Table 1 |.
Interface between RBPs and their effectors
| Effector | Effector proteina | Effector contact regionb | RBPa | RBP contact regionb | Kd (μM)c | Process regulated by the RBP-effector interaction |
|---|---|---|---|---|---|---|
| Spliceosome | SNRNP70 (U1-70K)d | RS domain (IDR) | SRSF1/2 (SC35) | RS domain (IDR) | Pre-mRNA splicing | |
| SNRPA (U1A)d | RRM1 domain (SD) | SAM68 (KHDRBS1) | Y-rich (YY) region (IDR) | |||
| SNRPC (U1C)d | N terminus (SD) | TIA1 | Q-rich domain (IDR) | |||
| U1 snRNAd | SL3 of U1 snRNA | FUS | RRM domain (SD) | |||
| U2AF65 | RS domain (IDR) | YBX1 | Basic/acidic repeats (IDR) | |||
| SMN | SMN | Tudor domain (SD) | ELAVL4 (HuD) | NR | mRNA transport, translation | |
| IGF2BP1 (ZBP1) | KH domain region | |||||
| KHSRP (FUBP2) | NR (methylated Arg) (IDR) | mRNA stability | ||||
| FUS | RGG box (IDR) and RRM (SD) | Pre-mRNA splicing | ||||
| Tudor domain (SD) and YG box (SD) | HNRNPR | RGG box (IDR) | mRNA transport, pre-mRNA splicing | |||
| SYNCRIP | RGG box (IDR) | |||||
| EWSR1 | RG domain (IDR) | NR | ||||
| YG box (SD) | FMRP | Internal segment (IDR) | mRNA transport, translation | |||
| NR | HNRNPU | RGG box (IDR) | NR | |||
| NIRs | TNPO1 | HEAT repeats (SD) | HNRNPA1 | PY-NLS SLiM (IDR)e | 0.042 | Nuclear import, RBP chaperoning/disaggregation |
| HNRNPA2B1 | ||||||
| EWSR1 | ||||||
| TAF15 | ||||||
| FUS | 0.0095 | |||||
| HNRNPF | Nuclear import | |||||
| HNRNPM | 0.01 | |||||
| HNRNPD | 0.0032 | |||||
| HNRNPDL | 1 | |||||
| SAM68 (KHDRBS1) | ||||||
| ELAVL1 (HUR) | ||||||
| KAP104(yeast) | Nab2p(yeast) | 0.037 | ||||
| Hrp1p(yeast) | 0.032 | |||||
| Kapβ1/Impα | HEAT/Arm repeats (SD) | TDP43 (TARDBP) | cNLS SLiM (IDR)e | 0.066 | Nuclear import, RBP chaperoning/disaggregation | |
| Motor proteins | Myo4p(yeast) | C terminus (SD) | She3p(yeast) | Pseudocoiled-coil (SD) | 0.058 | mRNA transport |
| She3p-She2p(yeast)f | P/R sites (IDR)-structure (SD) | 1.6 | ||||
| KIF11 | Tail domain (IDR/SD) | IGF2BP1 (ZBP1) | RRM domains (SD) | |||
| KIF3C | C terminus (IDR) | FMRP | NR | |||
| UPF1 | UPF1 | Helicase domain (SD) | SLBP | N-terminal half (IDR) | mRNA stability | |
| RecA domain (SD) and Thr28 (IDR) | ZC3H12A (regnase 1) | Internal segment (IDR) and RNase domain (SD) | ||||
| N terminus | STAU1/2 | Tubulin-binding domain (IDR) | ||||
| CCR4-NOT | CNOT1 | HEAT domain (SD) | ZFP36 (TTP) | SLiM (IDR) | 2 | mRNA stability, translation |
| ZFP36L1 (BRF1) | ||||||
| NR | TNRC6C (GW182)g | W-containing motifs (IDR) | ||||
| CNOT9 | Concave surface (SD) | Bam | CBM SLiM (IDR) | 0.183 | ||
| RC3H1/2 (Roquin 1/2) | mRNA stability | |||||
| CNOT4 | mRNA stability | |||||
| Convex surface (W pockets) (SD) | ZFP36 (TTP) | Isolated W residues (IDR) | 5.5 | mRNA stability | ||
| TNRC6A/C (GW182)g | mRNA stability, translation | |||||
| NOT module | NR (SD) | RC3H1/2 (Roquin 1/2) | C terminus (IDR) | mRNA stability | ||
| HELZ | mRNA stability, translation | |||||
| PUM1/2 | N-terminal domain (IDR) | |||||
| Bicaudal C | KH domains (SD) | |||||
| SHD (SD) | NANOS1–3 | SLiM (IDR) | Translation | |||
| YTHDF2 | P/Q/N-rich region (IDR) | RNA stability | ||||
| CNOT4 | C terminus (IDR) | mRNA stability | ||||
| PABPC | PABPC1 | MLLE domain (SD) | ATXN2 | PAM2 SLiM (IDR) | 0.7 | RBP chaperoning |
| HELZ | NR | |||||
| NR | USP10 | 26 | NR | |||
| Multiple domains | MKRN1 | RQC, translation | ||||
| PABPC1/4 | NR | NFX1 | mRNA stability | |||
| 4EHP | 4EHP | Dorsal surface (SD) | Bicoid (Bcd) | SLiM (IDR) | Translation | |
| NR | PKNOX1 (Prep1) | |||||
| eIF4G | TIF4631/2(yeast) | C terminus | Scd6(yeast) | RGG box (IDR) | ||
| Khd1(yeast) | NR | |||||
| Internal region | Sbp1(yeast) | RGG box (IDR) | ||||
| Internal region and C terminus | Npl3(yeast) |
CBM, CAF40-binding motif; IDR, intrinsicaLLy disordered region; Kd, dissociation constant; NIR, nuclear import receptor; NLS, nuclear localization sequence; NR, not reported; PABPC, cytoplasmic poly(A)-binding protein; PY-NLS, proline-tyrosine-rich NLS; RBP, RNA-binding protein; RQC, ribosome quality control; RRM, RNA recognition motif; SD, structured domain; SLiM, short linear motif; SMN, survival motor neuron protein; snRNP, small nuclear ribonucleoprotein; STAU, Staufen; TNPO1, transportin 1.
Only those direct RBP-effector interactions are listed where a contact region has been mapped in at least one of the interacting proteins. For a fully referenced list of direct and indirect interactions, see Supplementary Table 2. Effectors and RBPs are named by their official gene symbol with text in brackets indicating popular aliases. All interacting proteins are metazoan except for the indicated yeast proteins.
IDR (or its part) or SD (or its part) in brackets indicates peptide organization of the contact region in its non-bound state. Where not reported, this information was obtained through modelling of the protein structure using the structure prediction algorithm AlphaFold173.
The Kd in most cases pertains to an in vitro interaction between SLiM of an RBP and the interacting effector domain or the full-length effector protein.
Part of U1 snRNP.
Both She2p and She3p are RBPs in contact with the transported mRNA62.