Table 3. Ribosomal and nuclear genes required for the down regulation of the Ribi gene NSR1 in stress.
| Name | Description | Loc | [NSR1] | Down TOR | Phys Net |
|---|---|---|---|---|---|
| ELP3 | Subunit of Elongator complex | N | 2.8 | Yes | Yes |
| ELP6 | Subunit of Elongator complex | 1.8 | Yes | Yes | |
| IKI3 | Subunit of Elongator complex | N | 1.8 | Yes | Yes |
| VHS1 | Cytoplasmic serine/threonine protein kinase | 2.5 | No | Yes | |
| RPD3 | Histone deacetylase, component of Rpd3S and Rpd3L | N | 2.1 | No | Yes |
| SIN3 | Component of Rpd3S and Rpd3L | N | 2.6 | Yes | Yes |
| PHO23 | Component of Rpd3L | N | 2.4 | Yes | Yes |
| SAP30 | Component of Rpd3L | N | 2.2 | Yes | Yes |
| DEP1 | Component of the Rpd3L | N | 2.6 | Yes | Yes |
| RXT2 | Component of Rpd3L | N | 2.4 | Yes | Yes |
| HOS1 | Class I histone deacetylase | N | 1.9 | No | Yes |
| STB4 | Putative transcription factor | N | 2.4 | No | Yes |
| RPS6A | Protein component of the small (40S) ribosomal subunit | R | 2.4 | Yes | Yes |
| RPS7B | Protein component of the small (40S) ribosomal subunit | R | 1.4 | Yes | Yes |
| RPS9A | Protein component of the small (40S) ribosomal subunit | R | 1.9 | No | Yes |
| RPS22A | Protein component of the small (40S) ribosomal subunit | R | 1.4 | No | Yes |
| RPS17A | Protein component of the small (40S) ribosomal subunit | R | 2.4 | Yes | Yes |
| RPL2B | Ribosomal 60S subunit protein L2B | R | 1.3 | No | Yes |
| RPL6A | Ribosomal 60S subunit protein L6A | R | 2.1 | No | Yes |
| RPL6B | Ribosomal 60S subunit protein L6B | R | 2.6 | Yes | Yes |
| RPL7A | Ribosomal 60S subunit protein L7A | R | 2.1 | No | Yes |
| RPL13A | Ribosomal 60S subunit protein L13A | R | 1.8 | No | Yes |
| RPL16B | Ribosomal 60S subunit protein L16B | R | 1.8 | No | Yes |
| RPL22A | Ribosomal 60S subunit protein L22A | R | 1.9 | No | Yes |
| RPL24A | Ribosomal 60S subunit protein L24A | R | 2.0 | Yes | Yes |
| SSZ1 | Hsp70 protein that interacts with Zuo1p (a DnaJ homolog) | 2.0 | Yes | Yes | |
| ZUO1 | Ribosome-associated chaperone | R/N | 1.9 | Yes | Yes |
| NOP12 | Nucleolar protein involved in pre25S rRNA processing | N | 2.1 | No | Yes |
| RQC1 | Component of the ribosome quality control complex (RQC) | R | 2.0 | No | Yes |
| RPL38 | Ribosomal 60S subunit protein L38 | R | 2.0 | Yes | No |
| RPL43B | Ribosomal 60S subunit protein L43B | R | 1.6 | No | No |
| RPS27A | Protein component of the small (40S) ribosomal subunit | R | 2.1 | No | No |
| CLU1 | Subunit of the eukaryotic translation initiation factor 3 (eIF3) | 2.3 | Yes | Yes | |
| EFT1 | Elongation factor 2 (EF-2), also encoded by EFT2 | R | 1.6 | No | Yes |
| TIF1 | Translation initiation factor eIF4A | R | 1.6 | No | Yes |
| YGR054W | Eukaryotic initiation factor (eIF) 2A | R | 2.2 | No | Yes |
| CAF20 | Phosphoprotein of the mRNA cap-binding complex | 2.0 | No | Yes | |
| ASK10 | Component of RNA polymerase II holoenzyme | N | 2.4 | No | Yes |
| CAF130 | Subunit of the CCR4-NOT transcriptional regulatory complex | 1.6 | No | Yes | |
| ELA1 | Elongin A; Required for Pol II degradation | N | 2.6 | No | Yes |
| ELC1 | Elongin C; Required for Pol II degradation | N | 1.5 | No | Yes |
| PGD1 | Subunit of the RNA polymerase II mediator complex | N | 2.0 | No | Yes |
| NUT1 | Component of the RNA polymerase II mediator complex | N | 1.7 | No | Yes |
| GIS1 | Histone demethylase and transcription factor | N | 1.7 | No | Yes |
| HIR2 | Subunit of HIR nucleosome assembly complex | N | 2.0 | No | Yes |
| HIR3 | Subunit of the HIR complex | N | 2.5 | No | Yes |
| HPA2 | Tetrameric histone acetyltransferase | 1.9 | No | Yes | |
| HTA1 | Histone H2A | N | 2.4 | Yes | Yes |
| IES4 | Component of the INO80 chromatin remodeling complex | N | 1.8 | Yes | Yes |
| ITC1 | Subunit of Isw2p-Itc1p chromatin remodeling complex | N | 1.6 | No | Yes |
| DPB4 | Subunit of ISW2 chromatin accessibility complex | N | 2.0 | No | Yes |
| JHD2 | JmjC domain family histone demethylase | N | 2.2 | Yes | Yes |
| RLF2 | Largest subunit (p90) of the Chromatin Assembly Complex (CAF-1) | N | 2.5 | Yes | Yes |
| SAS5 | Subunit of the SAS complex (Sas2p, Sas4p, Sas5p) | N | 2.2 | No | Yes |
| SWI3 | Subunit of the SWI/SNF chromatin remodeling complex | N | 2.5 | Yes | Yes |
The top three groups of genes encode proteins highlighted in the bottom portion of the physical interaction network shown in Figure 6; Elongator, Rpd3L, and Ribosome, respectively. Note that three ribosomal proteins not connected to the others by physical interactions were included in the list. The fourth group lists other genes found in our screen involved in transcription and chromatin remodeling, all of which are part of the lower half of the physical interaction network in Figure 6. The third column lists the localization (Loc) of each protein: The fourth column [NSR1] lists the log2 NSR1/PEX6 expression ratio from the screen. The fifth column notes if the gene acts downstream of TORC1 (has log2 > 1 normalized NSR1/PEX6 ratio in rapamycin). The sixth column states whether the genes is part of the physical interaction network (Phys Net) shown in Figure 6. N, nuclear; R, ribosome.