| 2002 |
Set9 (SETD7) was isolated from human cells and shown to specifically monomethylate lysine 4 of histone H3 (H3-K4). This methylation precludes association of the NuRD histone deacetylase complex with the H3 tail, and also impairs Suv39h1-mediated methylation at H3-K9, thereby promoting transcription activation. |
Biochemical isolation, in vitro histone methyltransferase assay, histone tail binding assay, cross-inhibition assay with Suv39h1 and G9a |
Genes & development |
High |
11850410
|
| 2003 |
Crystal structure of a ternary complex of human SET7/9 with a histone H3 peptide and cofactor (AdoMet) revealed that the peptide substrate and cofactor bind on opposite surfaces of the enzyme, the target lysine inserts its side chain into a narrow channel connecting the two surfaces, and SET7/9 is exclusively a mono-methylase due to active-site geometry. |
High-resolution X-ray crystallography of ternary complex; solution studies confirming mono-methylase activity |
Nature |
High |
12540855
|
| 2004 |
SET9 (SETD7) monomethylates the TBP-associated factor TAF10 at a single lysine in its histone-fold domain (loop 2 region), and this methylation increases TAF10 affinity for RNA polymerase II, potentiating transcription of a subset of TAF10-dependent genes in a promoter-specific manner. |
In vitro methyltransferase assay, affinity pull-down, reporter assays, TAF10-null cell complementation with methylation-deficient mutant |
Molecular cell |
High |
15099517
|
| 2006 |
Crystal structures of SET7/9 bound to TAF10 and other substrate peptides revealed that the enzyme recognizes a conserved K/R-S/T/A motif preceding the target lysine, and has preference for aspartates/asparagines C-terminal to the target lysine, defining the substrate-specificity consensus motif. TAF7 was identified as a novel substrate (methylated at Lys5 in vitro) using this motif. |
X-ray crystallography, substrate peptide mutagenesis, in vitro methyltransferase assays with multiple substrates |
Nature structural & molecular biology |
High |
16415881
|
| 2007 |
QM/MM molecular dynamics simulations of SET7/9 identified Tyr-335 as the general base for deprotonation of the methylated lysine after AdoHcy dissociation, and showed that conformational changes bring Y335 to the target lysine for proton abstraction, explaining mono-methylase product specificity. Y305F and Y335F mutants were analyzed to support the mechanism. |
Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics and free-energy simulations; mutant analysis (Y305F, Y335F) |
Proceedings of the National Academy of Sciences of the United States of America |
Medium |
17517655
|
| 2008 |
SETD7 directly methylates estrogen receptor alpha (ERα) at lysine 302. SET7-mediated K302 methylation stabilizes ERα protein and is required for efficient recruitment of ERα to its target gene promoters and their transactivation. A breast cancer-associated mutation K303R alters K302 methylation in vitro and in vivo. Crystal structure of the SET7-ER peptide complex revealed the molecular basis of recognition. |
In vitro methyltransferase assay, X-ray crystallography of SET7-ER peptide complex, Co-IP, ChIP, mutagenesis, K303R cancer mutation analysis |
Molecular cell |
High |
18471979
|
| 2008 |
SET7/9 acts as a novel coactivator of NF-κB. SET7/9 knockdown in monocytes inhibits TNF-α-induced H3K4 methylation at NF-κB target gene promoters, reduces NF-κB p65 recruitment to those promoters, and attenuates inflammatory gene expression and monocyte adhesion. |
siRNA knockdown, ChIP, gene expression analysis (microarray), monocyte adhesion assay |
The Journal of biological chemistry |
Medium |
18650421
|
| 2008 |
Set7/9 methylates p53 at K369 (mouse)/K372 (human) in vivo. Cells from Set7/9 knockout mice fail to methylate p53 K369, cannot induce p53 downstream targets upon DNA damage, and are predisposed to oncogenic transformation. Mechanistically, Set7/9-mediated p53 methylation is required for binding of the acetyltransferase Tip60 to p53 and for subsequent p53 acetylation. |
Set7/9 knockout mouse generation, MEF-based DNA damage assays, Co-IP (Tip60-p53), p53 acetylation analysis, transformation assays |
Molecular cell |
High |
18280244
|
| 2009 |
SET7 directly interacts with DNMT1, colocalizes with it, and specifically monomethylates DNMT1 at Lys-142. This methylation promotes proteasome-mediated DNMT1 degradation, peaking during S and G2 phases. SET7 overexpression decreases DNMT1 levels; SET7 siRNA knockdown stabilizes DNMT1. |
Co-IP, colocalization (immunofluorescence), in vitro methyltransferase assay, proteasome inhibitor experiments, siRNA KD, SET7 overexpression |
Proceedings of the National Academy of Sciences of the United States of America |
High |
19282482
|
| 2009 |
Set9 (SETD7) physically associates with the RelA subunit of NF-κB and monomethylates RelA at lysine residues 314 and 315 in vitro and in vivo. This methylation inhibits NF-κB action by inducing proteasome-mediated degradation of promoter-associated RelA, limiting the duration of NF-κB target gene expression. |
Co-IP, in vitro methyltransferase assay, mutational analysis, mass spectrometry, siRNA KD, reporter assays |
The EMBO journal |
High |
19262565
|
| 2010 |
Set7/9 (KMT7) monomethylates lysine 51 in the RNA-binding domain of HIV-1 Tat. Set7/9 associates with the HIV promoter in vivo, binds TAR RNA by itself and in complex with Tat and P-TEFb. Knockdown of Set7/9 suppresses Tat transactivation in a methylation-dependent manner (K51A Tat is refractory to Set7/9 KD). |
In vitro methyltransferase assay, ChIP, RNA binding assay (TAR RNA), siRNA KD, luciferase reporter assay with K51A mutant |
Cell host & microbe |
High |
20227666
|
| 2010 |
SETD7 directly methylates and regulates the androgen receptor (AR). SET9 methylates AR at lysine 632 (also reported as K630 in a parallel study), which is necessary for enhancing AR transcriptional activity by facilitating inter-domain N-C communication and recruitment to androgen-target gene promoters. |
In vitro methyltransferase assay, Co-IP, ChIP, mutagenesis (K632A), N-C interaction assay |
Nucleic acids research |
High |
20959290 21273441
|
| 2011 |
Set7/9 interacts with SIRT1 both in vitro and in vivo. Upon DNA damage, Set7/9-SIRT1 interaction is enhanced, suppressing SIRT1-p53 interaction and abrogating SIRT1-mediated p53 deacetylation, thereby promoting p53-mediated transactivation. This regulation operates in addition to direct p53 methylation. |
Co-IP (in vitro and in vivo), p53 acetylation analysis, SIRT1 methylation analysis, reporter assays, DNA damage response assays |
Proceedings of the National Academy of Sciences of the United States of America |
Medium |
21245319
|
| 2011 |
Two independent Set7/9 knockout mouse strains showed that Set7/9 is dispensable for p53-dependent cell cycle arrest, apoptosis, and p53 acetylation following DNA damage or oncogene activation in vivo, contradicting the earlier finding (PMID:18280244) that p53 methylation by Set7/9 is required for p53 activation. |
Independent Set7/9 knockout mouse strain, DNA damage assays (irradiation, genotoxic agents), p53 target gene expression, p53 acetylation analysis |
Molecular cell |
High |
21855805 21855806
|
| 2011 |
Set7 directly interacts with MyoD and promotes skeletal muscle differentiation. Set7 knockdown or dominant-negative expression impairs myoblast differentiation with decreased H3K4me1, reduced expression of myocyte enhancer factor 2 and contractile proteins, and myofibril assembly defects. Set7 activates muscle genes by precluding Suv39h1-mediated H3K9 methylation on myogenic gene promoters. |
Co-IP (Set7-MyoD), siRNA KD, dominant-negative overexpression, ChIP (H3K4me1, H3K9me), differentiation assays |
The Journal of cell biology |
Medium |
21859860
|
| 2011 |
Set9 directly methylates FoxO3 at lysine 271 (identified by tandem mass spectrometry and methyl-specific antibody). Set9-mediated FoxO3 methylation decreases FoxO3 protein stability while moderately increasing its transcriptional activity. |
In vitro methyltransferase assay, tandem mass spectrometry, methyl-specific antibody, protein stability assay |
Aging |
Medium |
22820736
|
| 2011 |
SET7/9 can methylate multiple new peptide substrates from human proteins. Confirmed methylation of nine nonhistone proteins (AKA6, CENPC1, MeCP2, MINT, PPARBP, ZDH8, Cullin1, IRF1, TTK) and H2A and H2B in vitro and in vivo. Phosphorylation of substrate proteins adjacent to the target lysine inhibits SET7/9 methylation. MINT protein can be dimethylated by SET7/9 showing context-dependent product specificity. |
Peptide array methylation, in vitro methyltransferase assays with protein domains, in vivo methylation validation with antibodies |
Chemistry & biology |
Medium |
21276944
|
| 2012 |
Set7 (Setd7) monomethylates YAP at lysine 494. This methylation is critical for cytoplasmic retention of YAP. Set7 knockout mice have a larger intestinal progenitor compartment with increased YAP target gene expression, placing Set7-mediated YAP methylation as a regulatory checkpoint in the Hippo pathway. |
Set7 knockout mouse model, intestinal progenitor analysis, in vitro methyltransferase assay, YAP subcellular localization studies, YAP target gene expression |
Developmental cell |
High |
23850191
|
| 2012 |
SET7/9 directly methylates SUV39H1 at lysines 105 and 123 (identified by mass spectrometry and methyl-specific antibodies). Methylation dramatically down-regulates SUV39H1 methyltransferase activity, leading to decreased H3K9 trimethylation in heterochromatin, heterochromatin relaxation (increased Sat2 and α-Sat expression), and genome instability in response to DNA damage. |
Co-IP, GST pulldown, in vitro methyltransferase assay, mass spectrometry, methyl-specific antibody, micrococcal nuclease sensitivity assay, immunofluorescence |
Proceedings of the National Academy of Sciences of the United States of America |
High |
23509280
|
| 2012 |
SET7/9 directly methylates the farnesoid X receptor (FXR) at lysine 206 in vivo and in vitro. Methylation enhances FXR/RXRα binding to the FXRE and potentiates transactivation of FXR target genes (SHP, BSEP). Methylation-deficient K206R mutant FXR shows impaired transactivation; SET7/9 methyltransferase-dead mutant is also inactive. |
In vitro methyltransferase assay, Co-IP, GST pulldown, mammalian two-hybrid, EMSA, luciferase reporter assay, K206R mutagenesis, siRNA KD |
American journal of physiology. Gastrointestinal and liver physiology |
High |
22345554
|
| 2012 |
SET7/9 methylates histone H1.4 at multiple lysine residues (K121, K129, K159, K171, K177, K192) in KAK motifs of the C-terminal domain. ADP-ribosylation of H3 by ARTD1 prevents H3 methylation by SET7/9 but allows subsequent SET7/9 methylation of H1. H1 and H3 compete for SET7/9-dependent methylation, revealing substrate competition as a regulatory mechanism. |
In vitro methyltransferase assay with isolated histones, mass spectrometry identification of methylation sites, competition assays |
Epigenetics & chromatin |
Medium |
23289424
|
| 2013 |
SET7/9 directly methylates ARTD1 (PARP1) at K508 in vitro and in vivo. ARTD1 methylation by SET7/9 enhances poly-ADP-ribose (PAR) synthesis upon oxidative stress in vivo, and promotes ARTD1 recruitment to sites of laser-induced DNA damage in a SET7/9-dependent manner. ARTD1 auto-modification inhibits its methylation by SET7/9. |
In vitro methyltransferase assay, in vivo methylation detection, laser irradiation/PAR formation assay, live-cell imaging of ARTD1 recruitment |
Open biology |
Medium |
24088713
|
| 2013 |
Negative regulation of TGF-β signaling: Set9 methylates Smad7 (an inhibitory TGF-β effector), promoting Smad7 interaction with the E3 ligase Arkadia and subsequent ubiquitination-dependent degradation of Smad7. Set9 depletion or pharmacological inhibition elevates Smad7 levels and inhibits TGF-β-dependent extracellular matrix gene expression. Set9-deficient mice show severely compromised lung fibrosis. |
In vitro methyltransferase assay, Co-IP (Smad7-Arkadia), ubiquitination assay, Set9 KO mouse model of pulmonary fibrosis (bleomycin/Ad-TGF-β), siRNA and pharmacological inhibitor studies |
Cell reports |
High |
27292644
|
| 2014 |
(R)-PFI-2 was identified as a potent (Ki = 0.33 nM), selective, cofactor-dependent, substrate-competitive inhibitor of SETD7. Crystal structure showed it occupies the substrate peptide binding groove including the lysine-binding channel and contacts the methyl group of SAM. In murine embryonic fibroblasts, (R)-PFI-2 phenocopied Setd7 deficiency on Hippo pathway signaling via YAP modulation; in confluent MCF7 cells it rapidly altered YAP localization. |
Biochemical inhibitor characterization (Ki determination), X-ray crystallography, chemoproteomics (biotinylated probe competition), cell-based YAP localization assay |
Proceedings of the National Academy of Sciences of the United States of America |
High |
25136132
|
| 2014 |
Set7/9 physically interacts with Mdm2 and regulates expression of Mdm2 at the transcriptional level, affecting the DNA damage response. Multiple cancer cell lines with inverse expression of Set7/9 and Mdm2 show diminished survival in response to genotoxic stress. |
Co-IP, gene expression analysis, cell viability assays under genotoxic stress, bioinformatics |
Oncotarget |
Low |
26317544
|
| 2014 |
Set7/9 is a critical co-activator of E2F1-dependent transcription in response to DNA damage. Set7/9 indirectly modulates histone modifications at E2F1-dependent gene promoters, promotes CCNE1 expression (proliferation), and represses TP73 gene expression (anti-apoptotic). Cell cycle progression through G1/S checkpoint depends on threshold expression of both E2F1 and Set7/9. |
Co-IP, ChIP, gene expression analysis, cell biology assays (G1/S progression), bioinformatics across lung tumor cell lines |
Cell death and differentiation |
Medium |
25124555
|
| 2015 |
Set7 methylates HIF-1α at lysine 32 and HIF-2α at lysine K29, inhibiting HIF-α transcriptional activity by impairing occupancy of HIF-α on hypoxia response elements of target gene promoters. Set7-null fibroblasts and Set7 KD/inhibited cells show upregulated HIF target genes and increased glucose uptake. |
In vitro methyltransferase assay, ChIP (HIF-α at HRE), Set7 KO fibroblasts, shRNA KD, Set7 inhibitor treatment, glucose uptake assay |
Nucleic acids research |
Medium |
25897119
|
| 2015 |
Set7 monomethylates Gli3 full-length (but not truncated form) at K436 and K595. Methylation at K436 increases Gli3 stability and methylation at K595 increases Gli3 DNA binding ability, together enhancing Shh signaling activation and contributing to tumor growth/metastasis in non-small cell lung cancer. |
In vitro methyltransferase assay, mutagenesis (K436A, K595A), protein stability assay, DNA binding assay, Shh target gene expression, in vitro/in vivo tumor assays |
eLife |
Medium |
27146893
|
| 2015 |
Set7/9 methylates the transcription factor Pdx1 at K123 and K131 (identified by mass spectrometry and mutagenesis of purified proteins). K131 methylation (but not K123) is required for transcriptional augmentation by Set7/9. Conditional deletion of Set7/9 in β cells causes glucose intolerance and impaired glucose-stimulated insulin secretion with reduced Pdx1 target gene expression. |
In vitro methyltransferase assay, mass spectrometry, mutagenesis, luciferase reporter assay, conditional knockout mouse (Set(Δ)β), islet glucose-stimulated insulin secretion assay |
The Journal of biological chemistry |
High |
25713082
|
| 2015 |
SET7/9 directly methylates β-catenin at lysine 180 (identified by mutagenesis and mass spectrometry). Methylated β-catenin is recognized by GSK-3β for degradation. K180R mutant β-catenin has a longer half-life. SET7/9 depletion or K180R mutation enhances Wnt/β-catenin target gene expression and promotes cancer cell growth. |
Co-IP, in vitro methyltransferase assay, mutagenesis (K180R), mass spectrometry, protein half-life assay, luciferase reporter assay |
FASEB journal |
High |
26116705
|
| 2016 |
SETD7-mediated methylation of YAP (K494) facilitates Wnt-induced nuclear accumulation of β-catenin. SETD7 is part of a complex containing YAP, AXIN1, and β-catenin. SETD7 is required for Wnt-driven intestinal tumorigenesis and regeneration, linking the Wnt/β-catenin and Hippo/YAP pathways. |
SETD7 KO mouse model (intestinal tumorigenesis/regeneration), Co-IP complex analysis (YAP-AXIN1-β-catenin-SETD7), β-catenin nuclear localization assay |
Developmental cell |
High |
27046831
|
| 2016 |
SET7/9 methylates transcription factor YY1 at two lysine residues, K173 and K411. This methylation regulates YY1 DNA-binding activity in vitro and at specific genomic loci in cells, affecting YY1-regulated gene transcription and cell proliferation. |
In vitro methyltransferase assay, mutagenesis, EMSA (DNA binding), ChIP, luciferase reporter assay, cell proliferation assay |
Scientific reports |
Medium |
26902152
|
| 2018 |
SETD7 controls cardiac differentiation by reading H3K36 marks independently of its enzymatic activity. During mesodermal formation, SETD7 associates with SWI/SNF chromatin-remodeling factors; in cardiac progenitors it associates with NKX2.5. SETD7 binds methylated H3K36 in gene bodies of target genes to facilitate RNA Pol II-dependent transcription. |
ChIP-seq, Co-IP (SETD7 with SWI/SNF and NKX2.5), enzymatic activity mutant analysis, H3K36me binding assay, differentiation assays from hPSCs |
Cell stem cell |
High |
29499155
|
| 2018 |
SET7 methylates SOX2 at K119 (mouse)/K117 (human) and K42, triggering ubiquitin-dependent SOX2 proteolysis. LSD1 demethylase removes methyl groups from both sites preventing degradation, while PHF20L1 binds monomethylated K42 and K117 to protect SOX2 from proteolysis. SET7/LSD1/PHF20L1 dynamically regulate SOX2 stability in pluripotent stem cells. |
In vitro methyltransferase assay, methylation-specific antibody, Co-IP, siRNA KD (LSD1, PHF20L1), protein stability assay, SET7 inactivation |
The Journal of biological chemistry |
Medium |
29358331
|
| 2018 |
Rpl29 lysine 5 (Rpl29K5) is methylated exclusively by Set7/9 and can be demethylated by Lsd1. Rpl29 methylation has no effect on global protein synthesis but affects Rpl29 subcellular localization. Rpl29K5 methylation was validated as a specific cellular biomarker for Set7/9 activity, responsive to (R)-PFI-2 inhibitor treatment. |
In vitro methyltransferase assay (substrate identification), methylation-specific antibody, subcellular fractionation, Set7/9 inhibitor treatment, global translation assay |
The Journal of biological chemistry |
Medium |
29959229
|
| 2019 |
UHRF1 is methylated by SET7 and demethylated by LSD1. UHRF1 phosphorylation in S phase is a prerequisite for its interaction with SET7. SET7-mediated UHRF1 methylation catalyzes polyubiquitin chain conjugation to PCNA and promotes homologous recombination for DNA double-strand break repair. UHRF1 methylation is induced in response to DNA damage. |
In vitro methyltransferase assay, Co-IP, phosphorylation mutant analysis, polyubiquitination assay (PCNA), homologous recombination assay, cell viability assay |
Nucleic acids research |
Medium |
30357346
|
| 2019 |
SUMO-specific isopeptidase SENP3 associates with SETD7 and deSUMOylates it. By recruiting SETD7 to the MyHC-II gene locus, SENP3 promotes SETD7 association with active RNA polymerase II and precludes opposing Suv39h1 activity. SENP3 is degraded in cachexia, impairing this SENP3-SETD7 regulatory axis, resulting in disrupted MyHC-II expression and disorganized sarcomeres. |
Co-IP (SENP3-SETD7), deSUMOylation assay, ChIP (SETD7 and Pol II at MyHC-II), SENP3 KD functional assay, cachexia model |
Cell reports |
Medium |
31141694
|
| 2020 |
SETD7 methylates PLK1 at K191 (dimethylation), tuning down PLK1 kinase activity by limiting ATP utilization at kinetochores during early mitosis. Non-methylatable PLK1 K191 mutant or chemical inhibition of SETD7 causes mitotic arrest due to destabilized kinetochore-microtubule attachments, revealing that SETD7-mediated PLK1 methylation promotes dynamic kinetochore-microtubule attachments for accurate error correction. |
In vitro methyltransferase assay, mutagenesis (K191), PLK1 kinase activity assay, kinetochore-microtubule attachment assay, SETD7 inhibitor treatment, mitosis assay |
Journal of molecular cell biology |
Medium |
31863092
|
| 2021 |
SETD7 methylates Tau at K132, an event that facilitates subsequent methylation at K130. Methylated Tau (identified by mass spectrometry in human AD brain) preferentially localizes to cell soma and nuclear fractions (absent from neurites) in hiPSC-derived neurons and mouse brain, and methylated Tau levels increase with Tau pathology stage. |
Mass spectrometry (human AD brain), methylation-specific antibody development, knockdown and inhibitor studies, subcellular fractionation, proteomics |
Molecular neurodegeneration |
Medium |
34215303
|
| 2023 |
SETD7 methylates the Hippo pathway effector YAP upon energy deprivation in cardiomyocytes, leading to YAP cytosolic retention and impaired transcription of antioxidant genes MnSOD and CAT. This impairment causes mitochondrial ROS accumulation, organelle swelling, and apoptosis. Pharmacological inhibition of SETD7 by (R)-PFI-2 restores YAP nuclear localization and prevents myocardial ischemia/reperfusion injury in mice. |
NRVM culture (energy deprivation), SETD7 KO mouse I/R injury model, (R)-PFI-2 pharmacological inhibition, YAP localization assay, MnSOD/CAT expression, mtROS measurement, LV function assay |
Cardiovascular research |
High |
35709329
|
| 2016 |
TRIM21 physically associates with SETD7 and functions as a major negative regulator upstream of SETD7 through a proteasome-dependent ubiquitination mechanism, leading to SETD7 degradation. SETD7 promotes breast cancer malignant processes via activation of RUNX2. |
Mass spectrometry, Co-IP, GST pulldown, ubiquitination assay, ChIP-seq, ChIP, cell functional assays, xenograft model |
Cell death & disease |
Medium |
32102992
|