Table 1.
Features and requirements of UPF1-mediated RNA decay pathways.
| UMD | RNA Target | NMD Effectors | Translation Termination | Selected Other Effectors 1 | UPF1 Functions | UPF1 Phosphorylation | (p)-UPF1 Binding Factor | |
|---|---|---|---|---|---|---|---|---|
| ATPase | Helicase | |||||||
| NMD | mRNAs, (lncRNAs; snoRNA hosts) | UPF1+ (in variable combinations): UPF2, UPF3A, UPF3B, SMG1c, SMG6, SMG5/7 |
yes | EJC, Mov10, DHX34, SRSF1, NBAS, long 3′UTR decapping and deadenylation factors, 3–5′ and 5′–3′ exonucleases, PNRC2 |
yes | yes | yes | RNA? |
| SMD | mRNA | UPF1, UPF2, SMG1 | yes | STAU1, STAU2, dsRNA structures, PNRC2 | yes | yes | yes | UPF2 (STAU) |
| HMD | Histone mRNA | UPF1, SMG1 | yes | RNA stem loop SLBP, ATR, DNA–PK, 3‘hExo, PNRC2 |
yes | yes | yes | 3′UTR of histone mRNAs |
| RMD | Proinflammatory cytokine transcripts | UPF1, SMG1 | yes | Stem loop, with Py–Pu-Py-loop, regnase-1 |
yes | yes | yes | regnase-1 |
| SRD | mRNAs, circular RNAs | UPF1 | yes | GRBP1 | yes | yes | n.d. | Structured RNA |
| TRIM71-MD | CDKN1A/p21 mRNA | UPF1, SMG1, SMG7 | n.d. | TRIM71, TRIM71-binding stem loop in 3′UTR | n.d. | n.d. | implied 2 | TRIM71? |
| GC-rich 3′UTR-MD | mRNAs with GC-rich 3′UTRs | UPF1, UPF2, SMG1 | n.d. | n.d. | implied | implied | implied | GC-rich mRNA |
| UPF1/SMG7/miRNA-MD | mRNAs with CUG sequences embedded in miRNA seed sequences in 3′UTR | UPF1, SMG7, | n.d. | miRNA loaded AGO, NOT1, NOT3 | n.d. | no | n.d. | CUG embedded in 7mer miRNA seed sequence |
| TumiD | miRNA | UPF1 | no | Tudor staphylococcal/ micrococcal-like nuclease (TSN), AGO2, GW182 | n.d. | yes | No (by implication 2) | TSN |
| GMD | mRNA with GR-binding site often in 5′UTR | UPF1 | no | glucocorticoid, glucocorticoid receptor (GR), ATM, PNRC2, DCP1A, YBX1, HRSP12 | yes | yes | yes | GR-PNRC2 complex |
| ER NMD | ER-localized mRNAs | UPF1 (others?) |
n.d. | NBAS, SEC61β | n.d. | n.d. | No (by implication) | NBAS |
1 This list represents a selection of effectors as reported in the literature discussed in the text without claim to be exhaustive. 2 “implied” or “by implication“ indicates that the respective UPF1 function or feature was not tested directly but concluded upon by using UPF1 variants with mutations that interfere with these functions. N.d.: not determined.