Table 1. Mass-spectrometric analysis of NRPD1 affinity purifications.
| Pol IV subunits | |||||||
| Protein | Re-designation | AGI code | Spectra | Unique Peptides | % Coverage | NSAF | % NRPD1 |
| NRPD1 | At1g63020 | 363 | 72 | 38 | 1178.1 | 100 | |
| NRPD2/E2 | At3g23780 | 274 | 51 | 24.5 | 1130.6 | 96 | |
| NRPB3/D3/E3A | At2g15430 | 125 | 23 | 44.2 | 1847.8 | 157 | |
| NRPE3B | NRPD3B/E3B | At2g15400 | 46 | 13 | 24.8 | 680.0 | 58 |
| NRPD4/E4 | At4g15950 | 23 | 3 | 12.7 | 677.9 | 58 | |
| NRPB5/D5 | At3g22320 | 60 | 14 | 44.9 | 1380.2 | 117 | |
| NRPE5B | NRPD5B/E5B | At2g41340 | 17 | 8 | 35.8 | 367.7 | 31 |
| NRPB6A/D6A/E6A | At5g51940 | 4 | 2 | 17.4 | 131.0 | 11 | |
| NRPD7 | NRPD7A | At3g22900 | 10 | 3 | 19.5 | 271.0 | 23 |
| NRPE7 | NRPD7B/E7B | At4g14660 | 2 | 2 | 14.6 | 53.0 | 4 |
| NRPB8B/D8B/E8B | At3g59600 | 0 | 0 | 0 | 0.0 | 0 | |
| NRPB9A/E9A | NRPB9A/D9A/E9A | At3g16980 | 28 | 8 | 43.9 | 1158.2 | 98 |
| NRPB9B/D9B/E9B | At4g16265 | 37 | 7 | 46.5 | 1530.5 | 130 | |
| NRPB10/D10/E10 | At1g11475 | 29 | 2 | 12.7 | 1926.1 | 163 | |
| NRPB11/D11/E11 | At3g52090 | 21 | 6 | 26 | 853.7 | 72 | |
| NRPB12/D12/E12 | At5g41010 | 10 | 7 | 74.5 | 924.6 | 78 | |
| Other RdDM components | |||||||
| RDR2 | At4g11130 | 195 | 38 | 29.7 | 811.6 | 69 | |
| DMS4/RDM4 | At2g30280 | 20 | 7 | 11.6 | 272.6 | 23 | |
| CLSY1 | At3g42670 | 27 | 14 | 8 | 101.4 | 9 | |
| CLSY2 | At5g20420 | 28 | 14 | 11.8 | 104.7 | 9 | |
| CHR31 | CLSY3 | At1g05490 | 40 | 20 | 16.9 | 133.8 | 11 |
| CHR40 | CLSY4 | At3g24340 | 25 | 15 | 13.8 | 104.1 | 9 |
| SHH1 | At1g15215 | 13 | 6 | 25.2 | 237.6 | 20 | |
Table summarizing the polymerase subunits (upper) and other known or putative RNA directed DNA methylation (RdDM) components (lower) found to co-purify with NRPD1. Based on these MS analyses, several proteins have been given the additional designation of NRP “D#”, to indicate they are also present in the Pol-IV polymerase. The percent coverage (% coverage) column takes into account peptides that map only to the AGI code indicated in the third column (see also Figure S1). The percentage of NRPD1 (% NRPD1) column indicates the approximate stoichiometry of each co-purifying protein as a function of the Normalized Spectral Abundance Factor (NSAF)×10e5 [43].