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

Zheng Ma; Huangbin Chu; Fapei Li; Guochao Han; Yingqiu Cai; Jianing Yi; Mingrou Lu; Hai Xiang; Huimin Kang; Fei Ye; Siyu Chen; Hua Li

doi:10.3390/ani14172594

Animals (Sep 2024)

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

Zheng Ma,
Huangbin Chu,
Fapei Li,
Guochao Han,
Yingqiu Cai,
Jianing Yi,
Mingrou Lu,
Hai Xiang,
Huimin Kang,
Fei Ye,
Siyu Chen,
Hua Li

Affiliations

Zheng Ma: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Huangbin Chu: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Fapei Li: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Guochao Han: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Yingqiu Cai: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Jianing Yi: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Mingrou Lu: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Hai Xiang: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Huimin Kang: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Fei Ye: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Siyu Chen: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China
Hua Li: Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China

DOI: https://doi.org/10.3390/ani14172594
Journal volume & issue: Vol. 14, no. 17
p. 2594

Abstract

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Krüppel-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 Krüppel 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.

Published in Animals

ISSN: 2076-2615 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Agriculture: Animal culture: Veterinary medicine; Science: Zoology
Website: http://www.mdpi.com/journal/animals/

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