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>
Project description:This study aims to investigate the DNA methylation patterns at transcription factor binding regions and their evolutionary conservation with respect to binding activity divergence. We combined newly generated bisulfite-sequencing experiments in livers of five mammals (human, macaque, mouse, rat and dog) and matched publicly available ChIP-sequencing data for five transcription factors (CEBPA, HNF4a, CTCF, ONECUT1 and FOXA1). To study the chromatin contexts of TF binding subjected to distinct evolutionary pressures, we integrated publicly available active promoter, active enhancer and primed enhancer calls determined by profiling genome wide patterns of H3K27ac, H3K4me3 and H3K4me1.