Table 1.
Overview of cCREs in the PRDM13 and IRX1 loci
| cCRE | Coordinates (hg38) | cCRE characteristics | In vitro luciferase assay | In vivo enhancer detection assay |
|---|---|---|---|---|
| PRDM13 locus | ||||
| PRDM13_cCRE1 | chr6:99,588,208–99,589,239 | UMI-4C peak, DHS, ChIP-seq (H3K4me2, CRX, NRL, OTX2) | not significant | eye and brain |
| PRDM13_cCRE2 | chr6:99,590,566–99,591,414 | UMI-4C peak, DHS | ND | ND |
| PRDM13_cCRE3 | chr6:99,592,841–99,593,364 | Mutational hotspot-1, DHS, ChIP peak (CRX, OTX2) | positive | no activity |
| PRDM13_cCRE4 | chr6:99,595,852–99,596,746 | UMI-4C peak, DHS | ND | ND |
| PRDM13_cCRE5 | chr6:99,598,651–99,599,224 | Mutational hotspot-2, UMI-4C peak, DHS | not significant | eye and brain |
| PRDM13_cCRE6 | chr6:99,617,828–99,619,867 | UMI-4C peak, DHS, ChIP-seq (H3K27me2) | positive | ND |
| PRDM13_cCRE7 | chr6:99,645,605–99,647,017 | UMI-4C peak, DHS, highly conserved region | ND | ND |
| PRDM13_cCRE8 | chr6:99,749,318–99,752,123 | UMI-4C peak, DHS, ChIP-seq (H3K4me2, H3K27ac), UCNE | not significant | ND |
| IRX1 locus | ||||
| IRX1_cCRE1 | chr5:3,224,667–3,227,420 | UMI-4C peak, DHS, ChIP-seq (H3K4me2, H3K27ac), UCNE | positive | ND |
| IRX1_cCRE2 | chr5:3,426,706–3,428,595 | UMI-4C peak, DHS, UCNE | positive | ND |
| IRX1_cCRE3 | chr5:3,488,008–3,490,747 | UMI-4C peak, DHS, ChIP-seq (H3K27ac), UCNE | positive | ND |
| IRX1_cCRE4 | chr5:3,529,207–3,531,844 | UMI-4C peak, UCNE | negative | ND |
| IRX1_cCRE5 | chr5:3,620,470–3,622,600 | UMI-4C peak, DHS | negative | ND |
| IRX1_cCRE6 | chr5:3,628,385–3,630,819 | UMI-4C peak, DHS, conserved region | not significant | ND |
| IRX1_cCRE7 | chr5:3,649,694–3,651,723 | UMI-4C peak, DHS, conserved region | positive | eye, brain, neural crest |
| IRX1_cCRE8 | chr5:3,729,667–3,732,532 | UMI-4C peak, DHS, conserved region | positive | ND |
| IRX1_cCRE9 | chr5:3,786,388–3,788,778 | UMI-4C peak, DHS, conserved region | ND | ND |
| IRX1_cCRE10 | chr5:4,424,583–4,425,559 | shared duplicated region, DHS, UCNE | not significant | eye and brain |
The cCREs are obtained after integration of the UMI-4C profiles in the retina-specific multi-omics database (Figure S3). For each cCRE, it is indicated which characteristics contributed to their identification. The two right columns indicate whether cCRE activity was assessed using in vitro luciferase assays or in vivo enhancer detection assays, as well as the outcome of these experiments. When the cCRE of interest was not determined using in vitro luciferase assays or in vivo enhancer detection assays, this is indicated by ND. cCRE, candidate CRE; DHS, DNase I hypersensitive site; ChIP-seq, chromatin immunoprecipitation sequencing; ND, not determined; UCNE, ultraconserved non-coding element.