Table I.
Targets with RNAi phenotypes
| Gene name | ESC death | MEF death | Known or predicted function |
| Rnf2a | 3 | 0 | Histone ubiquitylation |
| Mettl5 | 2 | 0 | DNA, RNA, or ribosomal protein methylase |
| Setd8a | 4 | 3 | Histone H4K20 methyltransferase |
| Brca1 | 1 | 0 | E3 ubiquitin ligase |
| Ighmbp2 | 4 | 0 | Transcription regulation |
| Sin3aa | 4 | 0 | Scaffold for HDACs |
| Arid4a | 2 | 0 | Recruitment of HDACs |
| Cbx3a | 3 | 2 | Chromatin binding |
| Brd4 | 3 | 3 | Transcription initiation |
| Chaf1b | 3 | 0 | Chromatin assembly |
| Tpr | 3 | 0 | Nuclear envelope |
| Tcp1 | 4 | 0 | Protein chaperone, chromosome binding |
| Rif1 | 3 | 0 | Telomere length regulation |
| Stat3 | 1 | 0 | Transcription factor |
| Ints4 | 3 | 0 | RNA 3′ end processing |
| Trim28a | 3 | 0 | Transcriptional corepressor |
| Cdc5l | 3 | 0 | Transcription factor |
| Ssrp1b | 4 | 0/2 | Transcriptional elongation |
| Supt16h | 4 | 4 | Transcriptional elongation |
| Ruvbl1a | 3 | 0 | Chromatin remodeling |
| Ruvbl2a | 2 | 0 | Chromatin remodeling |
| Dmap1a | 1 | 0 | Chromatin remodeling |
| Ep400a | 2 | 0 | Chromatin remodeling |
| Htatipa | 1 | 0 | Chromatin remodeling |
| Trrapa | 1 | 0 | Chromatin remodeling |
| Yeats4a | 2 | 0 | Chromatin remodeling |
| H2afz | 1 | 0 | Chromatin structure |
| Smc2 | 4 | 0 | Mitotic chromosome condensation |
| Smc4a | 4 | 0 | Mitotic chromosome condensation |
| Smc1a | 1 | 0 | Chromosome cohesion |
| Gmnn | 4 | 0 | DNA replication |
| Mcm7 | 3 | 0 | DNA replication |
| Mcm2a | 3 | 0 | DNA replication |
| Mcm6 | 3 | 0 | DNA replication |
| Mcm4 | 3 | 0 | DNA replication |
| Eif4a3a | 4 | 4 | NMD, ribosome biogenesis |
| Ddx54 | 4 | 3 | Ribosome biogenesis |
| Ddx56 | 2 | 0 | Ribosome biogenesis |
| Ddx18a | 4 | 0 | Ribosome biogenesis |
| Ddx47a | 3 | 0 | Ribosome biogenesis |
| Utp3 | 2 | 0 | Processome, ribosome biogenesis |
| Snrpd1 | 4 | 0 | RNA splicing |
| Snrpd2 | 4 | 3 | RNA splicing |
| Snrpd3 | 4 | 0 | RNA splicing |
| Snrpe | 4 | 2 | RNA splicing |
| Snrpfa | 4 | 0 | RNA splicing |
| Snrpg | 4 | 0 | RNA splicing |
| Snrpn | 4 | 0 | RNA splicing |
| Lsm2a | 3 | 0 | RNA splicing |
| Lsm6a | 4 | 0 | RNA splicing |
| Lsm7 | 3 | 0 | RNA splicing |
| Dhx15 | 3 | 0 | RNA splicing |
| Ascc3l1 | 4 | 0 | RNA splicing |
| Skiv2l2 | 3 | 0 | RNA splicing |
| Ddx41 | 3 | 0 | RNA splicing |
| Dhx37 | 3 | 0 | RNA splicing |
| Dhx8 | 4 | 3 | RNA splicing |
| Ddx39 | 4 | 4 | RNA splicing |
| Aqr | 4 | 3 | RNA splicing |
| Sf3b1 | 4 | 3 | RNA splicing |
| Phf5a | 4 | 0 | RNA splicing |
| Ddx19a | 4 | 0 | mRNA export |
ESC, ES cell; HDAC, histone deacetylase complex; NMD, nonsense-mediated mRNA decay. For ES cell and MEF death, the numerical scale of cell division/viability defects is as follows: 0, no effect; 1, minor; 2, moderate; 3, moderate to severe; and 4, severe. Genes indicated in bold exhibit viability defects upon KD in both ES cells and iMEFs.
a
Tested with second esiRNA.
b
Initial esiRNA did not produce a phenotype in iMEFs, whereas a second esiRNA produced moderate cell death.