| 1997 |
PCF11 encodes an essential protein component of yeast Cleavage Factor I (CF I), required for pre-mRNA cleavage and polyadenylation. Thermosensitive pcf11 mutations cause shortening of poly(A) tails and decreased mRNA levels; antibody neutralization of Pcf11 abolishes cleavage and polyadenylation in vitro. Pcf11 co-fractionates with Rna15 in CF I fractions and was identified via two-hybrid interaction with Rna14 and Rna15. |
Two-hybrid screen, co-fractionation by anion-exchange chromatography, in vitro cleavage/polyadenylation assay with antibody neutralization, thermosensitive mutant analysis |
Molecular and cellular biology |
High |
9032237
|
| 2005 |
A 140-amino acid fragment of yeast Pcf11 containing the CTD-interaction domain (CID) dismantles elongating RNA Pol II complexes in vitro by bridging the CTD to the nascent transcript, causing dissociation of both Pol II and transcript from DNA without nucleotide hydrolysis. This mechanism requires both the CTD of the Pol II largest subunit and the CID of Pcf11. |
In vitro elongation complex dismantling assay using purified yeast Pol II; CID mutant analysis |
Genes & development |
High |
15998810
|
| 2005 |
The Pcf11 CTD-interacting domain (CID) binds phosphorylated Pol II CTD heptad repeats by induced fit: the disordered phospho-CTD adopts a structured conformation upon binding to Pcf11 CID. Binding is regulated by CTD phosphorylation and proline cis-trans isomerization (only the all-trans CTD proline form is selected). |
NMR spectroscopy, structural and biophysical interaction analyses |
Nature structural & molecular biology |
High |
15665873
|
| 2006 |
Drosophila Pcf11 (dPcf11) is directly involved in transcription termination in metazoans: it localizes to the 3' end of the hsp70 gene and to most transcribed loci on polytene chromosomes. RNAi depletion causes Pol II readthrough at normal termination sites. Biochemically, dPcf11 dismantles elongation complexes by bridging the CTD to RNA in a CTD-dependent but nucleotide-independent manner, and preferentially dismantles paused (low nucleotide) elongation complexes. |
RNAi knockdown with Pol II ChIP readthrough assay; immunolocalization on polytene chromosomes; in vitro elongation complex dismantling assay |
Molecular cell |
High |
16387654
|
| 2006 |
The Pcf11 CID also weakly binds RNA, and CTD phosphopeptides compete with RNA for the same binding surface on the CID. This competition between CTD and RNA at the CID is proposed to be mechanistically important for disengaging polyadenylation factors from Pol II. |
NMR chemical shift perturbation and competitive binding assays with CTD phosphopeptides and RNA |
RNA (New York, N.Y.) |
Medium |
16497660
|
| 2006 |
Crystal structure of a ternary Clp1–ATP–Pcf11 complex reveals that Clp1 contains three domains with a central ATP-binding site resembling SIMIBI-class ATPases but without hydrolysis activity. Three conserved Pcf11 residues mediate the Clp1–Pcf11 interaction at the central domain, maintaining coupling between the nucleotide-binding subunit and the polyadenylation machinery. |
X-ray crystallography; ATPase activity assay |
Nucleic acids research |
High |
17151076
|
| 2007 |
Human PCF11 (hPcf11) is required for efficient transcription termination by Pol II and for degradation of the downstream 3' cleavage product of the poly(A) site in human (HeLa) cells. Both functions require an intact poly(A) signal. |
siRNA knockdown in HeLa cells; RT-PCR and nuclear run-on termination assays; RNA processing assays |
Nucleic acids research |
Medium |
18086705
|
| 2011 |
Yeast Clp1 interacts with the CPF complex through its N-terminal and central domains, bridging CF IA and CPF. Mutations in the Clp1 ATP-binding site that displace ATP do not affect ATP binding per se but disrupt the Clp1–Pcf11 interaction, and a Pcf11 mutation that disrupts the Clp1 contact causes defects in 3'-end processing and transcription termination in vivo. |
Yeast genetics, growth assays, in vitro 3'-end processing assays, co-immunoprecipitation |
Nucleic acids research |
High |
21993299
|
| 2015 |
In S. cerevisiae, Pcf11 is generally required for NRD-dependent transcription termination of short ncRNAs, acting downstream of Nrd1. Pcf11 recruitment depends on Nrd1, and mutation of the Pcf11 CID causes Nrd1 retention on chromatin, delayed ncRNA degradation, restricted Pol II CTD Ser2 phosphorylation, and impaired Sen1–Pol II interaction. An exchange of Nrd1 and Pcf11 on chromatin facilitates Pol II pausing and CTD Ser2-P phosphorylation required for Sen1-dependent NRD termination. |
ChIP-seq, RNA-seq, genetic analysis with CID mutants, chromatin fractionation |
Genes & development |
High |
25877920
|
| 2016 |
The C-terminal domain of Pcf11 (conserved from yeast to humans) forms a novel zinc-finger fold resembling a trillium flower. A conserved surface on this zinc finger is required for both cleavage and polyadenylation activities, as determined by structural, biochemical, and genetic analyses. |
X-ray crystallography, NMR, in vitro cleavage/polyadenylation assay, yeast genetics |
RNA (New York, N.Y.) |
High |
27780845
|
| 2017 |
Yeast Pcf11 contains two separate Zn2+-binding zinc-finger domains flanking the Clp1-recognition region. These zinc-finger domains are not required for CF IA assembly or Pol II termination but contribute to different extents to pre-mRNA 3'-end cleavage and polyadenylation. |
Structural characterization (NMR/X-ray), mass spectrometry, in vitro cleavage/polyadenylation assays, yeast genetic complementation |
Nucleic acids research |
High |
28973460
|
| 2017 |
Nuclear-localized WNK1 kinase phosphorylates the PCF11 CID, which weakens PCF11's interaction with Pol II CTD. This phosphorylation event promotes transcript release from chromatin-associated Pol II and facilitates mRNA export to the cytoplasm. |
In vitro kinase assay, co-immunoprecipitation, chromatin RNA-seq, mRNA export assay in mammalian cells |
Genes & development |
High |
29196535
|
| 2019 |
Vertebrate PCF11 enhances transcription termination and stimulates early (premature) cleavage and polyadenylation genome-wide. PCF11 preferentially binds between closely spaced genes to prevent transcriptional interference. PCF11 is sub-stoichiometric to the CPA complex and autoregulates its own levels via premature termination of its own transcript. PCF11 selectively attenuates transcriptional regulators by premature CPA/termination and is essential for vertebrate development. |
mNET-seq, 3' mRNA-seq, chromatin RNA-seq, ChIP-seq, PCF11 depletion in human cells and zebrafish CRISPR/morpholino knockdown |
Molecular cell |
High |
30819644
|
| 2019 |
PCF11 modulates gene expression according to gene size: downregulation of PCF11 inhibits short gene expression while upregulating long genes by suppressing intronic polyadenylation (IPA) enriched in large introns. PCF11 autoregulates itself through a conserved IPA site; removing this IPA site leads to global activation of promoter-proximal poly(A) sites. |
siRNA knockdown, 3' mRNA-seq (poly(A)-seq), CRISPR deletion of IPA site, cell differentiation assays |
Cell reports |
High |
30840896
|
| 2018 |
PCF11 is a critical regulator of alternative polyadenylation (APA) in neuroblastoma, directing APA of hundreds of transcripts including a differentiation RNA-operon. PCF11 shapes inputs converging on WNT signaling and governs cell cycle, proliferation, apoptosis, and neurodifferentiation. Postnatal PCF11 downregulation induces a neurodifferentiation program. |
Extensive RNAi screening, 3' mRNA-seq, functional assays for proliferation/apoptosis/differentiation in neuroblastoma cell lines |
Nature communications |
High |
30552333
|
| 2023 |
PCF11 represses HIV-1 transcription by promoting premature transcription termination independently of the CPA complex or the 5' LTR poly(A) signal. PCF11 interacts with WDR82, and together they are recruited interdependently to the promoter-proximal region of the HIV-1 provirus. Knockdown of PCF11 or WDR82 reactivates HIV-1 expression in latently infected cells, and they act on the same pathway. |
Co-immunoprecipitation, ChIP-seq, siRNA knockdown in latently infected T cells, HIV-1 reactivation assay |
Proceedings of the National Academy of Sciences of the United States of America |
High |
38015843
|
| 2024 |
PCF11 is identified as a reader of the cap-specific RNA modification m6Am (N6,2'-O-dimethyladenosine). m6Am sequesters PCF11 away from proximal Pol II near transcription start sites, suppressing PCF11-mediated premature transcription termination and promoting full-length transcription. This anti-terminator function is enhanced when PCF11 levels are reduced (as during neuroblastoma differentiation therapy), and it operates through ATF3 upregulation to repress MYCN. |
Quantitative proteomics (m6Am-modified RNA pulldown), direct quantification of mature vs. nascent RNA, PCF11 knockdown, m6Am depletion assays in neuroblastoma cells |
Molecular cell |
High |
39481383
|
| 2025 |
In Drosophila germ line, Pcf11 and Spt5 form condensates that stall RNA Pol II to facilitate transcription termination and piRNA-guided heterochromatin formation. Pcf11 enforced tethering causes co-transcriptional repression and Pol II stalling dependent on an α-helical condensate-forming region. Pcf11 preferentially forms condensates with unphosphorylated Spt5, promoted by PP1/PNUTS phosphatase activity during termination. |
RNAi screening, tethering assays, phase separation/condensate assays, Pol II ChIP, piRNA pathway genetic epistasis |
Molecular cell |
High |
40015272
|
| 2025 |
PCF11 collaborates with SPT6 and PNUTS in transcription termination: SPT6 depletion causes readthrough transcription, and SPT6 facilitates termination by recruiting PNUTS and PCF11 to Pol II. SPT6 and PNUTS jointly restrict PROMPTs, while PCF11 presence is required for PROMPT accumulation at hundreds of genes in the absence of SPT6. |
siRNA knockdown, ChIP-seq, RNA-seq for readthrough and PROMPT detection in human cells |
Nucleic acids research |
Medium |
40103229
|
| 2025 |
PCF11 and Cbc (the two components of Cleavage Factor complex II) change subnuclear localization during male germ cell differentiation in Drosophila, moving from homogeneous nuclear distribution in spermatogonia to concentrated around the nucleolus in later spermatocyte stages, coinciding with developmentally regulated 3'UTR shortening via alternative polyadenylation. |
Immunofluorescence, confocal microscopy in Drosophila spermatocytes |
microPublication biology |
Medium |
40896257
|
| 2025 |
PCF11 interacts with swine influenza virus NP protein to promote viral polymerase activity, facilitating vRNP assembly and viral mRNA synthesis. PCF11 negatively regulates the IFN-β signaling pathway, further facilitating RNA virus replication. |
Co-immunoprecipitation, viral polymerase activity assay, siRNA knockdown, IFN-β reporter assay |
Microbiological research |
Medium |
40252262
|