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Table 2 Summary of SILAC MS analysis of proteins associated with wild-type (WT) vs. CID-mutated (MT) RPRD1B

From: Proteomics studies of the interactome of RNA polymerase II C-terminal repeated domain

Gene name

Median of (WT/MT)

Number of unique peptides

Amino acid coverage (%)

POLR2A

9.090909091

20

18.1

POLR2B

7.142857143

17

19.7

RECQL5

4

5

6.2

POLR2C

2.941176471

9

45.8

POLR2D

2.941176471

4

33.8

POLR2E

2.739726027

4

26.2

POLR2I

2.666666667

4

62.4

RPLP2

2.127659574

7

51.3

SKIV2L2

1.5625

3

2.9

NOLC1

1.418439716

4

7.3

EIF2C3

1.408450704

3

17.4

SUPT4H1

1.298701299

3

27.4

SF3A3

1.282051282

3

6.2

DDX3X|DDX3Y

1.265822785

11

32

CSTF3

1.25

5

11.9

TOP3B

1.25

3

9.2

NHP2

1.242236025

6

28.1

DDX5

1.234567901

14

13.3

PARP1

1.234567901

6

9.1

RBM42

1.234567901

4

7.5

RUVBL2

1.234567901

6

12.2

SFRS15

1.234567901

3

2.4

TNRC6B

1.234567901

9

12.6

TFG

1.204819277

5

21

DPF2

1.19760479

8

30.7

PRPF19

1.19047619

5

19.2

CSTF1

1.183431953

6

22.3

DDX5|DDX17

1.183431953

6

30.5

MRPL15

1.176470588

3

18.6

RUVBL1

1.176470588

8

26.8

SNRPD2

1.176470588

10

68.6

SMARCC1

1.169590643

8

20.5

TNRC6C

1.169590643

4

6.2

GTF2I

1.162790698

7

11.9

HMGN2

1.162790698

5

36.7

NUP153

1.162790698

11

10.8

NUP214

1.162790698

9

6.6

RPRD1B

1.156069364

22

77

DDX42

1.149425287

3

3.6

SEC23B

1.149425287

6

15.5

SEC31A

1.149425287

17

18.9

ZNF638

1.149425287

3

5

NUP98

1.142857143

8

7.8

SNRNP70

1.142857143

12

35

DPYSL2

1.136363636

3

13.9

SMARCC2|SMARCC1

1.136363636

11

20.5

DDX3X

1.123595506

3

32

FAU

1.123595506

3

32

SNRPG

1.123595506

3

48.7

RPS7

1.117318436

10

42.6

CDKN2AIP

1.111111111

15

36

CNOT1

1.111111111

3

2.1

EIF2C1

1.111111111

9

21

HNRNPH3

1.111111111

4

15

TP53

1.104972376

6

22.9

PRKRA

1.098901099

3

14.1

PCBP1

1.092896175

4

25

PCF11

1.092896175

6

4.4

FAM98B|FAM98A

1.086956522

3

57.9

FMR1

1.086956522

3

5.5

LRRC59

1.086956522

3

20.5

SF3B3

1.086956522

9

11

DDX17

1.081081081

22

42.4

WDR33

1.081081081

4

5.4

CPSF1

1.075268817

15

14.3

HIST1H1A

1.075268817

3

50.2

SEC24C

1.075268817

16

18.2

CPSF2

1.069518717

10

17.9

HMGA1

1.069518717

4

36.5

DHX9|NPL

1.063829787

3

19.1

EIF2C2

1.063829787

11

30.4

HNRNPD

1.063829787

15

48.4

RBM17

1.063829787

15

20.4

SNRPA

1.063829787

9

36.1

CHERP

1.052631579

8

9.9

DAP3

1.052631579

3

5.8

RPS17

1.052631579

4

34.8

RPS2

1.052631579

3

14.2

SNRPD1

1.052631579

3

58.8

  1. Lists proteins that were identified to preferentially associate with wild type (WT) RPRD1B, but not CID-mutated (MT) RPRD1B utilizing a SILAC mass spectrometry strategy where heavy and light isotope labeling was conducted after tetracycline-induced expression of the WT and MT RPRD1B in HEK293T cells. The official gene symbols of the identified proteins are listed in the first column. The column labeled Median WT/MT is the median ratio between a heavy and light matching peptide identified for that protein. Unique peptides column shows the total number of peptides that were identified and exists in only one protein regardless of peptide length. Amino acid coverage column shows the percentage of the protein’s sequence represented by the peptides identified in the MS analysis
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BMC Research Notes

ISSN: 1756-0500

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