Table 1 RNA-binding proteins identified to interact with HIV-RNA using HyPR-MS.

From: Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry

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	^70,71,72
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	^{8,11,73,74,75,76}
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

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Table 1 RNA-binding proteins identified to interact with HIV-RNA using HyPR-MS.

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