Genome-Wide Identification, Evolution, and miRNA-22 Regulation of Kruppel-Like Factor (KLF) Gene Family in Chicken (Gallus gallus)

Kruppel-like factors (KLFs) are essential transcription factors found in many eukaryotes. In this study, the focus is on identifying and analyzing the KLF gene family members in chickens using bioinformatic tools, and comparing them with representative classes such as fish, amphibians, birds, and mammals. The analysis includes the structural characterization, evolutionary relationship assessment, and functional predictions. Additionally, in this study, the impact of miRNA-22 is explored, associated with lipid metabolism, on the expression of KLF genes in the liver, heart, and muscle tissues of Qingyuan partridge chickens. The results indicate that the avian KLF gene family is evolutionarily closer to that of mammals, and all chicken KLFs are non-transmembrane proteins. Moreover, the effect of miRNA-22 on KLF expression varies across different tissues. These findings provide a scientific basis for further research into the functions of KLFs in chickens. Kruppel-like factors (KLFs) are a class of fundamental transcription factors that are widely present in various eukaryotes from nematodes to humans, named after their DNA binding domain which is highly homologous to the Kruppel factor in fruit flies. To investigate the composition, organization, and evolutionary trajectory of KLF gene family members in chickens, in our study, we leveraged conserved sequences of KLF genes from representative classes across fish, amphibians, birds, and mammals as foundational sequences. Bioinformatic tools were employed to perform homology alignment on the chicken genome database, ultimately identifying the KLF family members present in chickens. The gene structure, phylogenetic analysis, conserved base sequences, physicochemical properties, collinearity analysis, and protein structure were then analyzed using bioinformatic tools. Additionally, the impact of miRNA-22, related to poultry lipid metabolism, on the expression of the KLF gene family in the liver, heart, and muscle of Qingyuan partridge chickens was explored. The results showed that: (1) compared to fish, the KLF family in birds is more closely related to mammals and amphibians; (2) KLFs within the same subgroups are likely to be derived from a common ancestral gene duplication; (3) KLF3/8/12 in the same subgroup may have some similar or overlapping functions; (4) the motif 4 of KLF5 was most likely lost during evolution; (5) KLF9 may perform a similar function in chickens and pigs; (6) there are collinear relationships between certain KLF genes, indicating that there are related biomolecular functions between these KLF genes; (7) all members of the KLF family in chickens are non-transmembrane proteins; and (8) interference and overexpression of miRNA-22 in Qingyuan partridge chickens can affect the expression levels of KLF genes in liver, heart, and muscle.