Table 1.

Detection of most highly expressed PARylated proteins in iPSCs using poly(ADP-ribose)-resin pulldown

No. Protein name Accession no. Gene name kD/pl Pep # (unique) PEP 
1 Poly [ADP-ribose] polymerase 1 P11103 Parp1 113.10/9.05 70 (17) <1.00−307 
2 FACT complex subunit SPT16 Q92089 Supt16h 119.82/5.50 16 (16) 5.92−148 
3 Poly [ADP-ribose] polymerase 2 O88554 Parp2 63.40/8.65 15 (15) 3.28−134 
4 Chromodomain-helicase-DNA-binding protein 1-like Q9CXF7 Chd1l 101.44/6.20 11 (11) 1.54−54 
5 DNA ligase 3 P97386 Lig3 113.07/9.16 10 (10) 3.32−104 
6 FACT complex subunit SSRP1 Q08943 Ssrp1 80.86/6.33 4 (4) 9.96−9 
7 Leucine-rich repeat flightless-interacting protein 2 Q91WK0 Lrrfip2 47.15/5.54 3 (3) 4.01−61 
8 x-ray repair cross-complementing protein 6 P23475 Xrcc6 69.48/6.35 3 (3) 2.00−10 
9 x-ray repair cross-complementing protein 1 Q60596 Xrcc1 68.97/5.97 3 (3) 8.30−7 
10 Splicing factor U2AF 35 kD subunit Q9D883 U2af1 27.82/9.09 2 (2) 3.35−34 
11 Protein timeless homolog Q9R1X4 Timeless 137.50/5.35 2 (2) 1.11−22 
12 Nucleolar RNA helicase 2 Q9JIK5 Ddx21 93.55/9.19 2 (2) 3.57−5 
13 U1 small nuclear ribonucleoprotein A Q62189 Snrpa 31.84/9.81 2 (2) 3.52−4 
14 Tyrosyl-DNA phosphodiesterase 1 Q8BJ37 Tdp1 68.69/7.67 2 (2) 1.81−4 
15 Aprataxin and PNK-like factor Q9D842 Aplf 54.97/5.05 2 (2) 2.55−3 
16 Replication protein A 70 kD DNA-binding subunit Q8VEE4 Rpa1 69.04/8.13 2 (2) 2.24−3 
17 Apoptotic chromatin condensation inducer in the nucleus Q9JIX8 Acin1 150.72/5.71 1 (1) 3.75−10 
18 Heterogeneous nuclear ribonucleoprotein A3 Q8BG05 Hnrnpa3 39.65/9.10 1 (1) 5.56−5 
19 Fragile X mental retardation protein 1 homolog P35922 Fmr1 68.99/7.27 1 (1) 4.56−3 
20 Recombining binding protein suppressor of hairless P31266 Rbpj 58.54/8.43 1 (1) 2.56−3 
21 Splicing factor U2AF 65 kD subunit P26369 U2af2 53.52/9.19 1 (1) 1.14−3 
No. Protein name Accession no. Gene name kD/pl Pep # (unique) PEP 
1 Poly [ADP-ribose] polymerase 1 P11103 Parp1 113.10/9.05 70 (17) <1.00−307 
2 FACT complex subunit SPT16 Q92089 Supt16h 119.82/5.50 16 (16) 5.92−148 
3 Poly [ADP-ribose] polymerase 2 O88554 Parp2 63.40/8.65 15 (15) 3.28−134 
4 Chromodomain-helicase-DNA-binding protein 1-like Q9CXF7 Chd1l 101.44/6.20 11 (11) 1.54−54 
5 DNA ligase 3 P97386 Lig3 113.07/9.16 10 (10) 3.32−104 
6 FACT complex subunit SSRP1 Q08943 Ssrp1 80.86/6.33 4 (4) 9.96−9 
7 Leucine-rich repeat flightless-interacting protein 2 Q91WK0 Lrrfip2 47.15/5.54 3 (3) 4.01−61 
8 x-ray repair cross-complementing protein 6 P23475 Xrcc6 69.48/6.35 3 (3) 2.00−10 
9 x-ray repair cross-complementing protein 1 Q60596 Xrcc1 68.97/5.97 3 (3) 8.30−7 
10 Splicing factor U2AF 35 kD subunit Q9D883 U2af1 27.82/9.09 2 (2) 3.35−34 
11 Protein timeless homolog Q9R1X4 Timeless 137.50/5.35 2 (2) 1.11−22 
12 Nucleolar RNA helicase 2 Q9JIK5 Ddx21 93.55/9.19 2 (2) 3.57−5 
13 U1 small nuclear ribonucleoprotein A Q62189 Snrpa 31.84/9.81 2 (2) 3.52−4 
14 Tyrosyl-DNA phosphodiesterase 1 Q8BJ37 Tdp1 68.69/7.67 2 (2) 1.81−4 
15 Aprataxin and PNK-like factor Q9D842 Aplf 54.97/5.05 2 (2) 2.55−3 
16 Replication protein A 70 kD DNA-binding subunit Q8VEE4 Rpa1 69.04/8.13 2 (2) 2.24−3 
17 Apoptotic chromatin condensation inducer in the nucleus Q9JIX8 Acin1 150.72/5.71 1 (1) 3.75−10 
18 Heterogeneous nuclear ribonucleoprotein A3 Q8BG05 Hnrnpa3 39.65/9.10 1 (1) 5.56−5 
19 Fragile X mental retardation protein 1 homolog P35922 Fmr1 68.99/7.27 1 (1) 4.56−3 
20 Recombining binding protein suppressor of hairless P31266 Rbpj 58.54/8.43 1 (1) 2.56−3 
21 Splicing factor U2AF 65 kD subunit P26369 U2af2 53.52/9.19 1 (1) 1.14−3 

Posterior error probability (PEP) was obtained from statistical analysis of total peptide identification for a protein in one sample. The value essentially operates as a statistical value, and low PEP indicates high statistical significance. pl, isoelectric point.

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