Fig. 5: Identification of a retina-specific Crb1 isoform in mouse and human retina. | Nature Communications

Fig. 5: Identification of a retina-specific Crb1 isoform in mouse and human retina.

From: Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease

Fig. 5: Identification of a retina-specific Crb1 isoform in mouse and human retina.The alternative text for this image may have been generated using AI.

Transcript maps of most abundant Crb1 isoforms from mouse retina (a) and cortex (b). Map depicts reverse strand of mouse chromosome 1 at indicated location (Mb, megabase). 5′ and 3′ ends of Crb1 transcripts are indicated. A is the canonical isoform; A2 is a minor splice variant of A. These isoforms are shared between retina and cortex, whereas Cortex 1, Cortex 2, and Crb1-B are tissue-specific. Corresponding exon coverage (dark blue) and sashimi plots (red lines) were generated from lrCaptureSeq dataset. Note prevalence of reads associated with Crb1-B isoform (a). c Assay for chromatin accessibility (ATAC-seq; GSE102092, GSE83312) identifies likely promoters of Crb1-A and -B isoforms. Colored bars indicate location of putative A (green) and B (blue) promoters. Maps in a–c are aligned with each other. Crb1-A promoter is more open during development, but stays accessible in mature retina. Crb1-B promoter is open and presumed active in mature rods and both types of cones. Dnase I hypersensitivity data from ENCODE project reveals distinct chromatin environment in frontal cortex, consistent with expression of A isoform, as well as shorter cortex isoforms (cortex 1 and 2; gray bar at top). d Transcript maps of most abundant human retinal CRB1 isoforms, identified by lrCaptureSeq. Map depicts forward strand of human chromosome 1 at indicated location. A and B isoforms are highly homologous to mouse (a). CRB1-C encodes a putative secreted form of the protein; it was also identified in the mouse dataset but its relative abundance in mouse was much lower than A and B. Note that Crb1-A2 was not detected in the human dataset. Exon coverage (dark blue) and sashimi plots (red lines) were generated from lrCaptureSeq data. e ATAC-seq (GSE99287) of human peripheral (per.) and macular (mac.) retina show open regulatory sites corresponding to putative promoters for CRB1-A (green bar) and CRB1-B (blue bar). Two biological replicates are shown. Maps in d, e are aligned with each other.

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