Table 1.
A representative list of potential RBPs revealed by HuProt arrays. This list includes 53 oxidative-reductases, 17 small GTPases and 87 transcriptional and chromatin regulators. Proteins detected in previously reported RNA interactomes are labeled with ‘√’ or as indicated (10–17). Potential RBPs uniquely detected by HuProt arrays are indicated as ‘only in this study’ with maximal z-scores shown in brackets
| RNA interactomes reported in vivo | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| mRNA interactomes by oligo (dT) capture | RBD mapping | aRICK-16 h | RICK-0.5 h, 1 h, 2 h | |||||||||||
| Proteins bound to RNA on HuProt arrays | Kwon et al., 2013 | Baltz et al., 2012 | Castello et al., 2012 | Bao et al., 2018 | Beckmann et al., 2015 | Castello et al., 2016 | Liao et al., 2016 | He et al., 2016 | Bao et al., 2018 | |||||
| Category | Protein hits | Max z-score | # of times identified | mESCs | HEK293 | HeLa | HeLa | HuH-7 | HeLa | HL-1 | mESCs | HeLa | HeLa | |
| Metabolic enzymes (53) | Reported previously | QDPR | 3352 | 1 | √ | |||||||||
| IDH1 | 1935 | 3 | √ | √ | √ | |||||||||
| MTHFD1 | 429 | 3 | √ | √ | √ | |||||||||
| BLVRB | 52 | 2 | √ | √ | ||||||||||
| ACOX1 | 41 | 1 | √ | |||||||||||
| IMPDH2 | 36 | 1 | √ | |||||||||||
| ENOX1 | 36 | 1 | √ | |||||||||||
| PDIA5 | 35 | 1 | √ | |||||||||||
| AKR1B1 | 33 | 1 | √ | |||||||||||
| COX4I1 | 24 | 2 | √ | √ | ||||||||||
| GBE1 | 20 | 1 | √ | |||||||||||
| PGK1 | 19 | 4 | √ | √ | √ | √ | ||||||||
| ENO1 | 19 | 6 | √ | √ | √ | √ | √ | √ | ||||||
| PRDX1 | 18 | 9 | √ | √ | √ | √ | √ | √ | √ | √ | √ | |||
| AKR1C3 | 16 | 1 | √ | |||||||||||
| DHCR7 | 15 | 1 | √ | |||||||||||
| GYS1 | 13 | 1 | √ | |||||||||||
| DLD | 12 | 4 | √ | √ | √ | √ | ||||||||
| G6PD | 11 | 3 | √ | √ | √ | |||||||||
| Only in this study | TP53I3 (3440) | BDH2 (1433) | ALDH1L1 (2603) | AKR1D1 (798) | COQ6 (87) | NDUFB11 (64) | CRYZ (60) | D2HGDH (43) | DECR2 (42) | CYB561 (38) | IMPDH1 (37) | ZADH2 (36) | ALDH1A1 (30) | |
| DCT (32) | CPOX (30) | HACL1 (29) | GLRX2 (29) | AKR7A2 (27) | PFKL (24) | MECR (24) | FOXRED2 (20) | DDO (19) | PIR (18) | ACAA1 (17) | CYBA (14) | CYP8B1 (13) | ||
| MLYCD (13) | HK3 (12) | LOXL3 (12) | SCCPDH (12) | GFOD1 (12) | AKR7A3 (11) | PTGIS (11) | CRAT (10) | |||||||
| Small GTPases (17) | Reported previously | RAB11A | 39 | 1 | √ | |||||||||
| CDC42 | 29 | 1 | √ | |||||||||||
| RAB14 | 11 | 1 | √ | |||||||||||
| Only in this study | RAB1A (11) | RAB2A (39) | RAB4A (22) | RAB4B (38) | RAB5B (15) | RAB7L1 (49) | RAB9B (109) | RAB17 (21) | RAB43 (14) | RHOA (27) | RHOB (10) | RHOG (17) | RAC2 (26) | |
| RABL3 (31) | ||||||||||||||
| Transcriptional & chromatin regulators (87) | Reported previously | TRIM28 (30) | TRIM24 (21) | DNMT3A (38) | SMARCE1 (44) | EED (18) | CBX1 (13) | HOXB6 (27) | CHD2 (11) | NACA (26) | ZNF326 (17) | HIST1H1C (29) | H1F0 (11) | H1FX (56) |
| GTF2I (39) | RBBP5 (18) | PAF1 (62) | SET (10) | SMARCC1 (11) | SMARCC2 (10) | RNF10 (10) | TRIP6 (28) | NAP1L1 (22) | HMGN1 (112) | NUCKS1 (13) | H2AFY2 (30) | ASCC1 (26) | ||
| CTNNB1 (14) | NDC80 (16) | PQBP1 (32) | SND1 (16) | G3BP1 (13) | ZCCHC9 (11) | CDC73 (12) | GTF3C2 (11) | ILF3 (24) | TARDBP (36) | UBE2N (42) | IFI16 (11) | |||
| Only in this study | MED8 (26) | DAXX (62) | PRDM15 (29) | POU4F2 (10) | FOXG1 (42) | APP (12) | ASXL2 (74) | BCOR (29) | CENPN (15) | EAF1 (14) | EYA4 (16) | HIST1H1A (35) | IKZF3 (17) | |
| RBBP8 (45) | TAF7 (15) | APBB1 (55) | MEF2C (16) | MNDA (12) | NEUROD1 (10) | NFYA (22) | NIF3L1 (19) | OVOL2 (16) | PCGF3 (17) | ING3 (17) | JDP2 (10) | PRMT8 (45) | ||
| SCMH1 (12) | SEH1L (12) | SIRT5 (23) | SSBP2 (30) | SUDS3 (16) | RORC (11) | TCEAL5 (305) | TCEAL6 (132) | TERF2IP (14) | TLX2 (10) | TP53 (11) | TTN (50) | VGLL4 (17) | ||
| WT1 (13) | ZNF226 (19) | ZNF274 (22) | ZNF350 (21) | ZNF485 (17) | ZNF502 (13) | ZNF528 (12) | ZNF791 (11) | ZXDC (34) | PIR (18) | |||||
aRICK (capture of the newly transcribed RNA interactome using click chemistry) (13).