香猪ENTPD1基因3'UTR的SINE插入下调其基因表达

doi:10.11843/j.issn.0366-6964.2025.09.015

Abstract

Abstract:

The study aimed to investigate the population polymorphism of short interspersed nuclear element (SINE) insertions/deletions in the 3'UTR of the ENTPD1 gene and their effect on gene expression in the Xiang pig. Xiang pigs were used as research subjects and Large White pigs were used as controls. The detection of population polymorphism of SINE insertions/deletions in the 3'UTR region of the ENTPD1 gene in Xiang pig and Large White pig populations was performed by PCR. The functional elements in SINE sequences was analyzed using databases and softwares such as UCSC, SINE Base, miRNA Base, PITA and RBP suite; The mRNA levels of ENTPD1 in different tissues (heart, liver, spleen, lung and kidney) of individuals of 6-month-old and mRNA levels of ENTPD1 in lung tissues of individuals with different genotypes of healthy adult Xiang pig was detected using Real-time fluorescence quantitative PCR (RT-qPCR) technology. The protein levels of ENTPD1 in lung tissues of individuals with different genotypes was detected using Western blotting technique. The results showed that there was a 297 bp SINE polymorphism site in the 3'UTR of ENTPD1 in Xiang pig, it was located at 466 bp downstream of the terminator codon. Bioinformatic analysis revealed that the SINE belonged to the Pre0_SS tRNA family and contained the RNA polymerase Ⅲ promoter, multiple RNA-binding proteins, and binding sites for miRNAs; Three genotypes, insertion (SINE+/+), deletion (SINE-/-) and heterozygote (SINE+/-), were detected in Xiang pigs and Large White pigs. The frequency of deletion (SINE-/-) genotype in Xiang pigs was significantly higher than that in Large White pigs (P < 0.01), and the frequency of SINE- allele was significantly higher than that in Large White pigs (P < 0.05). The variation showed moderate polymorphism in both populations, but only in Xiang pig population conformed to Hardy-Weinberg equilibrium. Detection of ENTPD1 mRNA in different tissues of Xiang pig showed higher mRNA levels in spleen and lung tissues. The mRNA and protein assays of ENTPD1 in lung tissues of individuals with different genotypes of Xiang pigs showed that the mRNA levels of SINE-/- and SINE+/- genotypes were highly significantly higher than those of SINE+/+, and the protein levels of SINE-/- genotypes were highly significantly higher than those of SINE+/- and SINE+/+. The results suggest that SINE insertion negatively regulates the expression of ENTPD1 gene.

Key words: ENTPD1, 3'UTR, SINE, gene expression, Xiang pig

CLC Number:

S828.2

TIAN Jiao, LONG Juyan, CHEN Xia, CEN Xiaoli, NIU Xi, HUANG Shihui, WANG Jiafu, RAN Xueqin. Down-regulation of Gene Expression by SINE Insertion in the 3'UTR of the ENTPD1 Gene in the Xiang Pig[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(9): 4303-4314.

Figures/Tables 9

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引物名称 Primer name	引物序列(5′→3′) Primer sequence	产物长度/bp Length	退火温度/℃ Annealing temperature	用途 Application
ENTPD1-3′UTR-F	GAACTGAGAATCCTGAGTCCTGT	571/274	58	SV分型
ENTPD1-3′UTR-R	CATAAGTTCCTTCACAAGCCTCT
qENTPD1-F	CTCCCACTCCACCTATGTCTTC	160	60	mRNA水平分析
qENTPD1-R	AGTTTTCTTCTCACTCCAGCCA
qGAPDH-F	AGGTCGGAGTGAACGGATTTG	118	60
qGAPDH-R	ACCATGTAGTGGAGGTCAATGAAG

序号 Number	RNA结合蛋白 RNA-binding protein	结合位置 Binding position	结合序列 Binding sequence	数量 Number	分数 Score
1	富脯氨酸和谷氨酰胺的剪接因子(SFPQ)	112~118	GUGGUGU	1	0.58
2	Lin-28同系物A(LIN28A)	113~119;159~165	UGGUGUA	2	0.98
3	多聚结合蛋白1(PCBP1)	194~200 67~73	CCUAGCC CCUGCCC	1 1	0.72 0.56
5	脆性X信使核糖核蛋白1(FMR1)	35~41	CGACUAG	1	0.83
6	富丝氨酸和精氨酸的剪接因子7(SRSF7)	33~40	UCCGACUA	1	0.99
7	富丝氨酸和精氨酸的剪接因子9(SRSF9)	14~20	UGGCGCA	1	0.99
8	FUS RNA结合蛋白(FUS)	114~117;160~163	GGUG	2	0.67
9	FMR1常染色体同系物2(FXR2)	126~132	AGACGCG	1	0.97
10	胰岛素样生长因子2 mRNA结合蛋白1(IGF2BP1)	138~148	GAUCCUGCGUU	1	0.60
11	多聚嘧啶区结合蛋1(PTBP1)	72~78	CCUUGCU	1	0.51
12	Pumilio RNA结合家族成员1(PUM1)	116~119;162~165	UGUA	2	0.67

序号 Number	miRNA名称 miRNA	结合位置 Binding position	序列(5′→3′) Sequence	自由能/(kJ·mol^-1) Free energy
1	ssc-miR-744	209~217	AGCTCCGAT	-10.67
2	ssc-miR-4331-3p	209~215	AGCTCCG	-11.61
3	ssc-miR-214-5p	195~203	AGGCTGGCA	-10.52
4	ssc-miR-9802-3p	100~107	GCCCTTGC	-11.57
5	ssc-miR-326	258~266	GCCCAAAGA	-11.06
6	ssc-miR-330	258~266	GCCCAAAGA	-12.02
7	ssc-miR-885-3p	128~135	CGTTGCCG	-10.32
8	ssc-miR-99b	84~91	TGCGGGTT	-10.75
9	ssc-miR-652	78~86	TGGGGTTGC	-10.23
10	ssc-miR-9805-3p	168~176	GATCCTGCG	-10.87
11	ssc-miR-7137-5p	34~42	GTTCCCGTC	-10.62
12	ssc-miR-193a-5p	254~262	AAAGACCAA	-14.65
13	ssc-miR-140-5p	255~263	AAGACCAAA	-11.56

群体 Population	样本数/头 Sample	基因型频率(%) Genotype frequency			等位基因频率/% Allele frequency		HWE test P	群体遗传特征 Population genetic characteristics
群体 Population	样本数/头 Sample	SINE+/+	SINE+/-	SINE-/-	SINE+	SINE-	HWE test P	纯合度 Ho	杂合度 He	有效等位基因数Ne	多态信息含量PIC
香猪 Xiang pig	302	70 (23.18)	124 (41.06)	108 (35.76)^A	43.71	56.29^A	0.13	0.51	0.49	1.97	0.37
大白猪 Large White pig	170	54 (31.76)	102 (60.00)	14 (8.24)^C	61.76	38.24^B	0.03	0.53	0.47	1.90	0.36

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Down-regulation of Gene Expression by SINE Insertion in the 3'UTR of the ENTPD1 Gene in the Xiang Pig

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