideroflexin-1	SFXN1	○
73	O96008	TOM40_HUMAN	Mitochondrial import receptor subunit TOM40 homolog	TOMM40	○
74	O75746	CMC1_HUMAN	Calcium-binding mitochondrial carrier protein Aralar1	SLC25A12	○
75	Q9Y4W6	AFG32_HUMAN	AFG3-like protein 2	AFG3L2	○
	Lipid metabolism
76	P40939	ECHA_HUMAN	Trifunctional enzyme subunit alpha, mitochondrial	HADHA	○
77	P55084	ECHB_HUMAN	Trifunctional enzyme subunit beta, mitochondrial	HADHB	○
	Others
78	P42704	LPPRC_HUMAN	Leucine-rich PPR motif-containing protein, mitochondrial	LRPPRC	○
79	Q96EY1	DNJA3_HUMAN	DnaJ homolog subfamily A member 3, mitochondrial	DNAJA3	○
80	O00411	RPOM_HUMAN	DNA-directed RNA polymerase, mitochondrial	POLRMT	○
81	Q96TA2	YMEL1_HUMAN	ATP-dependent metalloprotease YME1L1	YME1L1	○
82	O76031	CLPX_HUMAN	ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial	CLPX	○
83	O95831	AIFM1_HUMAN	Apoptosis-inducing factor 1, mitochondrial	AIFM1	○
	ER protein
84	P43307	SSRA_HUMAN	Translocon-associated protein subunit alpha	SSR1	○
85	Q9UGP8	SEC63_HUMAN	Translocation protein SEC63 homolog	SEC63	○
86	P55072	TERA_HUMAN	Transitional endoplasmic reticulum ATPase	VCP	○
87	Q9NZ01	TECR_HUMAN	Trans-2,3-enoyl-CoA reductase	TECR	○
88	P16615	AT2A2_HUMAN	Sarcoplasmic/endoplasmic reticulum calcium ATPase 2	ATP2A2	○
89	Q13724	MOGS_HUMAN	Mannosyl-oligosaccharide glucosidase	MOGS	○
	Others
90	Q15836	VAMP3_HUMAN	Vesicle-associated membrane protein 3	VAMP3	○
91	Q93009	UBP7_HUMAN	Ubiquitin carboxyl-terminal hydrolase 7	USP7	○
92	P07437	TBB5_HUMAN	Tubulin beta chain	TUBB	○
93	Q14232	EI2BA_HUMAN	Translation initiation factor eIF-2B subunit alpha	EIF2B1	○
94	Q07157	ZO1_HUMAN	Tight junction protein ZO-1	TJP1	○
95	P48594	SPB4_HUMAN	Serpin B4	SERPIN B4	○
96	P29508	SPB3_HUMAN	Serpin B3	SERPIN B3	○
97	P48651	PTSS1_HUMAN	Phosphatidylserine synthase 1	PTDSS1	○
98	Q15758	AAAT_HUMAN	Neutral amino acid transporter B(0)	SLC1A5	○
99	Q8NFW8	NEUA_HUMAN	N-acylneuraminate cytidylyltransferase	CMAS	○
100	Q8WVX9	FACR1_HUMAN	Fatty acyl-CoA reductase 1	FAR1	○
101	P35613	BASI_HUMAN	Basigin	BSG	○
102	P06733	ENOA_HUMAN	Alpha-enolase	ENO1	○
	Unknown
103	Q96JP5	ZFP91_HUMAN	Zinc finger protein 91 homolog	ZFP91	○	○
104	Q9H5H4	ZN768_HUMAN	Zinc finger protein 768	ZNF768	○
105	Q14966	ZN638_HUMAN	Zinc finger protein 638	ZNF638	○
106	Q8NAF0	ZN579_HUMAN	Zinc finger protein 579	ZNF579	○
107	Q5VZL5	ZMYM4_HUMAN	Zinc finger MYM-type protein 4	ZMYM4	○
108	Q8N9Z2	YG034_HUMAN	Uncharacterized protein FLJ36031	FLJ36031	○
109	Q9Y4P3	TBL2_HUMAN	Transducin beta-like protein 2	TBL2	○
110	Q9UJZ1	STML2_HUMAN	Stomatin-like protein 2	STOML2	○
111	Q9P2N5	RBM27_HUMAN	RNA-binding protein 27	RBM27	○
112	Q5T8P6	RBM26_HUMAN	RNA-binding protein 26	RBM26	○
113	Q9NWS8	RMND1_HUMAN	Required for meiotic nuclear division protein 1 homolog	RMND1	○
114	Q6P158	DHX57_HUMAN	Putative ATP-dependent RNA helicase DHX57	DHX57	○
115	Q69YN4	VIR_HUMAN	Protein virilizer homolog	KIAA1429	○
116	Q9BX40	LS14B_HUMAN	Protein LSM14 homolog B	LSM14B	○
117	Q9Y520	BA2L2_HUMAN	Protein BAT2-like 2	BAT2L2	○
118	Q9ULL5	PRR12_HUMAN	Proline-rich protein 12	PRR12	○
119	Q96DN6	MBD6_HUMAN	Methyl-CpG-binding domain protein 6	MBD6	○
120	Q9UNF1	MAGD2_HUMAN	Melanoma-associated antigen D2	MAGED2	○
121	Q9NXS2	QPCTL_HUMAN	Glutaminyl-peptide cyclotransferase-like protein	QPCTL	○
122	Q96SL8	FIZ1_HUMAN	Flt3-interacting zinc finger protein 1	FIZ1	○
123	Q68CQ4	DEF_HUMAN	Digestive organ expansion factor homolog	C1orf107	○
124	Q9H0W5	CCDC8_HUMAN	Coiled-coil domain-containing protein 8	CCDC8	○

^a The proteins known to be associated with p32.