Table 2. The list of the chromatin proteins detected by mass spectrometry (MS) before and after enrichment on the MagIC-cryo-EM-beads.
The MS analysis was conducted to the sucrose gradient fractions 5, before (Figure 3C) and after (Figure 3E) enrichment with the GPF nanobody-MagIC-cryo-EM beads. Detectable MS signals for known chromatin proteins and the recombinant proteins used for assembling the MagIC-cryo-EM beads were manually selected and are listed here. See Supplementary file 2 of the full MS data.
| Description | Full name or functions | Input interphase, fraction 5 | Input metaphase, fraction 5 | MagIC-cryo-EM, interphase, fraction 5 | MagIC-cryo-EM, metaphase, fraction 5 |
|---|---|---|---|---|---|
| XBmRNA11963| h2ac17.L | histone H2A | 1.37x1010 | 4.12x109 | 2.08x108 | 1.49x108 |
| XBmRNA31731| LOC121402261 | histone H2B | 7.87x109 | 2.26x109 | 1.10x108 | 2.25x108 |
| XBmRNA31368| LOC121402047 | histone H4 | 7.34x109 | 2.00x109 | 1.11x108 | 1.63x108 |
| XBmRNA36987| h2aj.L | histone H2A.J | 6.74x109 | 3.64x109 | 2.44x108 | 1.29x108 |
| XBmRNA58735| h2ax.2.L | histone H2A.X | 6.56x109 | 1.73x109 | 2.44x108 | 1.75x108 |
| XBmRNA1949| h2az1.L | histone H2A.Z | 4.50x109 | 3.64x109 | 2.44x108 | 1.52x108 |
| XBmRNA75391| h3-3b.L | histone H3.3 | 3.33x109 | 1.19x109 | 3.84x107 | 5.29x107 |
| XBmRNA25971| npm2.L | Nucleoplasmin | 1.77x109 | n.d. | 1.89x108 | n.d. |
| XBmRNA28658| npm2.S | Nucleoplasmin | 1.76x109 | n.d. | 1.31x108 | n.d. |
| XBmRNA25690| pcna.L | PCNA | 1.29x109 | n.d. | n.d. | n.d. |
| XBmRNA28883| pcna.S | PCNA | 1.29x109 | n.d. | n.d. | n.d. |
| XBmRNA41314| h1-8.S | Linker histone H1.8 | 7.12x108 | 1.93x108 | 5.67x107 | 6.87x107 |
| XBmRNA9392| supt16h.S | supt16h (histone chaperone FACT complex component) | 3.14x108 | n.d. | n.d. | n.d. |
| XBmRNA4198| supt16h.L | supt16h (histone chaperone FACT complex component) | 3.04x108 | n.d. | n.d. | n.d. |
| XBmRNA62381| ssrp1.S | ssrp1 (histone chaperone FACT complex component) | 2.96x108 | n.d. | n.d. | n.d. |
| sfGFP | sfGFP (Tagged with H1.8) | 2.84x108 | 8.15x107 | 6.02x107 | 4.58x107 |
| XBmRNA26658| dnmt1.L | DNA methyltransferase 1 | 1.41x108 | n.d. | n.d. | n.d. |
| XBmRNA31618| dnmt1.S | DNA methyltransferase 1 | 1.35x108 | n.d. | n.d. | n.d. |
| XBmRNA5952| sub1.L | Activated RNA polymerase II transcriptional coactivator p15 | 8.60x107 | n.d. | n.d. | n.d. |
| XBmRNA24726| pclaf.L | PCNA-associated factor | 8.38x107 | n.d. | n.d. | n.d. |
| XBmRNA4881| ran.L | GTP-binding nuclear protein Ran | 7.38x107 | n.d. | n.d. | n.d. |
| XBmRNA42021| msh2.L | DNA repair protein MutS | 7.08x107 | n.d. | n.d. | n.d. |
| XBmRNA52420| mcm4.L | DNA replication licensing factor MCM4 | 6.61x107 | n.d. | n.d. | n.d. |
| XBmRNA51197| mcm6.L | DNA replication licensing factor MCM6 | 6.54x107 | n.d. | n.d. | n.d. |
| XBmRNA60815| rcc2.L | Regulator of chromosome condensation 2 | 6.29x107 | n.d. | n.d. | n.d. |
| XBmRNA29645| pclaf.S | PCNA-associated factor | 5.26x107 | n.d. | n.d. | n.d. |
| XBmRNA12919| rcc1.L | Regulator of chromosome condensation 1 | 5.24x107 | n.d. | n.d. | n.d. |
| XBmRNA27060| mcm7.L | DNA replication licensing factor MCM7 | 5.08x107 | n.d. | n.d. | n.d. |
| XBmRNA73621| LOC108700788 | Importin subunit beta-like isoform X2 | 5.03x107 | n.d. | n.d. | n.d. |
| XBmRNA42017| msh6.L | DNA repair protein MutS | 4.96x107 | n.d. | n.d. | n.d. |
| XBmRNA39469| top1.2.S | DNA topoisomerase I | 4.92x107 | n.d. | n.d. | n.d. |
| XBmRNA82329| kpna7.S | Importin subunit beta | 4.80x107 | n.d. | n.d. | n.d. |
| XBmRNA74418| csnk2a1.L | Casein kinase II subunit alpha | 4.65x107 | n.d. | n.d. | n.d. |
| XBmRNA25938| XB5867546.L | Nucleoplasmin isoform (lacking C-ter tail) | 4.31x107 | n.d. | n.d. | n.d. |
| XBmRNA7871| uhrf1.S | E3 ubiquitin-protein ligase UHRF1 | 4.27x107 | n.d. | n.d. | n.d. |
| XBmRNA12245| rpa1.L | Replication protein A | 4.10x107 | n.d. | n.d. | n.d. |
| XBmRNA41384| LOC100192369 | Sperm-specific nuclear basic protein 1 | 4.08x107 | n.d. | n.d. | n.d. |
| XBmRNA52377| mcm3.L | DNA replication licensing factor MCM3 | 4.04x107 | n.d. | n.d. | n.d. |
| XBmRNA36255| mcm5.L | DNA replication licensing factor MCM5 | 3.86x107 | n.d. | n.d. | n.d. |
| XBmRNA36962| mcm2.L | DNA replication licensing factor MCM2 | 3.73x107 | n.d. | n.d. | n.d. |
| XBmRNA60207| pold1.L | DNA polymerase | 3.63x107 | n.d. | n.d. | n.d. |
| XBmRNA33152| fen1.L | Flap endonuclease 1 A | 3.59x107 | n.d. | n.d. | n.d. |
| XBmRNA25831| pold2.L | DNA polymerase delta subunit 2 | 3.37x107 | n.d. | n.d. | n.d. |
| XBmRNA38234| ddb1.S | DNA damage-binding protein 1 | 2.98x107 | n.d. | n.d. | n.d. |
| XBmRNA78857| dppa2.L | Developmental pluripotency associated 2 | 2.96x107 | n.d. | n.d. | n.d. |
| XBmRNA34892| gins3.L | DNA replication complex GINS protein PSF3 | 2.93x107 | n.d. | n.d. | n.d. |
| XBmRNA83211| hirip3.S | HIRA-interacting protein 3 | 2.69x107 | n.d. | n.d. | n.d. |
| XBmRNA35380| nasp.L | histone chaperone NASP | 1.84x107 | n.d. | n.d. | n.d. |
| XBmRNA23497| hmga2.L | High mobility group AT-hook 2 | 1.45x107 | n.d. | n.d. | n.d. |
| XBmRNA30566| hmga2.S | High mobility group AT-hook 2 | 1.43x107 | n.d. | n.d. | n.d. |
| XBmRNA33324| pola2.L | DNA polymerase alpha subunit B | 1.10x107 | n.d. | n.d. | n.d. |
| Streptavidin | MagIC-cryo-EM beads proteins | n.d. | n.d. | 1.22x109 | 2.19x109 |
| SPY-tagGFPnanobody | MagIC-cryo-EM beads proteins | n.d. | n.d. | 7.69x108 | 1.41x109 |
| Spycatcher3 | MagIC-cryo-EM beads proteins | n.d. | n.d. | 5.99x108 | 7.82x108 |
| 11 nm_3HB | MagIC-cryo-EM beads proteins | n.d. | n.d. | 4.32x107 | 5.90x107 |
| 60 nm_SAH | MagIC-cryo-EM beads proteins | n.d. | n.d. | 1.21x107 | 7.73x106 |