Table 1.

RNA-binding proteins identified to interact with HIV-RNA using HyPR-MS.

Gene ID	Protein Name	Proposed Function in HIV Replication	Previous evidence of HIV-RNA binding?	Refs
Transcription/Regulation of Transcription
FUBP1	Far upstream element-binding protein 1	Unknown	No
HIST1H1B	Histone H1.5	Unknown	No
HSPD1	60 kDa heat shock protein	Yes	No	73
ILF2	Interleukin enhancer-binding factor 2	Yes	Yes	23,73,112
NPM1	Nucleophosmin	Transcription	Yes	23,73,103
TRIM28	Transcription intermediary factor 1-beta	Early HIV Replication	Yes	23,73,90,127
Splicing/Splicesome
DDX5	DEAD box protein 5	Nucleocytoplasmic Transport	Yes	23,55,73,126
EIF4A3	Eukaryotic initiation factor 4A-III	Yes	No	73
FUS	RNA-binding protein FUS	Yes	Yes	8,54
HNRNPA1	Heterogeneous nuclear ribonucleoprotein A1	Splicing, Nucleocytoplasmic Transport	Yes	23,61,62,73,116
HNRNPC	Heterogeneous nuclear ribonucleoprotein C	Yes	No	73
HNRNPD	Heterogeneous nuclear ribonucleoprotein D	Splicing, Nucleocytoplasmic Transport	Yes	23,63,73
HNRNPK	Heterogeneous nuclear ribonucleoprotein K	Splicing	Yes	23,65,73
HNRNPR	Heterogeneous nuclear ribonucleoprotein R	Yes	Yes	23,65,73
LUC7L2	Putative RNA-binding protein Luc7-like 2	Yes	No	73
PCBP2	Poly(rC)-binding protein 2	Yes	Yes	42
RBM8A	RNA-binding protein 8A	Unknown	No
SYNCRIP	Heterogeneous nuclear ribonucleoprotein Q	Splicing	Yes	23,73
Translation/Regulation of Translation
CALR	Calreticulin	Unknown	No
EEF1A1	Elongation factor 1-alpha 1	Early HIV Replication, Translation, RNA Packaging	Yes	23,73,111,122
EEF1D	Elongation factor 1-delta	Early HIV Replication, Translation	No	73,122
ELAVL1	ELAV-like protein 1 (HuR)	Translation	No	70–72
LRPPRC	Leucine-rich PPR motif-containing protein	Yes	No	73,120
NCL	Nucleolin	RNA Packaging/Budding	Yes	23,73,79
YBX3	Y-box-binding protein 3	Unknown	Yes	8
P-body/Stress Granule
CAPRIN1	Caprin-1	Yes	Yes	8,73
MOV10	Putative helicase MOV-10	Nucleocytoplasmic Transport, RNA Packaging	Yes	8,11,73–76
PSMA6	Proteasome subunit alpha type-6	Transcription	No	128
YBX1	Nuclease-sensitive element-binding protein 1	Yes	Yes	40,73,92
Structural Molecule/Cytoskeleton
ANXA1	Annexin A1	Unknown	No
FLNB	Filamin-B	Unknown	No
Gag/Gag-Pol	Gag/Gag-Pol polyprotein	Yes	No	15,45
RPL10A	60S ribosomal protein L10a	Unknown	No
RPL11	60S ribosomal protein L11	Unknown	No
RPL23	60S ribosomal protein L23	Unknown	No
RPL6	60S ribosomal protein L6	Yes	No	73
RPSA	40S ribosomal protein SA	Unknown	No
SPTBN1	Spectrin beta chain	Unknown	No	19,105
TUBA1B	Tubulin alpha-1B chain	Yes	Yes	8,17,105
Other
ARF1	ADP-ribosylation factor 1	Yes	No	102
CCT6A	T-complex protein 1 subunit zeta	Unknown	No
HSP90B1	Endoplasmin	Unknown	Yes	23
HSPA9	Stress-70 protein	Yes	No	73
HSPE1	10 kDa heat shock protein	Unknown	No
MDH2	Malate dehydrogenase	Unknown	No
P4HB	Protein disulfide-isomerase	Unknown	No
PDIA3	Protein disulfide-isomerase A3	Yes	No	119
PDIA4	Protein disulfide-isomerase A4	Unknown	No
PEBP1	Phosphatidylethanolamine-binding protein	Unknown	No
PPIA	Peptidyl-prolyl cis-trans isomerase A	Early HIV Replication	No	93,96
PRDX1	Peroxiredoxin-1	Unknown	No
PRMT1	Protein arginine N-methyltransferase 1	Unknown	No
STIP1	Stress-induced-phosphoprotein 1	Unknown	No
YWHAE	14-3-3 protein epsilon	Unknown	No
YWHAG	14-3-3 protein gamma	Unknown	No
YWHAZ	14-3-3 protein zeta/delta	Unknown	No