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Regulatory and structural variants in the CLCN2 gene are associated with modified skin colour pattern phenotypes in the corn snake

ABSTRACT: Background: Snakes exhibit a broad variety of adaptive colours and colour patterns, generated by the spatial arrangement of chromatophores, but little is known of the mechanisms responsible for these spectacular traits. Here, we investigate a monolocus trait with two recessive alleles that cause pattern aberrations in the corn snake: the motley and striped alleles. Results: We use mapping-by-sequencing to identify the genomic interval where the causal mutations reside. With our differential gene expression analyses, we find that CLCN2 (Chloride Voltage-Gated Channel 2), a gene within the genomic interval, is significantly downregulated in Motley embryonic skin. Furthermore, the insertion of a retrotransposon in CLCN2 results in a disruptive mutation in Stripe. We confirm the involvement of CLCN2 in colour pattern formation by producing knock-out snakes that present a phenotype similar to the Stripe one. In humans and mice, the disruption of CLCN2 results in leukoencephalopathy, as well as retinal and testes degeneration. Our single-cell transcriptomic analyses reveal that CLCN2 is indeed expressed in chromatophores during embryogenesis and in the adult brain. Although, we observe signs of vacuolation in the Stripe adult brain, the retina of Motley and Stripe animals is intact, and no fertility issues are reported for the carriers of both alleles. Conclusions: Our genomic, transcriptomic and functional analyses identify a plasma membrane anion channel to be involved in colour pattern development in Squamate reptiles and show that an active LTR-retrotransposon might be a key driver of trait diversification in corn snakes.

ORGANISM(S): Pantherophis guttatus

PROVIDER: GSE273631 | GEO | 2025/03/03

REPOSITORIES: GEO

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Project description:Background: Heliconius butterflies are an excellent model system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus and several genes in this region show expression pattern differences across races. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. It seems likely that miRNAs could act as downstream regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races. Results: We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs appeared to be differentially expressed between colour pattern races and this was tested further in different developing pupal wing stages using Northern blots. These revealed that differences in expression were due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified miR-193 and miR-2788; located 2380bp apart in an intergenic region. A search for miRNAs in all available H. melpomene BAC sequences (~2.5Mb) did not reveal any other miRNA genes and no novel miRNAs were predicted. There were several regions where other small RNA sequences assembled to the HmYb region and appeared to be differentially expressed.These might represent other regulatory RNAs. Conclusions: Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages. Two miRNAs were located in the HmYb region. Future work will examine the expression of these miRNAs in different colour pattern races and identify miRNA targets among wing patterning genes.

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Regulatory and structural variants in the CLCN2 gene are associated with modified skin colour pattern phenotypes in the corn snake

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