Nuclear High Mobility Group A2 (HMGA2) Interactome Revealed by Biotin Proximity Labeling
Abstract
:1. Introduction
2. Results
2.1. HMGA2-BioID2 Fusion Protein Biotinylates Nuclear Proteins
2.2. HMGA2 Proximity Labeling Identifies A Unique Nuclear HMGA2 Interactome
2.3. Nuclear HMGA2-BioID2 Interactome Confirms Known and Discovers New Interaction Partners
2.4. Bioinformatics Signature of the HMGA2 Proximity Interactome
3. Discussion
4. Materials and Methods
4.1. Creation of Stable HEK293 Cell Lines Expressing BioID2 and Miniturbo Fusion Proteins
4.2. Metabolic Labeling and Liquid Chromatography Mass Spectrometry (LC-MS/MS) Analysis
4.3. Western Blot Validation by Co-Immunoprecipitation (IP) or BioID
4.4. Bioinformatics Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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BioID2 AP/MS | miniTurbo AP/MS | |||||||
---|---|---|---|---|---|---|---|---|
Experiment 1 | Experiment 2 | |||||||
UniProt | Gene | # pep | log2 Ratio | # pep | log2 Ratio | # pep | log2 Ratio | Biogrid |
Bait | ||||||||
FSH2U8 | HMGA2 | 6 | Bait only | 4 | Bait only | 3 | Bait only | |
Histones | ||||||||
O75367 | H2AY | 13 | 8.52 | 9 | 2.95 | 4 | 1.28 | * |
P16403 | HIST1H1C | 11 | 2.96 | 12 | 1.49 | 12 | 0.68 | |
P10412 | HIST1H1E | 9 | Bait only | 11 | 1.46 | 11 | 0.42 | |
Q93077 | HIST1H2AC | 6 | 5.5 | 7 | 3.16 | 5 | 1.55 | * |
Q99878 | HIST1H2AJ | 8 | 6.22 | 8 | 3.22 | 5 | 1.57 | |
P62805 | HIST1H4F | 13 | 6.34 | 12 | 3.15 | 10 | 1.58 | |
Q71DI3 | HIST2H3D | 9 | 6.23 | 11 | 3.06 | 4 | 1.63 | |
Q99880 | H2B1L/M | 11 | 6.22 | 9 | 3.1 | 4 | 1.56 | |
Other Hits | ||||||||
P25440 | BRD2 | 10 | Bait only | 5 | Bait only | 7 | Bait only | |
Q13185 | CBX3 | 6 | Bait only | 6 | 1.07 | 7 | 1.38 | |
E9PEI0 | CDCA2 | 4 | Bait only | 1 | 1.73 | 7 | 3.26 | |
Q53HL2 | CDCA8 | 6 | Bait only | 2 | 2.53 | 10 | 5.55 | |
Q96JM3 | CHAMP1 | 18 | Bait only | 14 | 1.34 | 13 | 1.41 | |
Q5QJE6 | DNTTIP2 | 8 | Bait only | 3 | 2.05 | 7 | 1.41 | |
P78347 | GTF2I | 26 | Bait only | 16 | 1.59 | 20 | 0.46 | |
O14929 | HAT1 | 3 | Bait only | 4 | 2.48 | 1 | Bait only | |
Q5T7C4 | HMGB1 | 6 | 3.05 | 4 | 0.82 | 5 | 1.85 | |
D6R9A6 | HMGB2 | 5 | 4.13 | 4 | 0.82 | 4 | 1.66 | |
Q9H0C8 | ILKAP | 11 | Bait only | 9 | 1.8 | 5 | 0.85 | |
P42167 | LAP2B | 19 | Bait only | 22 | 1.08 | 9 | 2.19 | |
Q14676 | MDC1 | 32 | Bait only | 39 | 2.61 | 5 | 0.62 | |
P46013 | MKI67 | 4 | Bait only | 83 | 1.62 | 106 | 2.51 | |
Q14980 | NUMA1 | 91 | 3.25 | 46 | 2.49 | 12 | 1.29 | |
P09874 | PARP1 | 66 | 5.65 | 54 | 3.9 | 24 | 2.19 | * |
Q7Z3K3 | POGZ | 15 | Bait only | 6 | 4.23 | 4 | 1.19 | |
O75475 | PSIP1 | 16 | Bait only | 7 | 3.02 | 3 | Bait only | * |
Q08945 | SSRP1 | 17 | Bait only | 8 | 1.48 | 2 | 1.26 | |
P11388 | TOP2A | 55 | 4.13 | 33 | 1.9 | 15 | 1.86 | |
Q9ULW0 | TPX2 | 20 | Bait only | 20 | 1.56 | 23 | 2.96 | |
Q14669 | TRIPC | 25 | Bait only | 14 | 2.37 | 20 | 1.59 | |
B7ZM82 | WIZ | 13 | Bait only | 9 | 1.95 | 11 | Bait only | |
P13010 | XRCC5 | 32 | 4.13 | 20 | 2.8 | 10 | 0.86 | * |
P12956 | XRCC6 | 29 | 4.29 | 20 | 2.8 | 10 | 0.75 | * |
P17028 | ZNF24 | 6 | Bait only | 3 | Bait only | 2 | Bait only | |
Q96KM6 | ZNF512B | 3 | Bait only | 5 | 2.57 | 2 | Bait only |
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Gaudreau-Lapierre, A.; Klonisch, T.; Nicolas, H.; Thanasupawat, T.; Trinkle-Mulcahy, L.; Hombach-Klonisch, S. Nuclear High Mobility Group A2 (HMGA2) Interactome Revealed by Biotin Proximity Labeling. Int. J. Mol. Sci. 2023, 24, 4246. https://doi.org/10.3390/ijms24044246
Gaudreau-Lapierre A, Klonisch T, Nicolas H, Thanasupawat T, Trinkle-Mulcahy L, Hombach-Klonisch S. Nuclear High Mobility Group A2 (HMGA2) Interactome Revealed by Biotin Proximity Labeling. International Journal of Molecular Sciences. 2023; 24(4):4246. https://doi.org/10.3390/ijms24044246
Chicago/Turabian StyleGaudreau-Lapierre, Antoine, Thomas Klonisch, Hannah Nicolas, Thatchawan Thanasupawat, Laura Trinkle-Mulcahy, and Sabine Hombach-Klonisch. 2023. "Nuclear High Mobility Group A2 (HMGA2) Interactome Revealed by Biotin Proximity Labeling" International Journal of Molecular Sciences 24, no. 4: 4246. https://doi.org/10.3390/ijms24044246