Table S1:Selection of gene ontology (GO) terms for the proteins in the green box of the cluster analysis in Fig. 16C
GO term protein count (GO
term)
p% (count GO ter-min/count total list)
p-value
BP: gene expression 8 80 3.4 x 10−3
CC: chromosome 3 30 7.1 x 10−2
MF: nucleic acid binding 8 80 9.0 x 10−4
MF: protein binding 8 80 5.4 x 10−2
The number of proteins enriched for a specific GO term (protein count), the percentage of the protein count enriched for the specific GO term compared to the total number of proteins in the box and the p-value for the enrichment are given. BP = biological process, CC = cellular compartment, MF = molecular function
Table 1: Table S2: Selection of gene ontology (GO) terms for the proteins in the cyan box of the cluster analysis in Fig. 16C.
GO term protein count (GO
term)
p% (count GO ter-min/count total list)
p-value
CC: nucleus 9 90 1.2 x 10−3
MF: nucleic acid binding 9 90 6.6 x 10−5
The number of proteins enriched for a specific GO term (protein count), the percentage of the protein count enriched for the specific GO term compared to the total number of proteins in the box and the p-value for the enrichment are given. CC = cellular compartment, MF = molecular function
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Table S3: Selection of gene ontology (GO) terms for the proteins in the purple box of the cluster analysis in Fig. 16C.
GO term protein count
(GO term)
p% (count GO termin/count to-tal list)
p-value
BP: chromatin remod-eling
2 29 4.2 x 10−2
CC: chromosome 4 57 2.2 x 10−3
MF: transcription coactivator activity
3 43 5.5 x 10−4
The number of proteins enriched for a specific GO term (protein count), the percentage of the protein count enriched for the specific GO term compared to the total number of proteins in the box and the p-value for the enrichment are given. BP = biological process, CC = cellular compartment, MF = molecular function
Table S4: Selection of gene ontology (GO) terms for the proteins in the green box of the cluster analysis in Fig. 16C.
GO term protein count (GO term)
p% (count GO ter-min/count total list)
p-value
BP: gene expression 7 88 3.1 x 10−3
CC: nucleus 2 88 7.8 x 10−3
MF: DNA binding 4 50 4.5 x 10−2
The number of proteins enriched for a specific GO term (protein count), the percentage of the protein count enriched for the specific GO term compared to the total number of proteins in the box and the p-value for the enrichment are given. BP = biological process, CC = cellular compartment, MF = molecular function
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Table S5: Log2(GFP-Tet/GFP) values of the chromatin remodelling complex members which are more than twofold enriched and have a p-value < 0.05 in at least one of the Tet co-IPs compared to the control.
Complex Members
Tet1 Co-IP mESC
Tet3-CXXC Co-IP mESC
Tet3 Co-IP mESC
Tet1 Co-IP NPC
Tet3-CXXC Co-IP NPC
Actl6a pos 1.34 pos neg neg
Arid1a pos 0.92 1.67 neg neg
Dmap1 pos 3.00 1.84 pos pos
Hdac2 pos 2.23 neg 1.98 1.98
Mbd3 1.11 pos neg pos 1.92
Mta3 pos 1.66 3.20 neg neg
Ppp1cc neg 1.84 1.99 neg neg
Rbbp7 pos 2.39 3.02 pos 3.25
Ruvbl2 0.99 0.86 1.07 neg neg
Smarcc1 0.62 0.99 0.89 pos pos
Tox4 pos neg neg 1.09 pos
Wdr82 pos pos 1.69 pos 3.09
Ruvbl1 pos 1.34 pos neg neg
Morf4l1 pos 1.63 neg neg pos
Ppp1ca 0.83 1.31 0.87 neg pos
Rbbp4 1.08 1.51 0.94 pos pos
Mta2 pos pos pos neg pos
Ppp1r12a neg neg neg pos pos
Smarcd1 0.51 0.83 pos neg neg
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Complex Members
Tet1 Co-IP mESC
Tet3-CXXC Co-IP mESC
Tet3 Co-IP mESC
Tet1 Co-IP NPC
Tet3-CXXC Co-IP NPC
Smarcc2 2.24 neg pos neg pos
Smarca4 pos pos pos neg pos
Ppp1r10 neg pos pos neg neg
Smarcb1 neg pos pos neg neg
Gatad2a neg neg neg pos pos
Chd4 pos pos pos pos pos
Mta1 pos pos pos pos pos
Hdac1 pos pos neg pos 2.57
Meaf6 pos 2.27 neg pos pos
Smarce1 neg pos neg pos neg
Supt16 pos pos neg 1.75 2.36
Ssrp1 pos 1.42 pos 1.84 1.84
log2(GFP-Tet/GFP) values for the Tet1, Tet3 and Tet3-CXXCCo-IPs in mouse embryonal stem cells (mESCs) and neural progenitor cells (NPCs) are given.
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Table S6: Tet normalized values of the chromatin remodelling complex mem-bers which are more than twofold enriched and have a p-value < 0.05 in at least one of the Tet Co-IPs compared to the control.
Complex Members
Tet1 mESC normalized
Tet3-CXXC mESC nor-malized
Tet3 mESC normalized
Tet3 NPC
normalized
Tet3-CXXC NPC normal-ized
Ppp1cc 0.30 0.28
Actl6a 0.22
Arid1a 0.15 0.24
Dmap1 0.48 0.26
Hdac2 0.36 0.21 0.21
Mbd3 0.12 0.20
Mta3 0.27 0.45
Rbbp7 0.38 0.43 0.34
Ruvbl2 0.10 0.14 0.15
Smarcc1 0.06 0.16 0.13
Tox4 0.12
Wdr82 0.24 0.32
Ruvbl1 0.22
Morf4l1 0.26
Ppp1ca 0.09 0.21 0.12
Rbbp4 0.11 0.24 0.13
Smarcc2 0.23
Smarcd1 0.05 0.13
Meaf6 0.37
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Complex Members
Tet1 mESC normalized
Tet3-CXXC mESC nor-malized
Tet3 mESC normalized
Tet3 NPC
normalized
Tet3-CXXC NPC normal-ized
Ssrp1 0.23 0.20 0.19
Supt16 0.19 0.24
The normalized values for the Tet1, Tet3 and Tet3−CXXC Co-IPs in mouse embryonal stem cells (mESCs) and neural progenitor cells (NPCs) were calculated by dividing the log2 value of the complex member by the log2 value of Tet1, Tet3 or Tet3−CXXC.
Figure S1:Tet levels in mouse embryonic stem cells (mESC). RT-qPCR analysis of Tet1, Tet2 and Tet3 mRNA levels in mESCs shows that Tet1 and Tet2 are highly expressed whereas the amount of Tet3 mRNA is reduced but not zero.
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Figure S2: Validation of the Co-Immunoprecipitation workflow using Tet-loaded beads.
(A) Saturation of GFP-Tet1cd on GFP nanobody magnetic beads. (B) Successful pu-rification of GFP-Tet1cd shown by Coomassie stained 5% SDS PAGE gel.
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Figure S3:Data quality.(A) Multi scatter plot comparing the LFQ intensities from the four biological replicates of the Tet1 experiment with itself (red rectangle) and the control GFP Co-Immunoprecipitation (Co-IP) in mouse embryonic stem cells (mESCs).
Blue numbers indicate the Pearson correlation. (B) Histograms showing counts of LFQ intensities in the four different biological replicates of the control (GFP) and the Tet1 Co-IPs in mESCs. (C) Principal component analysis of the data from the different Tet Co-IPs and the GFP control experiment in mESCs.
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Figure S4: Co-localization of Tet1 and Ywhag in the mouse embryonic stem cells (mESCs). Immunocytochemistry in combination with fluorescence microscopy confirms that Tet1 and Ywhag interact in mESCs.
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Figure S5:The Co-Immunoprecipitation workflow using Tet-covered beads is not biased by competing endogenous Tet.(A) Multi scatter plot comparing the LFQ intensities from the four biological replicates of the Tet1 experiment with itself (reCluster heat map comparing three replicates of the Tet1 Co-IP and the GFP control in wildtype (wt) and triple knockout (TKO) mouse embryonic stem cells.
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