The landscape of submicroscopic structural variants at the OPN1LW/OPN1MW gene cluster on Xq28 underlying blue cone monochromacy

Abstract

Blue cone monochromacy (BCM) is an X-linked retinal disorder characterized by low vision, photoaversion, and poor color discrimination. BCM is due to the lack of long-wavelength-sensitive and middle-wavelength-sensitive cone photoreceptor function and caused by mutations in the OPN1LW/OPN1MW gene cluster on Xq28. Here, we investigated the prevalence and the landscape of submicroscopic structural variants (SVs) at single-base resolution in BCM patients. We found that about one-third (n = 73) of the 213 molecularly confirmed BCM families carry an SV, most commonly deletions restricted to the OPN1LW/OPN1MW gene cluster. The structure and precise breakpoints of the SVs were resolved in all but one of the 73 families. Twenty-two families-all from the United States-showed the same SV, and we confirmed a common ancestry of this mutation. In total, 42 distinct SVs were identified, including 40 previously unreported SVs, thereby quadrupling the number of precisely mapped SVs underlying BCM. Notably, there was no "region of overlap" among these SVs. However, 90% of SVs encompass the upstream locus control region, an essential enhancer element. Its minimal functional extent based on deletion mapping in patients was refined to 358 bp. Breakpoint analyses suggest diverse mechanisms underlying SV formation as well as in one case the gene conversion-based exchange of a 142-bp deletion between opsin genes. Using parsimonious assumptions, we reconstructed the composition and copy number of the OPN1LW/OPN1MW gene cluster prior to the mutation event and found evidence that large gene arrays may be predisposed to the occurrence of SVs at this locus.

Keywords: BCM; gene conversion; human visual pigment genes; locus control region; opsin gene deletion.

Fig. 1.

SVs in BCM families: Study overview. Root diagram of the study population and the subcategorization of SVs. Numbers on the right indicate numbers of BCM families in the respective subcategory.

Fig. 2.

Structure, extent, and composition of BCM-linked SVs observed in this study. (A) Map of the OPN1LW/OPN1MW gene array with a single OPN1LW and three downstream OPN1MW gene copies (according to the GRCh38/hg38 genome assembly). The OPN1LW and OPN1MW gene(s) are depicted by red and green arrows, respectively. The LCR is shown as a rectangle upstream of the OPN1LW gene. Flanking genes (MECP2, TEX28, and TKTL1) are shown by gray arrows. (B–F) Categories of BCM-linked SVs including deletions restricted to the LCR (B), SVs covering the LCR and parts of the OPN1LW/OPN1MW gene cluster (C), SVs covering OPN1LW/OPN1MW gene cluster but intact LCR (D), deletions of the OPN1LW/OPN1MW gene cluster (including the LCR) and extending into the downstream TEX28 and TEKTL1 genes (E), and complex structural rearrangements (F). The SV breakpoints are marked by brackets and deleted parts are indicated by lighter gray color. The presence of OPN1MW•OPN1LW hybrid genes is indicated by arrows half-colored in green and red. The blue box in SVar40 represents an interstitial insertion of chromosome 20 sequences. Additional copies of OPN1MW or OPN1MW•OPN1LW hybrid genes are indicated by the number in parentheses below the arrows. Note that the structure of SVar1, SVar2, and SVar42, which cannot be properly displayed at this scale, is displayed in SI Appendix, Figs. S5, S8, and S2, respectively.

Fig. 3.

Identical centromeric breakpoints and sequence-conserved telomeric breakpoints in SVar20 and SVar38 support a single lineage intrachromosomal NAHR event. (A) SVar20 and SVar38 share identical centromeric breakpoints while telomeric breakpoints share the same breakpoint sequence but differ by the presence/absence of a single OPN1MW gene copy. (B) Patient #11819/BCM 109 carrying SVar20 and patient #18281/BCM 89 carrying SVar38 share the same marker haplotype at Xq28. Markers including nine microsatellites and two SNPs are ordered according to their physical position (top to bottom). The localization of the OPN1LW/OPN1MW gene cluster is indicated by the arrow on the right. Shared alleles (microsatellite alleles coded in numbers) are depicted as gray squares. (C) Proposed sequence of events linking SVar20 and SVar38. Deletion of the LCR and parts of the OPN1LW/OPN1MW gene cluster results in SVar20, which retains a single OPN1MW gene copy. Subsequently, SVar20 undergoes intrachromosomal NAHR through homologous sequences downstream of the OPN1MW gene copies (relevant area of sequence homology indicated by the yellow patch; note that the intergenic sequence between OPN1MW gene copies is homologous to large parts of the TEX28 gene) which results in the loss of the terminal OPN1MW gene copy as seen in SVar38. In comparison with the structure of the normal gene cluster (Top), the SV breakpoints are marked by brackets and deleted parts are indicated by lighter gray color.