Genome-Wide Analysis of the KLF Gene Family in Chicken: Characterization and Expression Profile

SIMPLE SUMMARY: Broilers provide nutrition for people all around the world, and their muscle and fat contribute major roles. However, little is known about the relationships between the kruppel-like factor (KLF) and the development of muscle and fat. In recent years, studies have shown that KLFs are involved in many physiological processes such as cell development, adipocyte differentiation and neurodevelopment. In our study, we aim to learn the functions KLFs play in the muscle and fat development of chickens. Various bioinformatics analyses were used to illustrate the genomic information of KLFs. A qPCR was performed to show the relative expression level of KLFs. In addition, we collected RNA-seq data and we found that KLFs have different expression levels in the same tissues at different points in time. This study helps explore the regulation mechanism of KLFs in skeletal muscle and fat, and provides a theoretical basis for broiler breeding. ABSTRACT: The kruppel-like factor (KLF) gene family is a group of transcription factors containing highly conserved zinc-finger motifs, which play a crucial role in cell proliferation and differentiation. Chicken has been widely used as a model animal for analyzing gene function, however, little is known about the function of the KLF gene family in chickens. In this study, we performed genome-wide studies of chicken KLF genes and analyzed their biological and expression characteristics. We identified 13 KLF genes from chickens. Our phylogenetic, motif, and conserved domain analyses indicate that the KLF gene family has remained conserved through evolution. Synteny analysis showed the collinear relationship among KLFs, which indicated that they had related biomolecular functions. Interaction network analysis revealed that KLFs worked with 20 genes in biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that KLF2 was involved in Apelin and Forkhead Box O (FOXO) signaling pathways. Moreover, qPCR showed that 13 KLF genes were expressed in the nine selected tissues and displayed various gene expression patterns in chickens. RNA-seq showed that KLF3 and KLF10 genes were differentially expressed in the normal and high-fat diet fed groups, and KLF4, KLF5, KLF6, KLF7, KLF9, KLF12, and KLF13 genes were differentially expressed between undifferentiated and differentiated chicken preadipocytes. Besides, RNA-seq also showed that KLF genes displayed different expression patterns in muscle at 11 and 16 embryonic days old, and in 1-day-old chickens. These results indicated that the KLF genes were involved in the development of muscle and fat in chickens. Our findings provide some valuable reference points for the subsequent study of the function of KLF genes.