Table 1.
A growing list of the factors participating in transcriptional elongation
| Factor | Function | Related factors/notes | |
|---|---|---|---|
| GAGA-factor | Generate nucleosome free region (132) and promoter structure for pausing (121) | NURF(133) | |
| GTFs | TFIID | Generate promoter structure for pausing (121) | |
| TFIIF | Increase elongation rate (10, 130) | Near promoters (101) | |
| TFIIS | Rescue backtracked Pol II (10, 57) | Pol III (38) | |
| Pausing factors | NELF | Stabilize Pol II pausing (86, 144) | |
| DSIF | Stabilize Pol II pausing (135)/facilitate elongation (46, 143) | ||
| P-TEFb | Phosphorylates NELF (36), DSIF (58), Pol II CTD (105) for pause release | ||
| Processivity factors | Elongin | Increase elongation rate (5) | |
| ELL | Increase elongation rate (120) | AFF4 (71) | |
| SEC | Contains P-TEFb and ELL (71) | Mediator (129), PAF (47) | |
| Activator | c-Myc | Can directly recruit P-TEFb (32) | |
| NF-κB | Can directly recruit P-TEFb (7) | ||
| Coactivator | Brd4 | Recruits P-TEFb (53, 147) | |
| Mediator | Recruits P-TEFb via SEC (129) | ||
| Capping machinery | CE | Facilitates P-TEFb recruitment (70), counters NELF/DSIF (77) | |
| RNMT a | Methylates RNA 5′ end to complete capping | Myc (29) | |
| Premature termination factors | Dcp2 | De-caps nascent RNA for Xrn2 digestion (14) | Dcp1a/Edc3 (14) |
| Microprocessor | Cleaves hairpin structure for Xrn2 digestion (136) | Tat, Senx (136) | |
| Xrn2 | ‘Torpedo’s Pol II with RNA 5′-3′ exonucleation (14, 136) | ||
| TTF2 | Release Pol II from DNA (14, 136) | ||
| Gdown1 | Anti-termination and stabilize paused Pol II (22, 50, 54) | TFIIF (54), Mediator (50) | |
| Histone chaperone | FACT | H2A/H2B eviction and chaperon (9, 94) | Tracks with Pol II (117) |
| Nap1 a | H2A/H2B chaperon (51) | RSC (73), CHD (137) | |
| Spt6 | H3/H4 chaperon (13) | Tracks with Pol II (117) | |
| Asf1 a | H3/H4 chaperon (118) | H3K56ac (113) | |
| Chromatin remodeler | RSC a | SWI/SNF remodeling in gene body(20) | H3K14ac (56) |
| Chd1 a | Maintain gene body nucleosome organization (42) | FACT, DSIF (137) | |
| NURF | ISWI remodeling at promoter (133) | GAGA factor (132) | |
| PARP | Transcription independent nucleosome loss (98) | Tip60 (99) | |
| PAF complex | Loading dock for elongation factors (119) | SEC (47), FACT (96) | |
| Histone tail modifiers | MOF | H4K16ac, recruit Brd4 (153) | H3S10ph, 14-3-3 (153) |
| Tip60 | H2AK5ac, activate PARP (99) | ||
| Elongator a | Acetylates H3, facilitate nucleosomal elongation (59) | Also in cytoplasm (59) | |
| Rpd3C (Eaf3) a | Deacetylates and inhibit spurious initiation in gene body (21) | H3K36me3 (21) | |
| Set1 a | H3K4me3 (60, 88) | MLL/COMPASS | |
| Set2 a | H3K36me3 (63), regulate acetylation-deacetylation cycle (21) | Rpd3C (21) | |
| PIM1 | H3S10ph, recruit 14-3-3 and MOF (152) | ||
| RNF20/40 | H2BK123ub1, facilitate nucleosomal DNA unwrapping (96) | UbcH6, PAF | |
a
Not directly covered in our main text.