Table 1.
Comparative analysis of Chromatin Immune Precipitation followed by whole genome sequencing (ChIP-seq) binding sites of Ring1 and YY1 binding RYBP, RNF2/RING1B, PCGF6, and RAR on retinoic acid (RA) pathway members, 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) |
|---|---|---|---|---|---|---|
| Adh1 | 0/0.7 | Inf | - | - | - | - |
| Adh4 | 0/5.65 | Inf | - | - | - | + |
| Rarb | 0/2.12 | Inf | - | + | - | + |
| Rxrg | 0/1.41 | Inf | - | + | + | + |
| Crabp1 | 36.8/218.5 | 5.94 | + | + | - | - |
| Rdh14 | 4.2/13.4 | 3.166 | - | - | - | - |
| Rxra | 29.7/38.2 | 1.285 | - | + | - | + |
Raw reads from genome-wide transcriptomics from wild type (Rybp+/+) and Rybp-/- embryonic stem (ES) cells reported by Ujhelly et al., 2015 [126]. ChIP-seq data for the binding targets of RYBP, RNF2/RING1B, PCGF6, and RAR (see Methods) were analyzed for upregulated RA pathway members in the Rybp-/- ES cells. ‘+’ represents identified ChIP binding targets and ‘–‘ represents no binding. RYBP, RING1 and YY1 binding protein. ES, embryonic stem. PCGF6, Polycomb group ring finger 6.