Table 3. Transcription factors identified by iPOND and aniPOND.
Transcription Factors | iPOND (Mutant) | aniPOND (8hpi) | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Experiment 1 | Experiment 2 | Experiment 1 | Experiment 2 | |||||||||||||
DNA-directed RNA polyermase II | Ctrl | 6hpi | 8hpi | 12hpi | Ctrl | 6hpi | 8hpi | 12hpi | Ctrl | Mutant | KOS | Ctrl | Mutant | KOS | ||
POLR2A | DNA-directed RNA polymerase II subunit RPB1 | P24928 | 0 | 33 | 36 | 7 | 0 | 95 | 49 | 48 | 0 | 54 | 10 | 0 | 111 | 74 |
POLR2B | DNA-directed RNA polymerase II subunit RPB2 | P30876 | 0 | 20 | 40 | 4 | 0 | 97 | 61 | 51 | 0 | 31 | 3 | 0 | 87 | 50 |
POLR2C | DNA-directed RNA polymerase II subunit RPB3 | P19387 | 0 | 0 | 2 | 0 | 0 | 5 | 0 | 2 | 0 | 2 | 2 | 0 | 6 | 10 |
POLR2D | DNA-directed RNA polymerase II subunit RPB4 | O15514 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | ||||
POLR2E | DNA-directed RNA polymerases II subunit RPB5 | P19388 | 0 | 3 | 7 | 2 | 0 | 3 | 0 | 2 | 0 | 4 | 3 | 0 | 6 | 7 |
POLR2F | DNA-directed RNA polymerases II subunit RPB6 | P61218 | 0 | 2 | 0 | |||||||||||
POLR2G | DNA-directed RNA polymerase II subunit RPB7 | P62487 | 0 | 2 | 0 | 0 | 0 | 5 | 0 | 0 | 7 | 5 | ||||
POLR2H | DNA-directed RNA polymerases II subunit RPB8 | P52434 | 0 | 2 | 2 | |||||||||||
POLR2I | DNA-directed RNA polymerase II subunit RPB9 | P36954 | 0 | 7 | 2 | |||||||||||
POLR2J | DNA-directed RNA polymerase II subunit RPB11-a | P52435 | 0 | 2 | 2 | 0 | ||||||||||
POLR2L | DNA-directed RNA polymerases II subunit RPB10 | P62875 | 0 | 2 | 0 | 0 | ||||||||||
Mediator of RNA polymerase II transcription | ||||||||||||||||
MED1 | Mediator of RNA polymerase II transcription subunit 1 | Q15648 | 0 | 6 | 8 | 0 | 52 | 32 | ||||||||
MED4 | Mediator of RNA polymerase II transcription subunit 4 | Q9NPJ6 | 0 | 2 | 0 | 0 | 7 | 6 | ||||||||
MED6 | Mediator of RNA polymerase II transcription subunit 6 | O75586 | 0 | 4 | 0 | 0 | 12 | 7 | ||||||||
MED7 | Mediator of RNA polymerase II transcription subunit 7 | O43513 | 0 | 7 | 0 | |||||||||||
MED8 | Mediator of RNA polymerase II transcription subunit 8 | Q96G25 | 0 | 7 | 5 | |||||||||||
MED10 | Mediator of RNA polymerase II transcription subunit 10 | Q9BTT4 | 0 | 4 | 0 | |||||||||||
MED11 | Mediator of RNA polymerase II transcription subunit 11 | Q9P086 | 0 | 3 | 2 | |||||||||||
MED12 | Mediator of RNA polymerase II transcription subunit 12 | Q93074 | 0 | 14 | 0 | 0 | 82 | 46 | ||||||||
MED13 | Mediator of RNA polymerase II transcription subunit 13 | Q9UHV7 | 0 | 6 | 0 | |||||||||||
MED13L | Mediator of RNA polymerase II transcription subunit 13-like | Q71F56 | 0 | 11 | 0 | |||||||||||
MED14 | Mediator of RNA polymerase II transcription subunit 14 | O60244 | 0 | 22 | 10 | 0 | 156 | 119 | ||||||||
MED15 | Mediator of RNA polymerase II transcription subunit 15 | Q96RN5 | 0 | 15 | 3 | |||||||||||
MED16 | Mediator of RNA polymerase II transcription subunit 16 | Q9Y2X0 | 0 | 18 | 9 | 0 | 51 | 31 | ||||||||
MED17 | Mediator of RNA polymerase II transcription subunit 17 | Q9NVC6 | 0 | 9 | 5 | 0 | 37 | 27 | ||||||||
MED18 | Mediator of RNA polymerase II transcription subunit 18 | Q9BUE0 | 0 | 3 | 3 | 0 | 12 | 6 | ||||||||
MED20 | Mediator of RNA polymerase II transcription subunit 20 | Q9H944 | 0 | 6 | 4 | 0 | 11 | 11 | ||||||||
MED21 | Mediator of RNA polymerase II transcription subunit 21 | Q13503 | 0 | 2 | 0 | 0 | 4 | 2 | ||||||||
MED22 | Mediator of RNA polymerase II transcription subunit 22 | Q15528 | 0 | 4 | 3 | |||||||||||
MED23 | Mediator of RNA polymerase II transcription subunit 23 | Q9ULK4 | 0 | 59 | 27 | 0 | 132 | 110 | ||||||||
MED24 | Mediator of RNA polymerase II transcription subunit 24 | O75448 | 0 | 35 | 12 | 0 | 83 | 65 | ||||||||
MED25 | Mediator of RNA polymerase II transcription subunit 25 | Q71SY5 | 0 | 16 | 16 | |||||||||||
MED27 | Mediator of RNA polymerase II transcription subunit 27 | Q6P2C8 | 0 | 4 | 2 | 0 | 16 | 17 | ||||||||
MED28 | Mediator of RNA polymerase II transcription subunit 28 | Q9H204 | 0 | 2 | 2 | 0 | 3 | 4 | ||||||||
MED29 | Mediator of RNA polymerase II transcription subunit 29 | Q9NX70 | 0 | 3 | 2 | 0 | 8 | 10 | ||||||||
MED30 | Mediator of RNA polymerase II transcription subunit 30 | Q96HR3 | 0 | 4 | 0 | 0 | 7 | 4 | ||||||||
MED31 | Mediator of RNA polymerase II transcription subunit 31 | Q9Y3C7 | 0 | 7 | 6 | 0 | 13 | 8 | ||||||||
CCNC | Cyclin-C | P24863 | 0 | 2 | 3 | 0 | 6 | 5 | ||||||||
CDK8 | Cyclin-dependent kinase 8 | P49336 | 0 | 8 | 10 | |||||||||||
Transcription initiation factor TFIID | ||||||||||||||||
TAF1 | Transcription initiation factor TFIID subunit 1 | P21675 | 0 | 5 | 12 | |||||||||||
TAF2 | Transcription initiation factor TFIID subunit 2 | Q6P1X5 | 0 | 9 | 0 | 0 | 18 | 25 | ||||||||
TAF3 | Transcription initiation factor TFIID subunit 3 | Q5VWG9 | 0 | 0 | 3 | |||||||||||
TAF4 | Transcription initiation factor TFIID subunit 4 | O00268 | 0 | 5 | 0 | |||||||||||
TAF5 | Transcription initiation factor TFIID subunit 5 | Q15542 | 0 | 8 | 2 | 0 | 62 | 45 | ||||||||
TAF6 | Transcription initiation factor TFIID subunit 6 | P49848 | 0 | 20 | 6 | 0 | 48 | 41 | ||||||||
TAF9 | Transcription initiation factor TFIID subunit 9 | Q16594 | 0 | 8 | 10 | |||||||||||
TAF9B | Transcription initiation factor TFIID subunit 9B | Q9HBM6 | 0 | 8 | 3 | 0 | 6 | 0 | ||||||||
TAF10 | Transcription initiation factor TFIID subunit 10 | Q12962 | 0 | 2 | 0 | 0 | 2 | 2 | ||||||||
TAF12 | Transcription initiation factor TFIID subunit 12 | Q16514 | 0 | 4 | 0 | 0 | 2 | 3 | ||||||||
TAF15 | TATA-binding protein-associated factor 2N | Q92804 | ||||||||||||||
TBP | TATA-box binding protein | P20226 | 0 | 12 | 17 | |||||||||||
Transcription initiation factor TFIIH | ||||||||||||||||
XPB | TFIIH basal transcription factor complex helicase ERCC3 | P19447 | 0 | 0 | 9 | 0 | 39 | 60 | ||||||||
XPD | TFIIH basal transcription factor complex helicase ERCC2 | P18074 | 0 | 0 | 4 | 0 | 36 | 45 | ||||||||
CDK7 | Cyclin-dependent kinase 7 | P50613 | 0 | 15 | 19 | |||||||||||
MAT1 | CDK-activating kinase assembly factor MAT1 | P51948 | 0 | 8 | 9 | |||||||||||
CCNH | Cyclin-H | P51946 | 0 | 0 | 2 | 0 | 8 | 9 | ||||||||
GTF2H1 | General transcription factor 2H subunit 1 | P32780 | 0 | 6 | 14 | |||||||||||
GTF2H2 | General transcription factor 2H subunit 2 | Q6P1K8 | 0 | 2 | 6 | 0 | 21 | 38 | ||||||||
GTF2H3 | General transcription factor 2H subunit 3 | Q13889 | 0 | 0 | 3 | 0 | 13 | 13 | ||||||||
GTF2H4 | General transcription factor 2H subunit 4 | Q92759 | 0 | 0 | 5 | 0 | 17 | 36 | ||||||||
Viral transcription regulators | ||||||||||||||||
VP16 | Tegument protein VP16 | P06492 | 4 | 11 | 16 | 85 | 21 | 6 | 52 | 108 | 9 | 86 | 81 | 13 | 127 | 158 |
ICP4 | Major viral transcription factor | P08392 | 46 | 300 | 199 | 247 | 31 | 259 | 266 | 366 | 133 | 613 | 585 | 113 | 1146 | 1255 |
ICP22 | Transcriptional regulator ICP22 | P04485 | 8 | 60 | 18 | 46 | 6 | 51 | 69 | 74 | 0 | 26 | 17 | 0 | 29 | 44 |
Other cellular transcription factors | ||||||||||||||||
TRIM28 | Transcription intermediary factor 1-beta | Q13263 | 0 | 130 | 94 | 117 | 3 | 81 | 121 | 162 | 0 | 26 | 19 | 0 | 121 | 181 |
CTCF | Transcriptional repressor CTCF | P49711 | 0 | 2 | 6 | 24 | 0 | 26 | 12 | 0 | 41 | 54 | ||||
TFII-I | General transcription factor II-I | P78347 | 0 | 69 | 61 | 73 | 0 | 35 | 49 | 73 | 0 | 3 | 0 | 0 | 21 | 10 |
SPT5 | Transcription elongation factor SUPT5H (DSIF component) | O00267 | 0 | 25 | 7 | 6 | 0 | 33 | 20 | 27 | 0 | 15 | 2 | 0 | 37 | 21 |
SPT6 | Transcription elongation factor SUPT6H | Q7KZ85 | 0 | 5 | 6 | 0 | 0 | 28 | 10 | 14 | 0 | 17 | 0 | 0 | 38 | 14 |
CSK21 | Casein kinase II subunit alpha | P68400 | 0 | 7 | 3 | 0 | 9 | 12 | ||||||||
CSK2B | Casein kinase II subunit beta | P67870 | 0 | 6 | 2 | 2 | 10 | 7 | ||||||||
FUBP1 | Far upstream element-binding protein 1 | Q96AE4 | 2 | 25 | 32 | 47 | 7 | 32 | 31 | 39 | ||||||
FUBP2 | Far upstream element-binding protein 2 | Q92945 | 9 | 41 | 22 | 46 | 6 | 27 | 32 | 38 | ||||||
MATR3 | Matrin-3 | P43243 | 0 | 52 | 41 | 69 | 0 | 41 | 50 | 105 | 0 | 2 | 0 | 0 | 16 | 5 |
BCLF1 | Bcl-2-associated transcription factor 1 | Q9NYF8 | 0 | 0 | 14 | 15 | 0 | 12 | 13 | 29 | 10 | 23 | 14 | 16 | 54 | 47 |
CDC5L | Cell division cycle 5-like protein | Q99459 | 0 | 0 | 11 | 10 | 0 | 4 | 11 | 17 | 0 | 2 | 0 | 0 | 8 | 5 |
NONO | Non-POU domain-containing octamer-binding protein | Q15233 | 18 | 85 | 90 | 123 | 22 | 85 | 121 | 133 | 31 | 67 | 60 | 8 | 88 | 75 |
CN166 | UPF0568 protein C14orf166 | Q9Y224 | 0 | 9 | 5 | 10 | 0 | 2 | 3 | 14 | 0 | 2 | 6 | 0 | 7 | 16 |
Experiments, conditions, and complexes are indicated in bold. Columns 1, 2, and 3 include protein name, description, and accession number. Values indicate spectral counts determined by mass spectrometry.