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

PROVIDER: PRJNA1142529 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30059350_1.fastq.gz	Fastqsanger.gz
	SRR30059350_2.fastq.gz	Fastqsanger.gz
	SRR30059351_1.fastq.gz	Fastqsanger.gz
	SRR30059351_2.fastq.gz	Fastqsanger.gz

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

Project description: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.

2025-03-03 | GSE273807 | GEO

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

2025-03-03 | GSE273631 | GEO

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

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

| PRJNA1143394 | ENA

PMEL is involved in snake color pattern transition from blotches to stripes [scRNA-seq]

Project description:Our genomic, bulk and single-cell transcriptomic, functional, and developmental characterization of the Terrazzo corn snake color morph and the extensive comparison with wild-type snakes puts forward the dual role of PMEL in snake skin coloration, both in the differentiation of chromatophores during embryogenesis and the melanogenesis in melanophores.

2024-07-26 | GSE262160 | GEO

PMEL is involved in snake color pattern transition from blotches to stripes [bulk RNA-seq]

2024-07-26 | GSE262159 | GEO

Reorganization of HoxD regulatory landscapes during the evolution of a snake-like body plan (ChIP-seq)

Project description:While the vertebrate body plan is highly conserved amongst all species of this taxon, extreme variations thereof can be documented in snakes, which display both an absence of limbs and an unusually elongated trunk. As Hox genes are strong candidates both for the making and the evolution of this body plan, their comparative study in such a morphologically diverged group is informative regarding their potential causative importance in these processes. In this work we use an interspecies comparative approach where different aspects of regulation at the HoxD locus are investigated. We find that although spatial collinearity and associated epigenetic mark dynamics are conserved in the corn snake, other regulatory modalities have been largely restructured. A BAC transgenic approach indeed revealed that, while the majority of mesodermal enhancers in vertebrates appear to be mostly located outside of the cluster, the corn snake contains most mesodermal trunk enhancers within the HoxD cluster. We also find that, despite the absence of limbs and an altered Hoxd gene regulation in external genitalia, the bimodal chromatin structure at the corn snake HoxD locus is maintained. The analysis of particular enhancer sequences initially defined in the mouse and further isolated at the snake orthologous locus showed differences in their specificities for the limb and genital bud expression. Of particular interest, a snake counterpart of a mouse limb-only enhancer sequence evolved into a genital-only enhancer. Such a regulatory exaptation suggests that enhancer versatility may have been an important factor to accompany the transition towards the snake body plan. These results show that vertebrate morphological evolution is likely to have been associated with extensive reorganization at the HoxD regulatory landscapes while respecting a very conserved general regulatory framework.

2016-11-05 | GSE79047 | GEO