Annotation inferences using phylogenetic trees
Gene Ontology annotation based on curation of immunofluorescence data
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
Combined Automated Annotation using Multiple IEA Methods
AATF, a novel transcription factor that interacts with Dlk/ZIP kinase and interferes with apoptosis.
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AATF was identified as a 523-amino-acid nuclear phosphoprotein that interacts with the pro-apoptotic kinase Dlk/ZIP kinase and antagonizes Dlk-induced apoptosis.
"In search for interaction partners that might serve as regulators or targets of this kinase we identified apoptosis antagonizing transcription factor (AATF), a nuclear phosphoprotein of 523 amino acids."
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AATF contains an extremely acidic domain and a putative leucine zipper, and a Gal4-BD-AATF fusion protein exhibited strong transactivation activity, establishing AATF as a transcription factor.
"AATF contains an extremely acidic domain and a putative leucine zipper characteristic of transcription factors. Indeed, a Gal4-BD-AATF fusion protein exhibited strong transactivation activity."
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AATF interfered with Dlk-induced apoptosis, establishing its anti-apoptotic function.
"Interestingly, AATF interfered with Dlk-induced apoptosis."
Identification of a novel partner of RNA polymerase II subunit 11, Che-1, which interacts with and affects the growth suppression function of Rb.
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Che-1/AATF was identified as a novel interaction partner of hRPB11 (POLR2J), a core subunit of RNA polymerase II, and possesses a domain with high homology to E. coli RNA polymerase sigma factor 70.
"Here we describe Che-1, a novel human protein that interacts with hRPB11. Che-1 possesses a domain of high homology with Escherichia coli RNA polymerase final sigma-factor 70 and SV40 large T antigen."
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Che-1 interacts with Rb through two distinct domains and represses Rb growth suppression by counteracting the inhibitory action of Rb on E2F1 transactivation.
"Che-1 interacts with the retinoblastoma susceptibility gene (Rb) by two distinct domains. Functionally, we demonstrate that Che-1 represses the growth suppression function of Rb, counteracting the inhibitory action of Rb on the trans-activation function of E2F1."
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Che-1 may be part of a transcription regulatory complex bridging RNA Pol II and Rb.
"These results identify a novel protein that binds Rb and the core of pol II, and suggest that Che-1 may be part of transcription regulatory complex."
Functional proteomic analysis of human nucleolus.
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AATF was identified among 213 nucleolar proteins in HeLa cells by mass spectrometry-based proteomic analysis, establishing its nucleolar localization.
"we have carried out a proteomic analysis to draw up a list of proteins present within nucleoli of HeLa cells. This analysis allowed the identification of 213 different nucleolar proteins."
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The nucleolar proteome functional classification supports the plurifunctional nature of nucleoli including roles in ribosome biogenesis and gene expression control.
"Functional classification of these proteins allowed outlining several biological processes taking place within nucleoli. Notably, a role in ribosome biogenesis was proposed for 31 proteins."
Che-1 affects cell growth by interfering with the recruitment of HDAC1 by Rb.
Che-1 arrests human colon carcinoma cell proliferation by displacing HDAC1 from the p21WAF1/CIP1 promoter.
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Che-1/AATF is an RNA polymerase II binding protein that activates p21WAF1/Cip1 expression by displacing HDAC1 from SP1 binding sites on the p21 promoter, leading to histone H3 acetylation and growth arrest in colon carcinoma cells.
"Che-1 activates p21WAF1/Cip1 by displacing histone deacetylase (HDAC)1 from the Sp1 binding sites of the p21WAF1/Cip1 gene promoter and accumulating acetylated histone H3 on these sites."
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Che-1 can be considered a general HDAC1 competitor, and Che-1-specific RNAi negatively affects p21 transactivation and increases cell proliferation.
"Che-1-specific RNA interference negatively affects p21WAF1/Cip1 transactivation and increases cell proliferation in HCT116 cells. Taken together, our results indicate that Che-1 can be considered a general HDAC1 competitor."
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Che-1 previously demonstrated the ability to inhibit Rb growth-suppressing function by interfering with Rb-mediated HDAC1 recruitment on E2F target gene promoters.
"We previously demonstrated that Che-1 inhibits the Rb growth-suppressing function by interfering with Rb-mediated HDAC1 recruitment on E2F target gene promoters."
AATF inhibits aberrant production of amyloid beta peptide 1-42 by interacting directly with Par-4.
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AATF colocalizes with Par-4 in both cytoplasmic and nuclear compartments and interacts directly and selectively with Par-4 via the leucine zipper domain in neural cells.
"AATF colocalizes with Par-4 in both cytoplasmic and nuclear compartments, and it interacts directly and selectively with Par-4 via the leucine zipper domain in neural cells."
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Co-expression of AATF completely blocked aberrant production and secretion of Abeta-42 induced by Par-4, and AATF/Par-4 complex formation was essential for this inhibitory effect.
"Co-expression of AATF completely blocked aberrant production and secretion of Abeta-(1-42) induced by Par-4, and AATF/Par-4 complex formation was essential for the inhibitory effect of AATF on aberrant Abeta secretion."
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AATF is an endogenous antagonist of Par-4 activity, functioning as an effective inhibitor of aberrant Abeta production under apoptotic conditions.
"These results indicate that AATF is an endogenous antagonist of Par-4 activity and an effective inhibitor of aberrant Abeta production and secretion under apoptotic conditions."
AATF protects neural cells against oxidative damage induced by amyloid beta-peptide.
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AATF is expressed in cortical neurons and PC12 cells, and Abeta induces alterations in AATF expression; inhibition of AATF induction sensitizes neurons to Abeta toxicity.
"AATF (apoptosis-antagonizing transcription factor), a leucine zipper protein initially identified as an interaction partner of DAP like kinase (Dlk), is expressed in cortical neurons and in neural PC12 cells. Abeta induces alterations in AATF expression in cortical neurons. Inhibition of AATF induction sensitizes neurons to Abeta toxicity."
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AATF overexpression suppresses superoxide production, inhibits peroxynitrite formation and lipid peroxidation, and protects against Abeta-induced apoptosis, indicating AATF is a neuroprotective factor acting through ROS suppression.
"Overexpression of AATF suppressed superoxide production, inhibited peroxynitrite formation and membrane lipid peroxidation, and protected against Abeta-induced apoptosis in PC12 cells. These results suggest that AATF is a novel neuroprotective factor and it may protect against Abeta-induced apoptosis through its effects on suppressing the production of reactive oxygen species (ROS)."
Che-1 phosphorylation by ATM/ATR and Chk2 kinases activates p53 transcription and the G2/M checkpoint.
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Che-1 contributes to the DNA damage response; checkpoint kinases ATM/ATR and Chk2 interact with Che-1 and promote its phosphorylation and accumulation in response to DNA damage.
"Che-1 contributes to DNA damage response and its depletion sensitizes cells to anticancer agents. The checkpoint kinases ATM/ATR and Chk2 interact with Che-1 and promote its phosphorylation and accumulation in response to DNA damage."
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DNA damage-induced phosphorylation of Che-1 causes its specific recruitment to the TP53 and p21 promoters, with a profound effect on basal p53 expression that is preserved following DNA damage.
"These Che-1 modifications induce a specific recruitment of Che-1 on the TP53 and p21 promoters. Interestingly, it has a profound effect on the basal expression of p53, which is preserved following DNA damage."
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Che-1 contributes to maintenance of the G2/M checkpoint induced by DNA damage, revealing a mechanism by which checkpoint kinases regulate DNA damage responses.
"Notably, Che-1 contributes to the maintenance of the G2/M checkpoint induced by DNA damage. These findings identify a mechanism by which checkpoint kinases regulate responses to DNA damage."
AATF mediates an antiapoptotic effect of the unfolded protein response through transcriptional regulation of AKT1.
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AATF is induced by ER stress through the PERK-eIF2alpha pathway and is an antiapoptotic component of the unfolded protein response.
"We show that AATF is induced by ER stress through the PERK-eIF2alpha pathway and transcriptionally activates the v-akt murine thymoma viral oncogene homolog 1 (AKT1) gene through signal transducer and activator of transcription 3 (Stat3), which sustains Akt1 activation and promotes cell survival."
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AATF acts as a transcriptional cofactor that drives AKT1 expression via STAT3, sustaining AKT1 activation to promote cell survival under ER stress.
"Ectopic expression of AATF or a constitutively active form of AKT1 confers on cells resistance to ER stress-mediated cell death, whereas RNAi-mediated knockdown of AATF or AKT1 renders cells sensitive to ER stress."
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AATF and WFS1 form a positive feedback loop in pancreatic beta-cells, and loss of either drives a self-perpetuating cycle of ER-stress-mediated cell death.
"We also discovered a positive crosstalk between the AATF and WFS1 signaling pathways. Thus, WFS1 deficiency or AATF deficiency mediates a self-perpetuating cycle of cell death."
Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.
The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts.
AATF/Che-1 acts as a phosphorylation-dependent molecular modulator to repress p53-driven apoptosis.
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AATF is phosphorylated by checkpoint kinase MK2 upon genotoxic stress, and this phosphorylation releases AATF from cytoplasmic MRLC3, enabling nuclear translocation.
"Upon genotoxic stress, AATF is phosphorylated by the checkpoint kinase MK2. Phosphorylation results in the release of AATF from cytoplasmic MRLC3 and subsequent nuclear translocation."
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Nuclear AATF binds to PUMA, BAX, and BAK promoter regions to repress p53-driven expression of these pro-apoptotic genes, acting as a critical regulator that shifts the p53 response from apoptosis toward cell-cycle arrest and DNA repair.
"where AATF binds to the PUMA, BAX and BAK promoter regions to repress p53-driven expression of these pro-apoptotic genes."
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The p38/MK2/AATF signalling module is identified as a critical repressor of p53-driven apoptosis; AATF depletion dramatically enhances tumor response to genotoxic chemotherapy, while phospho-mimicking AATF causes adriamycin resistance in vivo.
"In xenograft experiments, mice exhibit a dramatically enhanced response of AATF-depleted tumours following genotoxic chemotherapy with adriamycin. The exogenous expression of a phospho-mimicking AATF point mutant results in marked adriamycin resistance in vivo. These data identify the p38/MK2/AATF signalling module as a critical repressor of p53-driven apoptosis."
A proteome-scale map of the human interactome network.
Che1/AATF interacts with subunits of the histone acetyltransferase core module of SAGA complexes.
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AATF interacts with ADA2A, ADA2B, and GCN5 (but not SGF29) of the SAGA/ATAC HAT module, as demonstrated by yeast two-hybrid, co-immunoprecipitation in HEK293 cells, and fluorescence co-localization in HEK293 and U2OS cells.
"Co-immunoprecipitation and co-localization experiments were used to demonstrate association of AATF both with two ADA2 isoforms, ADA2A and ADA2B and with GCN5 proteins in human cells and yeast two-hybrid assays to delineate domains in the ADA2 and GCN5 proteins required for these interactions."
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ADA2B shows the strongest interaction with AATF among HAT module subunits, and ADA2B co-localizes with AATF in both nucleoplasm and nucleolus, while GCN5 is excluded from the nucleolus.
"ADA2B produced the strongest interaction with AATF, while ADA2A and GCN5 displayed weaker, nonetheless definite interaction. ADA2B co-localization with AATF was primarily in the nucleoplasm with an additional nucleolar co-localization. Unlike AATF, GCN5 appeared to be excluded from the nucleolus."
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The GCN5 acetyltransferase domain is required for interaction with AATF; for ADA2 isoforms, the region between the SANT domain and Ada1 box is critical.
"For hGCN5, amino or carboxy-terminal truncations that removed the acetyltransferase domain no longer manifested interaction with AATF suggesting this domain is required for the association. For both ADA2 isoforms, the region between the SANT domain and the Ada1 box also may be critical for interaction with AATF while the SWIRM domain is not required."
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Co-expression of ADA2A, ADA2B, or GCN5 with AATF significantly reduced AATF-mediated transcriptional activation of the MDM2 promoter, indicating HAT module subunits negatively modulate AATF transactivation function.
"AATF expression activates the promoter while co-expression of ADA2A, ADA2B or GCN5 with AATF, significantly reduced the activation imparted by AATF on MDM2 promoter-directed transcription (p <0.01)."
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AATF is localized to both nucleoplasm and nucleolus, consistent with reported nuclear and nucleolar localization signals, and may participate in regulation of gene expression by modulating chromatin structure through HAT complex interactions.
"AATF was mostly found in the nucleoplasm. Like ADA2B, the AATF protein, was also localized in the nucleolus in addition to the nucleoplasm. Che-1/AATF could be participating in the regulation of gene expression by regulating chromatin structure."
Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei.
A reference map of the human binary protein interactome.
Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
Nucleolar maturation of the human small subunit processome.
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Cryo-EM structures at 2.7 to 3.9 angstrom resolution reveal AATF as a structural component of the human SSU processome, a 4.5-megadalton nucleolar assembly.
"We report the high-resolution cryo-electron microscopy structures of maturing human small subunit (SSU) processomes at resolutions of 2.7 to 3.9 angstroms."
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The SSU processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps, including targeted exosome-mediated RNA degradation and site-specific endonucleolytic cleavage.
"The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. RNA folding states within these particles are communicated to and coordinated with key enzymes that drive irreversible steps such as targeted exosome-mediated RNA degradation, protein-guided site-specific endonucleolytic RNA cleavage, and tightly controlled RNA unwinding."
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The SSU processome demonstrates impressive structural plasticity through conserved mechanisms, endowing it with the ability to mature the small ribosomal subunit from within the nucleolus.
"These conserved mechanisms highlight the SSU processome's impressive structural plasticity, which endows this 4.5-megadalton nucleolar assembly with the distinctive ability to mature the small ribosomal subunit from within."
OpenCell: Endogenous tagging for the cartography of human cellular organization.