Gene description for Trim28
Gene name tripartite motif-containing 28
Gene symbol Trim28
Other names/aliases AA408787
KAP-1
KRIP-1
MommeD9
Tif1b
Tif1beta
Species Mus musculus
 Database cross references - Trim28
ExoCarta ExoCarta_21849
Vesiclepedia VP_21849
Entrez Gene 21849
UniProt Q62318  
 Trim28 identified in sEVs derived from the following tissue/cell type
Colon cancer cells 37309723    
Melanoma cells 34957415    
Melanoma cells 34957415    
T-cell lymphoma cells 37309723    
 Gene ontology annotations for Trim28
Molecular Function
    DNA binding GO:0003677 IDA
    DNA binding GO:0003677 ISO
    chromatin binding GO:0003682 IBA
    chromatin binding GO:0003682 ISO
    transcription coactivator activity GO:0003713 IDA
    transcription corepressor activity GO:0003714 IEA
    transcription corepressor activity GO:0003714 ISO
    protein kinase activity GO:0004672 IDA
    ubiquitin-protein transferase activity GO:0004842 ISO
    protein binding GO:0005515 IPI
    zinc ion binding GO:0008270 IEA
    zinc ion binding GO:0008270 ISO
    SUMO transferase activity GO:0019789 ISO
    ubiquitin protein ligase binding GO:0031625 IEA
    ubiquitin protein ligase binding GO:0031625 ISO
    Krueppel-associated box domain binding GO:0035851 ISO
    Krueppel-associated box domain binding GO:0035851 ISS
    ubiquitin protein ligase activity GO:0061630 IBA
    ubiquitin protein ligase activity GO:0061630 IEA
    SUMO ligase activity GO:0061665 TAS
    chromo shadow domain binding GO:0070087 IEA
    chromo shadow domain binding GO:0070087 ISO
    promoter-specific chromatin binding GO:1990841 ISO
    promoter-specific chromatin binding GO:1990841 ISS
Biological Process
    negative regulation of transcription by RNA polymerase II GO:0000122 IDA
    negative regulation of transcription by RNA polymerase II GO:0000122 IGI
    in utero embryonic development GO:0001701 IMP
    epithelial to mesenchymal transition GO:0001837 IDA
    DNA repair GO:0006281 IEA
    DNA repair GO:0006281 ISO
    chromatin organization GO:0006325 IBA
    DNA methylation-dependent constitutive heterochromatin formation GO:0006346 IMP
    protein phosphorylation GO:0006468 IDA
    embryo implantation GO:0007566 IMP
    protein sumoylation GO:0016925 IBA
    protein sumoylation GO:0016925 IEA
    protein sumoylation GO:0016925 ISO
    positive regulation of protein import into nucleus GO:0042307 ISO
    positive regulation of protein import into nucleus GO:0042307 ISS
    epigenetic programming of gene expression GO:0043045 IMP
    proteasome-mediated ubiquitin-dependent protein catabolic process GO:0043161 IEA
    positive regulation of DNA binding GO:0043388 IDA
    positive regulation of DNA binding GO:0043388 IMP
    suppression of viral release by host GO:0044790 IEA
    suppression of viral release by host GO:0044790 ISO
    innate immune response GO:0045087 IBA
    innate immune response GO:0045087 IDA
    innate immune response GO:0045087 IGI
    innate immune response GO:0045087 ISO
    positive regulation of DNA repair GO:0045739 IEA
    positive regulation of DNA repair GO:0045739 ISO
    negative regulation of single stranded viral RNA replication via double stranded DNA intermediate GO:0045869 IDA
    negative regulation of single stranded viral RNA replication via double stranded DNA intermediate GO:0045869 IGI
    negative regulation of single stranded viral RNA replication via double stranded DNA intermediate GO:0045869 IMP
    negative regulation of single stranded viral RNA replication via double stranded DNA intermediate GO:0045869 IMP
    negative regulation of DNA-templated transcription GO:0045892 IBA
    negative regulation of DNA-templated transcription GO:0045892 IDA
    negative regulation of DNA-templated transcription GO:0045892 IMP
    negative regulation of DNA-templated transcription GO:0045892 ISO
    positive regulation of DNA-templated transcription GO:0045893 IDA
    positive regulation of DNA-templated transcription GO:0045893 IDA
    protein autophosphorylation GO:0046777 IDA
    convergent extension involved in axis elongation GO:0060028 IMP
    embryonic placenta morphogenesis GO:0060669 IMP
    genomic imprinting GO:0071514 IMP
Subcellular Localization
    chromatin GO:0000785 IDA
    euchromatin GO:0000791 IDA
    heterochromatin GO:0000792 IDA
    nucleus GO:0005634 IDA
    nucleus GO:0005634 ISO
    nucleoplasm GO:0005654 IDA
    nucleoplasm GO:0005654 ISO
    nucleoplasm GO:0005654 TAS
    nucleolus GO:0005730 IDA
    protein-containing complex GO:0032991 ISO
    RNA polymerase II transcription regulator complex GO:0090575 IBA
    RNA polymerase II transcription regulator complex GO:0090575 IDA
 Experiment description of studies that identified Trim28 in sEVs
1
Experiment ID 907
MISEV standards
✔
EM
Biophysical techniques
✔
Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a
Enriched markers
✔
HSPA5
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 37309723    
Organism Mus musculus
Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells
Authors "Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."
Journal name Proteomics
Publication year 2023
Sample Colon cancer cells
Sample name C26
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
2
Experiment ID 1117
MISEV standards
✘ Biophysical techniques
✔
Cd81|Icam1
Enriched markers
✘ Negative markers
✔
NTA
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 34957415    
Organism Mus musculus
Experiment description Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism
Authors "García-Silva S, Benito-Martín A, Nogués L, Hernández-Barranco A, Mazariegos MS, Santos V, Hergueta-Redondo M, Ximénez-Embún P, Kataru RP, Lopez AA, Merino C, Sánchez-Redondo S, Graña-Castro O, Matei I, Nicolás-Avila JÁ, Torres-Ruiz R, Rodríguez-Perales S, Martínez L, Pérez-Martínez M, Mata G, Szumera-Ciećkiewicz A, Kalinowska I, Saltari A, Martínez-Gómez JM, Hogan SA, Saragovi HU, Ortega S, Garcia-Martin C, Boskovic J, Levesque MP, Rutkowski P, Hidalgo A, Muñoz J, Megías D, Mehrara BJ, Lyden D, Peinado H."
Journal name Nat Cancer
Publication year 2021
Sample Melanoma cells
Sample name B16-F1R2
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
3
Experiment ID 1118
MISEV standards
✘ Biophysical techniques
✔
Cd81|Icam1
Enriched markers
✘ Negative markers
✔
NTA
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 34957415    
Organism Mus musculus
Experiment description Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism
Authors "García-Silva S, Benito-Martín A, Nogués L, Hernández-Barranco A, Mazariegos MS, Santos V, Hergueta-Redondo M, Ximénez-Embún P, Kataru RP, Lopez AA, Merino C, Sánchez-Redondo S, Graña-Castro O, Matei I, Nicolás-Avila JÁ, Torres-Ruiz R, Rodríguez-Perales S, Martínez L, Pérez-Martínez M, Mata G, Szumera-Ciećkiewicz A, Kalinowska I, Saltari A, Martínez-Gómez JM, Hogan SA, Saragovi HU, Ortega S, Garcia-Martin C, Boskovic J, Levesque MP, Rutkowski P, Hidalgo A, Muñoz J, Megías D, Mehrara BJ, Lyden D, Peinado H."
Journal name Nat Cancer
Publication year 2021
Sample Melanoma cells
Sample name B16-F1R2
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
4
Experiment ID 908
MISEV standards
✔
EM
Biophysical techniques
✔
Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a
Enriched markers
✔
HSPA5
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 37309723    
Organism Mus musculus
Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells
Authors "Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."
Journal name Proteomics
Publication year 2023
Sample T-cell lymphoma cells
Sample name EL4
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
 Protein-protein interactions for Trim28
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 Vezf1  
Affinity Capture-MS Mus musculus
2 Emd  
Co-fractionation Mus musculus
3 Cbx1  
Reconstituted Complex Mus musculus
Affinity Capture-MS Mus musculus
Affinity Capture-Western Mus musculus
Affinity Capture-Western Mus musculus
FRET Mus musculus
Biochemical Activity Mus musculus
Affinity Capture-Western Mus musculus
Two-hybrid Mus musculus
4 Tnik  
Affinity Capture-MS Mus musculus
5 Zfp819  
Two-hybrid Mus musculus
6 Lmna 16905
Affinity Capture-MS Mus musculus
7 Trim28 21849
Biochemical Activity Mus musculus
Affinity Capture-Western Mus musculus
Biochemical Activity Mus musculus
Affinity Capture-Western Mus musculus
8 ZNF331  
Affinity Capture-MS Homo sapiens
9 RCN1 5954
Affinity Capture-MS Homo sapiens
10 RRN3  
Affinity Capture-Western Homo sapiens
11 IPO8 10526
Affinity Capture-MS Homo sapiens
12 Fxr1 14359
Affinity Capture-MS Mus musculus
13 Cct3 12462
Co-fractionation Mus musculus
14 Nras 18176
Synthetic Lethality Mus musculus
15 Zfp53  
Affinity Capture-Western Mus musculus
16 Pde4dip  
Affinity Capture-MS Mus musculus
17 ZNF552  
Affinity Capture-MS Homo sapiens
18 Tsc1  
Affinity Capture-MS Mus musculus
19 Fmr1  
Affinity Capture-MS Mus musculus
20 Kctd13  
Affinity Capture-MS Mus musculus
21 ZFP1  
Affinity Capture-MS Homo sapiens
22 ZNF124  
Affinity Capture-MS Homo sapiens
23 Tfe3  
Affinity Capture-MS Mus musculus
24 Zfp354a  
Two-hybrid Mus musculus
25 Shank3  
Affinity Capture-MS Mus musculus
26 Cbx3 12417
Affinity Capture-Western Mus musculus
Reconstituted Complex Mus musculus
Affinity Capture-MS Mus musculus
Affinity Capture-Western Mus musculus
Affinity Capture-Western Mus musculus
FRET Mus musculus
Biochemical Activity Mus musculus
Affinity Capture-Western Mus musculus
Two-hybrid Mus musculus
27 POGK 57645
Affinity Capture-MS Homo sapiens
28 Iqcb1  
Affinity Capture-MS Mus musculus
29 Dnmt1 13433
Co-fractionation Mus musculus
30 FTH1 2495
Affinity Capture-MS Homo sapiens
31 Ywhae 22627
Affinity Capture-MS Mus musculus
32 RBAK  
Affinity Capture-MS Homo sapiens
33 Myb  
Two-hybrid Mus musculus
Reconstituted Complex Mus musculus
34 Lin28a  
Affinity Capture-Western Mus musculus
35 ZNF566  
Affinity Capture-MS Homo sapiens
36 Mettl21e  
Affinity Capture-MS Mus musculus
37 ZNF250  
Affinity Capture-MS Homo sapiens
38 Zfp42  
Affinity Capture-MS Mus musculus
39 Cbx5  
Affinity Capture-Western Mus musculus
Reconstituted Complex Mus musculus
Two-hybrid Mus musculus
Affinity Capture-MS Mus musculus
Affinity Capture-Western Mus musculus
Affinity Capture-Western Mus musculus
Biochemical Activity Mus musculus
Affinity Capture-Western Mus musculus
Two-hybrid Mus musculus
40 CALU 813
Affinity Capture-MS Homo sapiens
41 Zfp68  
Affinity Capture-Western Mus musculus
42 TRIM28 10155
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
43 Brcc3  
Co-fractionation Mus musculus
44 Nanog  
Affinity Capture-MS Mus musculus
Affinity Capture-MS Mus musculus
Affinity Capture-MS Mus musculus
45 Sertad1  
Two-hybrid Mus musculus
46 ZNF354A  
Two-hybrid Homo sapiens
47 ZNF324  
Affinity Capture-MS Homo sapiens
48 ZNF10  
Two-hybrid Homo sapiens
49 Zfp661  
Two-hybrid Mus musculus
50 Sfpq 71514
Co-fractionation Mus musculus
51 C1QBP 708
Affinity Capture-MS Homo sapiens
52 DDB1 1642
Affinity Capture-MS Homo sapiens
53 RCN2 5955
Affinity Capture-MS Homo sapiens
54 Mycbp2 105689
Affinity Capture-MS Mus musculus
55 ZNF460  
Affinity Capture-MS Homo sapiens
56 Eed  
Affinity Capture-MS Mus musculus
57 Nlrp3  
Affinity Capture-MS Mus musculus
Affinity Capture-Western Mus musculus
58 Sox17  
Affinity Capture-MS Mus musculus
59 Atxn1  
Proximity Label-MS Mus musculus
Affinity Capture-MS Mus musculus
60 Atg16l1  
Affinity Capture-MS Mus musculus
61 Ccdc6  
Co-fractionation Mus musculus
62 Nr0b1  
Affinity Capture-MS Mus musculus
63 ZNF8  
Affinity Capture-MS Homo sapiens
64 Fancd2  
Affinity Capture-MS Mus musculus
65 Socs1  
Affinity Capture-MS Mus musculus
View the network image/svg+xml



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