Bioinformatics Analysis of Porcine CREBRF Gene and Its Expression Pattern

doi:10.13304/j.nykjdb.2024.0154

Abstract

Abstract:

CREBRF gene plays an important regulatory role in the reproductive process of female animals. In order to deeply understand the characteristics and functions of CREBRF gene in pigs， bioinformatic analysis of the CREBRF gene was performed， and the expression pattern of CREBRF in ovarian tissues at different stages of Bama pigs was analyzed by RT-qPCR. The results showed that 20 mutations of CREBRF gene were identified in the genomes of 5 pig breeds， 7 of which were synonymous mutations and 13 were missense mutations. The CDS region of the porcine CREBRF gene was 1 920 bp in length， encoding a total of 639 amino acids， with a high instability coefficient， a hydrophilic protein， 85 high-confidence phosphorylation sites and 4 glycosylation sites， and the mRNA of CREBRF had 20 high-confidence m⁶A methylation modification sites. CREBRF proteins were more conserved in pig， human and mouse， and the secondary structures of pig and human CREBRF proteins were more similar. RT-qPCR results showed that the expression of the CREBRF gene in pig ovaries was higher at 0 and 28 d after birth， and with the growth and development of pigs， the expression decreased significantly at 180 d after birth， and the expression of CREBRF increased again at 38 and 80 d after gestation in sows. By comparing the base mutations in the CDS region of CREBRF gene in different breeds of pigs and analysing the physicochemical properties and expression pattern of the gene， CREBRF gene was highly expressed in the ovarian tissues of pigs at the fetal stage， early birth and gestation， and it was speculated that CREBRF plays an important role in the reproductive process of sows， which provided a reference for the mining of genes for high porcine fertility and the development of molecular markers.

Key words: pig, ovary, CREBRF, bioinformatics analysis, expression pattern

摘要：

CREBRF基因在雌性动物生殖过程中具有重要调控作用，为了深入了解猪的CREBRF基因特征和功能，对CREBRF基因进行生物信息学分析，并通过RT-qPCR分析不同阶段巴马猪卵巢组织中CREBRF的表达规律。结果显示，在5个品种猪基因组上鉴定到20个CREBRF基因的碱基突变，其中7个为同义突变，13个为错义突变。猪CREBRF基因的CDS区全长1 920 bp，共编码639个氨基酸，不稳定系数较高，为亲水性蛋白，有85个高置信度的磷酸化位点和4个糖基化位点，且CREBRF的mRNA具有20个高可信度的m⁶A甲基化修饰位点，猪、人和小鼠中的CREBRF蛋白保守性较强。RT-qPCR结果显示，猪卵巢中CREBRF基因的表达量在猪出生0和28 d时表达水平较高，随着猪生长发育，在出生180 d时表达量显著降低，在母猪妊娠38和80 d时CREBRF的表达再次升高。通过比对不同品种猪中CREBRF基因CDS区的碱基突变并分析该基因的理化性质及表达规律，发现了CREBRF基因在猪胎儿期、出生早期和妊娠期卵巢组织中的高表达，推测CREBRF在母猪生殖过程中起重要作用，为猪高繁殖力基因挖掘和分子标记开发提供参考。

关键词: 猪, 卵巢, CREBRF, 生物信息学分析, 基因表达

CLC Number:

S828

Xiaorong GUO, Ying LIU, Jiazhen FAN, Tao HUANG, Rong ZHOU. Bioinformatics Analysis of Porcine CREBRF Gene and Its Expression Pattern[J]. Journal of Agricultural Science and Technology, 2024, 26(9): 44-53.

郭肖蓉, 刘颖, 樊佳珍, 黄涛, 周荣. 猪CREBRF基因生物信息学和表达规律分析[J]. 中国农业科技导报, 2024, 26(9): 44-53.

Figures/Tables 11

References 28

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氨基酸 Amino acid	数量 Number	频率 Frequency/%	氨基酸 Amino acid	数量 Number	频率 Frequency/%
Ala （A）	29	4.5	Lys （K）	51	8.0
Arg （R）	25	3.9	Met （M）	11	1.7
Asn （N）	34	5.3	Phe （F）	17	2.7
Asp （D）	48	7.5	Pro （P）	40	6.3
Cys （C）	10	1.6	Ser （S）	65	10.2
Gln （Q）	31	4.9	Thr （T）	36	5.6
Glu （E）	67	10.5	Trp （W）	6	0.9
Gly （G）	29	4.5	Tyr （Y）	20	3.1
His （H）	10	1.6	Val （V）	34	5.3
Ile （I）	17	2.7	Pyl （O）	0	0.0
Leu （L）	59	9.2	Sec （U）	0	0.0

氨基酸 Amino acid	数量 Number	频率 Frequency/%	氨基酸 Amino acid	数量 Number	频率 Frequency/%
Ala （A）	29	4.5	Lys （K）	51	8.0
Arg （R）	25	3.9	Met （M）	11	1.7
Asn （N）	34	5.3	Phe （F）	17	2.7
Asp （D）	48	7.5	Pro （P）	40	6.3
Cys （C）	10	1.6	Ser （S）	65	10.2
Gln （Q）	31	4.9	Thr （T）	36	5.6
Glu （E）	67	10.5	Trp （W）	6	0.9
Gly （G）	29	4.5	Tyr （Y）	20	3.1
His （H）	10	1.6	Val （V）	34	5.3
Ile （I）	17	2.7	Pyl （O）	0	0.0
Leu （L）	59	9.2	Sec （U）	0	0.0

物种 Species	参数 Parameter	α-螺旋 α-helix	β-折叠 β-turn	无规则卷曲 Random coil	延伸链 Extended strand
猪Sus scrofa	数量Number	54	21	78	27
	氨基酸数Amino acid number	238	32	303	66
	占比Ratios/%	37.25	5.01	47.42	10.33
人Homo sapiens	数量Number	54	21	79	27
	氨基酸数Amino acid number	239	32	302	47.26
	占比Ratios/%	37.40	5.01	47.26	10.33
小鼠Mus musculus	数量Number	58	17	82	19
	氨基酸数Amino acid number	235	31	314	60
	占比Ratios/%	36.72	4.84	49.06	9.38

物种 Species	参数 Parameter	α-螺旋 α-helix	β-折叠 β-turn	无规则卷曲 Random coil	延伸链 Extended strand
猪Sus scrofa	数量Number	54	21	78	27
	氨基酸数Amino acid number	238	32	303	66
	占比Ratios/%	37.25	5.01	47.42	10.33
人Homo sapiens	数量Number	54	21	79	27
	氨基酸数Amino acid number	239	32	302	47.26
	占比Ratios/%	37.40	5.01	47.26	10.33
小鼠Mus musculus	数量Number	58	17	82	19
	氨基酸数Amino acid number	235	31	314	60
	占比Ratios/%	36.72	4.84	49.06	9.38

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