Table S1.

Proteins that are significantly enriched or depleted in H2Aub nucleosomes isolated from HeLa cells overexpressing HA-ubiquitin

Accession no.	Name	Gene	Log2 (fold-change)				In negative control IP	Mann–Whitney test (Bonferroni corrected)
			H2Aub depleted		H2A enriched
			SILAC labeled	Unlabeled	SILAC labeled	Unlabeled
P38159	RNA-binding motif protein, X chromosome	RBMX	−0.0119	−0.0247	2.9391	2.464	Yes	0.0031
Q96T58	Msx2-interacting protein	SPEN	0.2218	0.2813	3.3034	1.9627	No	0.032
Q13435	Splicing factor #B subunit 2	SF3B2	0.0452	0.0452	1.4797	1.9167	Yes	0.00015
C9JNJ1	Remodeling and spacing factor 1	RSF1	−0.0021	0	1.3044	1.8278	No	0.011
Q13573	SNW domain-containing protein 1	SNW1	−0.1363	−0.0432	1.6406	0.7747	Yes	0.039
A6NJZ9U	Nucleolar complex protein 3 homolog	NOC3L	0.0308	0.0308	0.5244	0.7512	No	0.00027
Q9NYF8-2	Bcl-2–associated transcription factor 1	BCLAF1	0.0164	0.0164	2.579	0.6463	Yes	0.0015
Q9Y2X3	Nucleolar protein 58	NOP58	−0.0963	−0.0963	0.7584	0.3893	Yes	0.0086
Q15029	116 kDa U5 small nuclear ribonucleoprotein component	EFTUD2	−0.0149	−0.0149	1.4838	0.3651	Yes	0.01
P02545	Prelamin-A/C	LMNA	0	0	−0.4099	−0.7106	—	0.017
P62701	40S ribosomal protein S4, X isoform	RPS4X	0.0639	0.0639	−0.2305	−0.9616	—	0.0053
Q12906	Interleukin enhancer-binding factor 3	ILF3	0	0	−1.2755	−1.2198	—	0.012
Q08945	FACT complex subunit SSRP1	SSRP1	−0.0457	−0.0457	−0.148	−1.2864	—	0.00024
P62750	60S ribosomal protein L23a	RPL23A	0	0	−0.5037	−1.2923	—	0.0011
P62805	Histone H4	HIST1H2A	0.0287	0.0287	−0.464	−1.8234	—	0.0014
P32969	60S ribosomal protein L9	RPL9	−0.018	−0.018	−2.006	−2.1686	—	0.026
P11387	DNA topoisomerase 1	TOP1	0	0	−1.124	−2.4621	—	0.012
B4E0E1	Highly similar to Poly(ADP ribose) polymerase 1		0.0182	0.0182	−1.8421	−2.7885	—	0.0011
P08133	Annexin A6	ANXA6	−0.0323	−0.0323	−4.2228	−5.1433	—	0.0081

A negative control, where parallel IP experiment was performed with parental cell lines, was included. Proteins that were not immunoprecipitated in negative control are in bold.