Table 2.
Comparative analysis of Chromatin Immune Precipitation followed by whole genome sequencing (ChIP-seq) binding sites of RYBP, RNF2/RING1B, PCGF6, and RAR on meiotic genes upregulated in the Rybp-/- ES cells.
| Gene Name | Transcriptome (Rybp+/+/Rybp-/-) Raw Counts |
Fold Change | RYBP ChIP-seq (GSM1041375) | RING1B ChIP-seq (GSM1041372) | PCGF6 ChIP-seq (GSE84905) | RAR ChIP-seq (GSM482749) |
|---|---|---|---|---|---|---|
| Xlr4a | 0/42.42 | Inf | - | - | - | - |
| Xlr4b | 0/42.43 | Inf | - | - | - | - |
| Tex11 | 5.65/223.44 | 39.50 | + | + | + | - |
| Dazl | 31.11/437.69 | 14.068 | + | + | + | - |
| Tex15 | 31.11/280.01 | 9.00 | + | + | - | + |
| Xlr3a | 7.07/63.63 | 9.00 | - | - | - | - |
| Piwil2 | 22.62/201.52 | 8.90 | + | + | + | + |
| Xlr3c | 1.41/12.02 | 8.50 | - | - | - | - |
| Tdrkh | 29.69/250.31 | 8.42 | + | + | + | - |
| Hormad2 | 16.97/110.30 | 6.50 | + | - | - | + |
| Sycp2 | 21.21/137.17 | 6.46 | + | + | + | + |
| Mov10l1 | 55.15/335.87 | 6.090 | + | + | + | + |
| Piwil4 | 5.65/33.94 | 6.00 | - | - | - | + |
| Mael | 87.68/415.77 | 4.74 | + | + | + | + |
| Ddx4 | 151.32/623.66 | 4.120 | + | + | + | + |
| Tdrd1 | 18.38/65.76 | 3.57 | + | + | + | + |
| Smc1b | 100.40/337.28 | 3.35 | + | + | + | + |
| Xlr3b | 9.89/32.52 | 3.285 | - | - | - | - |
| Cpeb1 | 11.31/36.06 | 3.187 | + | + | + | + |
| Stra8 | 48.08/152.73 | 3.176 | - | - | - | + |
| Boll | 7.07/20.5 | 2.90 | + | + | + | + |
| Meioc | 49.49/142.12 | 2.87 | + | + | + | + |
| Asz1 | 2.82/7.77 | 2.75 | + | + | - | + |
| Sycp1 | 251.73/412.95 | 1.640 | + | + | + | - |
| Prdm14 | 52.34/84.14 | 1.60 | - | + | - | + |
| Sycp3 | 322.44/381.83 | 1.184 | + | + | - | + |
Raw reads from genome-wide transcriptomics from wild type (Rybp+/+) and Rybp-/- ES cells reported by Ujhelly et al., 2015 [126] and ChIP-seq data for the binding targets of RYBP, RNF2/RING1B, PCGF6 and RAR (see Methods) were analyzed for upregulated meiotic targets in the Rybp-/- ES cells. Targets. which were identified in more than one independent experiment are included in the table. ‘+’ represents identified ChIP binding targets and ‘–‘ represents no binding.