Table 2.
Nucleosome-binding Proteins Regulated by CpG- and Lysine-Methylation as Identified by SNAP
| Enrichment/Exclusion (Ratio H/L forward) |
H3K4me3/ 601-Nuc |
H3K4me3/ 601me-Nuc |
H3K9me3/ 601-Nuc |
H3K9me3/ 601me-Nuc |
H3K27me3/ 601-Nuc |
H3K27me3/ 601me-Nuc |
|
|---|---|---|---|---|---|---|---|
| Enriched Proteins | Very Strong Enrichment (>10) |
Spindlin1 | IWS1# Spindlin1 |
CBX5/HP1α UHRF1 |
UHRF1 | ||
| Strong Enrichment (5 - 10) |
PHF8 CHD1 |
PHF8 | CBX3/HP1γ CDYL2 |
CBX5/HP1α Orc43 Orc23 Orc33 Orc53 LRWD1 MeCP2 |
|||
| Moderate Enrichment (2 - 5) |
DIDO1 UBF1 Sin3A6 |
PAX6 CHD1 MeCP2 MTERF MBD22 DIDO1 Orc23 Orc43 MBD4 |
LRWD1 CDYL FBXL11 UBF1 Orc23 Orc43 Orc53 Orc33 |
PAX6 CBX3/HP1γ CDYL MTERF MBD22 Orc13 |
C17orf96 LRWD1 EED4 Orc43 Orc53 SUZ124 Orc23 Orc33 EZH24 MTF2 CBX8 |
LRWD1 Orc23 Orc33 Orc43 Orc53 MeCP2 CBX8 UHRF1 PAX6 MTERF Orc13 |
|
| Weak Enrichment (1.5 - 2) |
SAP306 WDR82 EMG1 TAF9B PPIB VRK2 HNRNPA1* HNRNPA2B1* ING4 WDR61 HNRNPA0* FLYWCH1 BUB3 FUBP3 |
Orc53 LRWD1 PPIB ING4 TOX4 MTA22 CHD42 ZSCAN21 Orc33 NONO CDCA7L* WDR82* |
CHD1 SUZ124 EED4 PPIB NONO MTF2 SUB1 |
MTA22 MBD4 ZSCAN21 CHD42 NSD3 |
PPIB | CDCA7L BMI1 PPIB MTA22 MBD4* |
|
| Excluded Proteins | Weak Exclusion (0.5 - 0.67) |
SKP11 RCOR1 |
SKP11 CREB1 |
HCFC1 PHF14 SKP11 |
|||
| Moderate Exclusion (0.2 - 0.5) |
HMG20A HMG20B MTF2* |
RING11 SUB1 HMG20B NAIF MYC |
IMP4 | RCOR1 BANP RING11 SUB1 EED4 TIGD5 RNF21 MYC NAIF1 ARNT TCF7L2 HES7 |
SPTH167 SSRP17 TCF7L2 BANP* PRDM11 NAIF1 RPA15 BANP* SUB1 |
||
| Strong Exclusion (0.1 - 0.2) |
PHF14 | FBXL101 PHF14 BCOR1 PCGF11 |
MAX CXXC5 L3MBTL3 FBXL101 BCOR1 |
RPA25 BCOR1 MYC FBXL101 PCGF11 MAX |
|||
| Very Strong Exclusion (< 0.1) |
L3MBTL3 ARNT FBXL11 Syntenin1 Atherin USF2 USF1 HIF1A* bHLHB2 |
PCGF11 HIF1A Syntenin1 FBXL11 Atherin USF1 USF2 bHLHB2 |
L3MBTL3 HES7 Syntenin1 HIF1A Atherin ARNT FBXL11 USF1 USF2 bHLHB2 |
||||
*
Table 2 shows the proteins that were enriched or excluded by modified nucleosomes compared to unmodified nucleosomes at least 1.5-fold in both, the forward and reverse pulldown experiments. Proteins are grouped according to their ratio H/L in the forward experiments. Proteins marked by an asterisk are just below the threshold. For the values of the SILAC ratios see Tables S1 and S2. Protein complex subunits:
1
BCOR-complex,
2
NuRD-complex,
3
ORC complex,
4
PRC2-complex,
5
Replication factor A-complex,
6
Sin3A-complex,
7
FACT.
#
IWS should be treated with caution since it was found as a false positive outlier in the 601me-Nuc pulldown. Fbxl11/KDM2A is highlighted in bold.