Research note: Comparative identification of higher-order quadruplex structures in the LEP locus of galliformes

Four-stranded nucleic acid secondary structures known as quadruplexes, specifically G-quadruplexes (G4s) and i-motifs (iMs), form in G-rich and C-rich sequences, respectively. Although these quadruplex structures have been identified within regulatory regions and are involved in gene regulation, their distribution within the GC-rich avian LEP locus remains to be elucidated. Leptin (LEP) influences growth and nutrient utilization in vertebrates by regulating appetite; however, the regulatory mechanisms governing LEP expression in chickens are still poorly understood despite the importance of production efficiency in poultry systems. The objectives of this study were to characterize the GC-rich chicken LEP locus and perform comparative analyses of the avian LEP genomic landscape. Following the identification of LEP-containing chicken genomic sequences via the Basic Local Alignment Search Tool (BLAST), we employed approaches to identify G4- and iM-based potential higher-order quadruplex sequences (PHOQSs). Consequently, 23 G4-based PHOQSs and nine iM-based PHOQSs were identified in the Silkie chicken LEP locus. Moreover, G4 and iM configurations within these PHOQS structures were predicted, indicating distinct spatial arrangements between the two structural elements (G4s and iMs). Our comparative analyses revealed that these higher-order quadruplexes are conserved across chicken breeds and appear to be conserved in the quail LEP locus, whereas such conservation was absent in the mallard duck. These findings suggest a unique gene regulatory mechanism in the chicken and quail LEP loci, which appears distinct from that of the mallard duck and may contribute to the leptin biology within Galliformes.