PMEL is involved in snake color pattern transition from blotches to stripes [scRNA-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1090495 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28412033.fastq.gz | Fastqsanger.gz | |||
| SRR28412034.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
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
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 | GSE262159 | GEO
Project description:PMEL is involved in snake color pattern transition from blotches to stripes [bulk RNA-seq]
| PRJNA1090493 | ENA
Project description:Corn snakes are emerging models for animal colouration studies. Here, we focus on the Terrazzo morph, whose skin pattern is characterized by stripes rather than blotches. Using genome mapping, we discover a disruptive mutation in the coding region of the Premelanosome protein (PMEL) gene. Our transcriptomic analyses reveal that PMEL expression is significantly downregulated in Terrazzo embryonic tissues. We produce corn snake PMEL knockouts, which present a comparable colouration phenotype to Terrazzo and the subcellular structure of their melanosomes and xanthosomes is also similarly impacted. Our single-cell expression analyses of wild-type embryonic dorsal skin demonstrate that all chromatophore progenitors express PMEL at varying levels. Finally, we show that in wild-type embryos PMEL-expressing cells are initially uniformly spread before forming aggregates and eventually blotches, as seen in the adults. In Terrazzo embryos, the aggregates fail to form. Our results provide insights into the mechanisms governing colouration patterning in reptiles.
| S-EPMC11371805 | biostudies-literature
Project description:Phenotypic and genomic dissection of color pattern variation in a reef fish radiation
| PRJEB61240 | ENA
Project description:We apply developmental and single cell gene expression analysis to fetal skin of domestic cats, together with genetic characterization of Mendelian color variation, to identify when, where, and how, during fetal development, felid color patterns are established. Prior to the appearance of hair follicle placodes, we identify changes in epidermal thickness that represent a signature of color pattern establishment, and that are preceded by a pre-pattern of gene expression in which the secreted Wnt inhibitor encoded by Dickkopf 4 (Dkk4) plays a central role. We also demonstrate that mutations in Dkk4 underlie the Ticked pattern mutation in cats. Our results bring molecular understanding to how the leopard got its spots, suggest that similar mechanisms underlie periodic color pattern and periodic hair follicle spacing, and provide a genomic framework to explore natural selection for diverse pattern types in wild felids.
2021-02-25 | GSE152946 | GEO
Project description:Many animals exhibit typical color patterns that have been linked to key adaptive functions, yet the developmental mechanisms establishing these crucial designs remain unclear. Here, we surveyed color distribution in the plumage across a large number of passerine finches. Despite extreme apparent pattern diversity, we identified a small set of conserved color regions whose combinatory association can explain all observed patterns. We found these domains are instructed by signals from embryonic somites and lateral plate mesoderm, and through profiling and comparative analyses, produced a molecular map marking putative color domains in the developing skin. This revealed cryptic pre-patterning common to differently colored species, uncovering a simple molecular landscape underlying extensive color pattern variation.
2024-01-18 | GSE165119 | GEO
Project description:<p><strong>BACKGROUND:</strong> Reptiles exhibit a wide variety of skin colors, which serve essential roles in survival and reproduction. However, the molecular basis of these conspicuous colors remains unresolved.</p><p><strong>RESULTS:</strong> We investigate color morph-enriched Asian vine snakes (<em>Ahaetulla prasina</em>), to explore the mechanism underpinning color variations. Transmission electron microscopy imaging and metabolomics analysis indicates that chromatophore morphology (mainly iridophores) is the main basis for differences in skin color. Additionally, we assemble a 1.77 Gb high-quality chromosome-anchored genome of the snake. Genome-wide association study and RNA sequencing reveal a conservative amino acid substitution (p.P20S) in <em>SMARCE1</em>, which may be involved in the regulation of chromatophore development initiated from neural crest cells. <em>SMARCE1</em> knockdown in zebrafish and immunofluorescence verify the interactions among <em>SMARCE1</em>, iridophores, and <em>tfec</em>, which may determine color variations in the Asian vine snake.</p><p><strong>CONCLUSIONS:</strong> This study reveals the genetic associations of color variation in Asian vine snakes, providing insights and important resources for a deeper understanding of the molecular and genetic mechanisms related to reptilian coloration.</p>
2023-02-23 | MTBLS6927 | MetaboLights
Project description:Developmental Genetics of Color Pattern Establishment in Cats
| PRJNA641030 | ENA
Project description:We used gene expression accompanied by physical characteristics and gill Na+/K+-ATPase activity to analyze physiological differences associated with two life history variations of juvenile fall Chinook Salmon in the Snake River basin. Subyearlings originating in the Snake River typically migrate seaward as subyearlings, whereas many subyearlings from the Clearwater River delay seaward migration during summer and complete seaward migration the following spring as yearlings. We examined gill Na+/K+-ATPase activity and gene expression of subyearlings at different times during rearing and seaward emigration. Natural-origin Snake River subyearlings rearing under an increasing photoperiod and seasonally increasing temperatures showed a typical increasing pattern of parr to smolt gill Na+/K+-ATPase activity development, which then declined into autumn. In contrast, Clearwater River subyearlings that had experienced cooler temperatures showed no pattern of increasing gill Na+/K+-ATPase activities and were not different from parr. Liver transcription of genes involved in DNA repair and binding, the cell cycle, metabolism (steroid, fatty acid and other metabolic pathways) iron homeostasis, heme and oxygen binding, the immune response, and male sexual development were enriched amongst genes differentially expressed between Snake River parr versus smolts. Gene expression results confirmed that Clearwater River subyearlings were parr-like in their physiological status. By autumn, subyearlings had low gill Na+/K+-ATPase activities despite their large size and external smolt characteristics. We suggest that environmental factors like temperature and photoperiod influence subyearling physiological status in each river that ultimately dictates juvenile life history pathways. Non-migrating and migrating natural subyearling fall Chinook salmon were collected from the Snake River. Non-migrating natural subyearling fall Chinook salmon were collected from the Clearwater River. Twelve fish were collected at each of four different time points for a total of 48 fish. Total RNA was extracted from the liver of each fish. Equal amounts of RNA from three fish were pooled to create four pools of RNA per time point. Each RNA pool was hybridized to an array for a total of 16 arrays with four arrays per time point.
2014-06-20 | E-GEOD-58670 | biostudies-arrayexpress