Regulatory Single Nucleotide Polymorphism of the Bovine <i>IFITM3</i> Gene Induces Differential Transcriptional Capacities of Hanwoo and Holstein Cattle

Interferon-induced transmembrane protein 3 (IFITM3), a crucial effector of the host’s innate immune system, prohibits an extensive range of viruses. Previous studies have reported that single nucleotide polymorphisms (SNPs) of the <i>IFITM3</i> gene are associated with the expression lev...

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Autores principales:	Yong-Chan Kim, Min-Ju Jeong, Byung-Hoon Jeong
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	cattle IFITM3 FMDV IAV SNP promoter Genetics QH426-470
Acceso en línea:	https://doaj.org/article/1c46fb6827e74ebf9c36d4be6b7bf180
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spelling	oai:doaj.org-article:1c46fb6827e74ebf9c36d4be6b7bf1802021-11-25T17:40:24ZRegulatory Single Nucleotide Polymorphism of the Bovine <i>IFITM3</i> Gene Induces Differential Transcriptional Capacities of Hanwoo and Holstein Cattle10.3390/genes121116622073-4425https://doaj.org/article/1c46fb6827e74ebf9c36d4be6b7bf1802021-10-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1662https://doaj.org/toc/2073-4425Interferon-induced transmembrane protein 3 (IFITM3), a crucial effector of the host’s innate immune system, prohibits an extensive range of viruses. Previous studies have reported that single nucleotide polymorphisms (SNPs) of the <i>IFITM3</i> gene are associated with the expression level and length of the IFITM3 protein and can impact susceptibility to infectious viruses and the severity of infection with these viruses. However, there have been no studies on polymorphisms of the bovine <i>IFITM3</i> gene. In the present study, we finely mapped the bovine <i>IFITM3</i> gene and annotated the identified polymorphisms. We investigated polymorphisms of the bovine <i>IFITM3</i> gene in 108 Hanwoo and 113 Holstein cattle using direct sequencing and analyzed genotype, allele, and haplotype frequencies and linkage disequilibrium (LD) between the <i>IFITM3</i> genes of the two cattle breeds. In addition, we analyzed transcription factor-binding sites and transcriptional capacity using PROMO and luciferase assays, respectively. Furthermore, we analyzed the effect of a nonsynonymous SNP of the <i>IFITM3</i> gene using PolyPhen-2, PANTHER, and PROVEAN. We identified 23 polymorphisms in the bovine <i>IFITM3</i> gene and found significantly different genotype, allele, and haplotype frequency distributions and LD scores between polymorphisms of the bovine <i>IFITM3</i> gene in Hanwoo and Holstein cattle. In addition, the ability to bind the transcription factor Nkx2-1 and transcriptional capacities were significantly different depending on the c.-193T > C allele. Furthermore, nonsynonymous SNP (F121L) was predicted to be benign. To the best of our knowledge, this is the first genetic study of bovine <i>IFITM3</i> polymorphisms.Yong-Chan KimMin-Ju JeongByung-Hoon JeongMDPI AGarticlecattleIFITM3FMDVIAVSNPpromoterGeneticsQH426-470ENGenes, Vol 12, Iss 1662, p 1662 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	cattle IFITM3 FMDV IAV SNP promoter Genetics QH426-470
spellingShingle	cattle IFITM3 FMDV IAV SNP promoter Genetics QH426-470 Yong-Chan Kim Min-Ju Jeong Byung-Hoon Jeong Regulatory Single Nucleotide Polymorphism of the Bovine <i>IFITM3</i> Gene Induces Differential Transcriptional Capacities of Hanwoo and Holstein Cattle
description	Interferon-induced transmembrane protein 3 (IFITM3), a crucial effector of the host’s innate immune system, prohibits an extensive range of viruses. Previous studies have reported that single nucleotide polymorphisms (SNPs) of the <i>IFITM3</i> gene are associated with the expression level and length of the IFITM3 protein and can impact susceptibility to infectious viruses and the severity of infection with these viruses. However, there have been no studies on polymorphisms of the bovine <i>IFITM3</i> gene. In the present study, we finely mapped the bovine <i>IFITM3</i> gene and annotated the identified polymorphisms. We investigated polymorphisms of the bovine <i>IFITM3</i> gene in 108 Hanwoo and 113 Holstein cattle using direct sequencing and analyzed genotype, allele, and haplotype frequencies and linkage disequilibrium (LD) between the <i>IFITM3</i> genes of the two cattle breeds. In addition, we analyzed transcription factor-binding sites and transcriptional capacity using PROMO and luciferase assays, respectively. Furthermore, we analyzed the effect of a nonsynonymous SNP of the <i>IFITM3</i> gene using PolyPhen-2, PANTHER, and PROVEAN. We identified 23 polymorphisms in the bovine <i>IFITM3</i> gene and found significantly different genotype, allele, and haplotype frequency distributions and LD scores between polymorphisms of the bovine <i>IFITM3</i> gene in Hanwoo and Holstein cattle. In addition, the ability to bind the transcription factor Nkx2-1 and transcriptional capacities were significantly different depending on the c.-193T > C allele. Furthermore, nonsynonymous SNP (F121L) was predicted to be benign. To the best of our knowledge, this is the first genetic study of bovine <i>IFITM3</i> polymorphisms.
format	article
author	Yong-Chan Kim Min-Ju Jeong Byung-Hoon Jeong
author_facet	Yong-Chan Kim Min-Ju Jeong Byung-Hoon Jeong
author_sort	Yong-Chan Kim
title	Regulatory Single Nucleotide Polymorphism of the Bovine <i>IFITM3</i> Gene Induces Differential Transcriptional Capacities of Hanwoo and Holstein Cattle
title_short	Regulatory Single Nucleotide Polymorphism of the Bovine <i>IFITM3</i> Gene Induces Differential Transcriptional Capacities of Hanwoo and Holstein Cattle
title_full	Regulatory Single Nucleotide Polymorphism of the Bovine <i>IFITM3</i> Gene Induces Differential Transcriptional Capacities of Hanwoo and Holstein Cattle
title_fullStr	Regulatory Single Nucleotide Polymorphism of the Bovine <i>IFITM3</i> Gene Induces Differential Transcriptional Capacities of Hanwoo and Holstein Cattle
title_full_unstemmed	Regulatory Single Nucleotide Polymorphism of the Bovine <i>IFITM3</i> Gene Induces Differential Transcriptional Capacities of Hanwoo and Holstein Cattle
title_sort	regulatory single nucleotide polymorphism of the bovine <i>ifitm3</i> gene induces differential transcriptional capacities of hanwoo and holstein cattle
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/1c46fb6827e74ebf9c36d4be6b7bf180
work_keys_str_mv	AT yongchankim regulatorysinglenucleotidepolymorphismofthebovineiifitm3igeneinducesdifferentialtranscriptionalcapacitiesofhanwooandholsteincattle AT minjujeong regulatorysinglenucleotidepolymorphismofthebovineiifitm3igeneinducesdifferentialtranscriptionalcapacitiesofhanwooandholsteincattle AT byunghoonjeong regulatorysinglenucleotidepolymorphismofthebovineiifitm3igeneinducesdifferentialtranscriptionalcapacitiesofhanwooandholsteincattle
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Regulatory Single Nucleotide Polymorphism of the Bovine <i>IFITM3</i> Gene Induces Differential Transcriptional Capacities of Hanwoo and Holstein Cattle

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