猪CREBRF基因生物信息学和表达规律分析

doi:10.13304/j.nykjdb.2024.0154

中国农业科技导报 ›› 2024, Vol. 26 ›› Issue (9): 44-53.DOI: 10.13304/j.nykjdb.2024.0154

猪CREBRF基因生物信息学和表达规律分析

郭肖蓉¹^,²(), 刘颖³, 樊佳珍², 黄涛⁴, 周荣²()

^1.佛山大学生命科学与工程学院，广东省动物分子设计与精准育种重点实验室，广东佛山 528225
^2.中国农业科学院北京畜牧兽医研究所，北京 100193
^3.内蒙古科技大学生命科学与技术学院，内蒙古包头 014010
^4.石河子大学动物科技学院，新疆石河子 832000

收稿日期:2024-03-03 接受日期:2024-04-23 出版日期:2024-09-15 发布日期:2024-09-13
通讯作者: 周荣
作者简介:郭肖蓉 E-mail：guoxiaorong1117@163.com；
基金资助:
科技创新2030重大项目(2023ZD0404702);国家自然科学基金项目(32130102)

Bioinformatics Analysis of Porcine CREBRF Gene and Its Expression Pattern

Xiaorong GUO¹^,²(), Ying LIU³, Jiazhen FAN², Tao HUANG⁴, Rong ZHOU²()

^1.Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding，School of Life Science and Engineering，Foshan University，Guangdong Foshan 528231，China
^2.Institute of Animal Science，Chinese Academy of Agricultural Sciences，Beijing 100193，China
^3.College of Life Science and Technology，Inner Mongolia University of Science and Technology，Inner Mongolia Baotou 014010，China
^4.College of Animal Science and Technology，Shihezi University，Xinjiang Shihezi 831301，China

Received:2024-03-03 Accepted:2024-04-23 Online:2024-09-15 Published:2024-09-13
Contact: Rong ZHOU

摘要/Abstract

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

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

中图分类号:

S828

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.

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.

图/表 11

表1 引物序列信息

Table 1 Primer sequence information

基因名称

Gene name

上游引物

Sense primer（5’-3’）

下游引物

Antisense primer（5’-3’）

用途

Usage

CREBRF

ATGCCTCAGCCTAGCGTAA

TTACACTTTTGATGTTGGTATCC

CREBRF

图1 不同品种猪与杜洛克猪CREBRF基因的CDS区序列比对注：黑色为参考碱基，红色为同义突变，绿色为错义突变，“-”为碱基缺失。

Fig. 1 Comparison of the CDS region sequence of the CREBRF gene among different breedsNote： Black shows reference bases， red shows synonymous mutations， green shows missense mutations in， “-” shows base deletion.

表2 猪CRERBF蛋白的氨基酸组成

Table 2 Amino acid composition of porcine CRERBF protein

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

图2 猪CREBRF 蛋白亲/疏水性预测

Fig. 2 Bioinformatics analysis of hydrophilicity/hydrophobicity of CREBRF protein in Sus scrofa

图3 猪CREBRF 磷酸化位点预测

Fig. 3 Bioinformatics analysis of phosphorylation sites of CREBRF protein in Sus scrofa

图4 猪CREBR蛋白的糖基化位点预测

Fig. 4 Bioinformatics analysis of glycosylation site of CREBRF protein in Sus scrofa

图5 猪CREBRF基因m6A修饰位点预测

Fig. 5 Bioinformatics analysis of m6A modification sites in porcine CREBRF gene

图6 猪、人和小鼠CREBRF氨基酸序列比对

Fig. 6 Comparison of amino acid sequence of CREBRF in Sus scrofa， Homo sapiens and Mus musculus

图7 猪、人和小鼠CREBRF二级结构预测

Fig. 7 Bioinformatics analysis of CREBRF secondary structure in Sus scrofa， Homo sapiens and Mus musculus

表3 猪、人和小鼠CREBRF蛋白二级结构

Table 3 Secondary structure of CREBRF protein in Sus scrofa， Homo sapiens and Mus musculus

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

图8 猪CREBRF基因表达量注：E80—胚胎期80 d；PN0—出生后0 d；PN28—出生后28 d；PN180—出生后180 d；PG38—妊娠38 d；PG80—妊娠80 d。不同字母表示P <0.05水平差异显著。

Fig. 8 Expression of CREBRF geneNote： E80—80 d at embryonic stage； PN0—0 d after birth； PN28—28 d after birth； PN180—180 d after birth； PG38—38 d after gestation； PG80—80 d after gestation. Different letters indicate significant differences at P<0.05 level.

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猪CREBRF基因生物信息学和表达规律分析

Bioinformatics Analysis of Porcine CREBRF Gene and Its Expression Pattern

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