| 1997 |
RTF1 was identified as a nuclear protein whose mutation or deletion suppresses transcription start site alterations caused by a TBP specificity mutant, placing RTF1 as a regulator of TBP-dependent TATA site selection in vivo. |
Genetic suppressor screen, indirect immunofluorescence localization, transcription initiation analysis |
Molecular and cellular biology |
Medium |
9234706
|
| 2000 |
RTF1 functions as a transcription elongation factor, demonstrated by synthetic lethality with elongation factor genes (SPT4, SPT5, SPT16, PPR2, SRB5, CTK1, FCP1, POB3) and sensitivity to 6-azauracil and mycophenolic acid. |
Synthetic lethal screen, drug sensitivity assay (6-azauracil, mycophenolic acid), genetic epistasis |
Genetics |
Medium |
11014804
|
| 2002 |
Rtf1, Ctr9, and Leo1 are components of the Paf1-RNA Pol II complex, physically associating with Paf1, Cdc73, and Pol II but not with the Srb-mediator complex; deletion of RTF1 suppresses many paf1Δ phenotypes including reduced CLN1 expression. |
Tandem affinity purification, mass spectrometry, genetic analysis of double mutants |
Molecular and cellular biology |
High |
11884586
|
| 2003 |
Rtf1 is required for global histone H2B ubiquitination at K123, and this is the indirect mechanism by which Rtf1 promotes H3-K4 and H3-K79 methylation; Rtf1 is also required for Set1 recruitment to active genes for H3-K4 methylation but not for H3-K36 methylation. |
Chromatin immunoprecipitation, histone modification analysis by western blot, genetic deletion analysis |
The Journal of biological chemistry |
High |
12876293
|
| 2008 |
The NMR structure of the human Rtf1 Plus3 domain reveals structural similarity to PAZ and Tudor domains; the Plus3 domain binds single-stranded DNA via basic residues on the rim of its beta sheet in vitro, but does not bind double-stranded DNA or RNA. |
NMR structure determination, in vitro DNA/RNA binding assay |
Structure |
High |
18184592
|
| 2008 |
S. pombe Rtf1 (replication termination factor 1, a distinct protein from transcription factor Rtf1/Prf1) mediates site-specific replication termination at RTS1 via two myb/SANT DNA-binding domains and self-interaction through its C-terminal tail. NOTE: This paper describes the S. pombe replication termination Rtf1, which is a different protein from the transcription elongation Rtf1/Prf1 discussed in other papers. |
Domain characterization, DNA binding assays, genetic analysis with dominant-negative mutants |
Genetics |
Low |
18723894
|
| 2011 |
Single amino acid substitutions within the Rtf1 histone modification domain (HMD) abolish H2B ubiquitylation and impair H3 methylation, and also disrupt 3'-end formation of snoRNA transcripts, identifying H2B K123 ubiquitylation as required for noncoding RNA termination. |
Site-directed mutagenesis, histone modification assays, snoRNA 3'-end analysis, telomeric silencing and elongation assays |
Genetics |
High |
21441211
|
| 2012 |
A 90-amino acid histone modification domain (HMD) within Rtf1 is sufficient to promote H3 K4 and K79 methylation and H2B K123 ubiquitylation independently of other Paf1C subunits when expressed as the only source of Rtf1; this function requires Rad6-Bre1 and conserved HMD residues important for chromatin association. |
Domain truncation and expression analysis, chromatin immunoprecipitation, histone modification western blot, DNA binding domain fusion experiments |
PNAS |
High |
22699496
|
| 2013 |
A conserved domain of Rtf1 (Spt5-interacting domain) directly and physically interacts with the Spt5 C-terminal repeat domain (CTR), and this interaction is necessary and sufficient for tethering Paf1C to active chromatin; mutations disrupting this interaction or deletion of the Spt5 CTR release Paf1C from chromatin. |
In vitro binding assay, ChIP, genetic mutations, domain sufficiency experiments |
Molecular and cellular biology |
High |
23775116
|
| 2013 |
In S. pombe, Cdk9 phosphorylation of Spt5 creates a direct binding site for Prf1/Rtf1; Prf1 and the PAF complex are biochemically separable and exert opposing effects on the RNAPII elongation complex, with Prf1 negatively regulating elongation through H2B monoubiquitylation. |
Biochemical fractionation, genetic epistasis, phosphorylation-dependent binding assays |
PLoS genetics |
Medium |
24385927
|
| 2015 |
Human Rtf1 functions as a transcription elongation factor independently of the PAF1 complex; its Plus3 domain is critical for coactivator-dependent transcription activation in vitro; human Rtf1 and PAF1C regulate distinct gene subsets and PAF1C is recruited to genes independently of Rtf1 in human cells. |
In vitro transcription assay, RNA-seq, ChIP, mutational analysis |
Molecular and cellular biology |
Medium |
26217014
|
| 2016 |
The Rtf1 HMD directly interacts with the ubiquitin conjugase Rad6 and stimulates H2B monoubiquitylation independently of transcription; the crystal structure of the Rtf1 HMD was solved; site-specific in vivo crosslinking identified a conserved Rad6 interaction surface on the HMD; the HMD stimulates H2Bub in a transcription-free reconstituted in vitro system. |
Crystal structure determination, in vitro reconstitution, site-specific in vivo crosslinking, ChIP-exo, biochemical pulldown |
Molecular cell |
High |
27840029
|
| 2020 |
Cryo-EM structure of the complete Pol II elongation complex reveals RTF1 Plus3 domain associates with RPB12 and phosphorylated SPT5 CTR; RTF1 forms four α-helices extending along the Pol II protrusion and RPB10 to the polymerase funnel; a C-terminal 'fastener' helix retains PAF and a 'latch' reaches the bridge helix; RTF1 strongly stimulates Pol II elongation, requiring the latch, suggesting allosteric activation of translocation. |
Cryo-EM structure determination, in vitro transcription elongation assay, structure-function mutagenesis |
Nature structural & molecular biology |
High |
32541898
|
| 2020 |
In S. pombe, the Plus3 domain of Prf1/Rtf1 and phospho-Spt5 (pSpt5) function through parallel, distinct pathways to promote Prf1 function; the Plus3 domain has an alternate interface overlapping the pSpt5-binding site that can interact with single-stranded nucleic acid or PAF complex in vitro. |
Genetic epistasis, in vitro binding assay, domain mutational analysis |
Molecular and cellular biology |
Medium |
32366382
|
| 2023 |
The Rtf1 HMD interaction surface on Rad6 was mapped to the highly conserved N-terminal helix of Rad6; separation-of-function mutations disrupting the Rad6-HMD interface impair H2BK123 ubiquitylation but not other Rad6 functions; RNA-seq profiles of these mutants overlap extensively with those of H2B ubiquitylation-site mutants. |
In vitro crosslinking followed by mass spectrometry, genetic separation-of-function mutations, in vivo protein crosslinking, RNA-seq |
PNAS |
High |
37216505
|
| 2023 |
Rtf1 is essential for cardiogenesis in zebrafish and mammals; cardiac progenitors arrest in an immature state in rtf1 morphants/mutants; Rtf1's Plus3 domain (mediating Spt5 interaction) is required for cardiac progenitor formation; loss of Rtf1 reduces RNA Pol II occupancy at TSS of cardiac genes, reflecting reduced transcriptional pausing; pharmacological CDK9 inhibition restores cardiomyocyte formation in Rtf1-deficient embryos. |
Morpholino knockdown, genetic knockout (zebrafish and mouse), ChIP-seq, CDK9 inhibitor rescue experiments |
bioRxivpreprint |
Medium |
37873297
|
| 2026 |
Rtf1 promotes promoter-proximal pausing of RNA Pol II; its Plus3 domain mediating Spt5 interaction is required for cardiogenic activity; in Rtf1-deficient zebrafish embryos RNA Pol II TSS occupancy is reduced relative to downstream occupancy, and CDK9 inhibition restores TSS occupancy and cardiomyocyte formation. |
Genetic knockout (zebrafish and mouse), ChIP-seq, CDK9 morpholino and pharmacological inhibition rescue, structure-function analysis |
eLife |
Medium |
41537425
|
| 2025 |
An N-terminal region of Rtf1 directly interacts with the CHCT domain of Chd1 nucleosome remodeler; disruption of this interaction causes Chd1 accumulation at 5' gene ends, increased cryptic transcription, altered nucleosome positioning, and shifted histone modification profiles; a homologous region of mouse RTF1 also interacts with mouse CHD1 and CHD2 CHCT domains. |
Pull-down/co-IP interaction assays, domain mapping, mutagenesis, ChIP-seq, nucleosome positioning assays, cryptic transcription reporter |
Nucleic acids research |
High |
40867051
|
| 2025 |
RTF1 physically interacts with CLOCK in Drosophila pacemaker neurons and promotes CLK occupancy at per and other clock gene promoters; SET1 forms a complex with CLK and RTF1 and increases H3K4me3 at per/tim promoters; human RTF1 physically interacts with BMAL1/CLOCK and affects circadian rhythms in U2OS cells. |
Co-immunoprecipitation, ChIP, H3K4me3 assays, genetic knockdown with behavioral rescue, overexpression rescue |
The Journal of cell biology |
Medium |
41186576
|
| 2025 |
RTF1 facilitates histone H2B monoubiquitination (H2Bub1) through its HMD domain to support Th17 cell differentiation; cells lacking the H2Bub1 E3 ligase subunit RNF40 (a known RTF1 physical interactor) similarly impair Th17 differentiation, while Treg differentiation is unaffected. |
Conditional knockout, histone modification western blot, T cell differentiation assays, genetic epistasis with RNF40 |
Journal of immunology |
Medium |
40073106
|
| 2025 |
RTF1 stimulates H2B-K120 ubiquitylation and H3K4me3 but RTF1 (unlike PAF1) does not contribute to transcription restart after DNA damage, dissociating RTF1's histone modification activity from the PAF1C-dependent transcription restoration function. |
Transcription recovery assay after UV damage, histone modification analysis, siRNA knockdown |
bioRxivpreprint |
Low |
bio_10.1101_2025.07.23.666359
|