Characterization of the ABCA4cis-regulatory landscape in human retina. aABCA4 promoter interaction frequencies using UMI-4C in human neural retina and RPE/choroid from retinal donors (n = 3, interacting regions (IRs) indicated 1–12). Candidate cis-regulatory elements (cCREs) within IRs were identified using publicly available epigenomic data from human retina: ATAC-seq from bulk retina and scATAC-seq from photoreceptor cells; ChIP-seq for histone marks H3K27ac and H3K4me2, retinal transcription factors (TFs) (CRX, OTX2, and NRL) and the architectural protein CTCF. Epigenomic data for RPE/choroid included bulk ATAC-seq and ChIP-seq targeting H3K27ac and CTCF. All these data were integrated to finely map cCREs. b Close-up of the cCREs including the above-described datasets; retinal TF binding (CRX, OTX2, NRL, RORB, and MEF2D); and sequence motifs (Jaspar Core Pred. TFBS 2022) for TFs expressed in photoreceptors (i.e., MEIS1, NRL, NR2E3, OTX2, CRX, MEIS2, MEF2D, RORB, RXRG, SMAD2 and NEUROD1); and the TFs expressed in RPE (CRX, KLF4, KLF9, LHX2, MEIS1, MEIS2, OTX2, RORB, SMAD2, STAT5B, TEAD1, and TEAD3). c Overview of in vivo enhancer assays using zebrafish stable transgenic lines; dot plot (left) indicating in which tissues GFP + reporter expression was observed (retina, RPE, and lens, white arrows). d Overview of in vivo enhancer assays for the cCRE1–5 synthetic construct through transient transgenesis in zebrafish; bar plots (top) indicating the frequency of GFP + tissues (retina, pineal gland, lens, forebrain, heart, and nosepit) among total GFP + embryos at 1, 2, 3, and 4 days post-fertilization (dpf); example of reporter expression in retina and pineal gland at 3 and 4 dpf
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