牛TARDBP基因核心启动子鉴定与转录调控分析

doi:10.13560/j.cnki.biotech.bull.1985.2023-1048

生物技术通报 ›› 2024, Vol. 40 ›› Issue (4): 306-318.doi: 10.13560/j.cnki.biotech.bull.1985.2023-1048

牛TARDBP基因核心启动子鉴定与转录调控分析

张清兰¹^,²(), 张亚冉²^,³(), 鞠志花²^,³, 王秀革²^,³, 肖遥²^,³, 王金鹏²^,³, 魏晓超²^,³, 高亚平²^,³, 白福恒⁴, 王洪程¹()

1.贵州师范大学生命科学学院，贵阳 550025
2.山东省农业科学院畜牧兽医研究所山东省畜禽疫病防治与繁育重点实验室，济南 250100
3.农业农村部畜禽生物组学重点实验室，济南 250100
4.山东鲁润畜产品有限公司，德州 250523

收稿日期:2023-11-09 出版日期:2024-04-26 发布日期:2024-04-30
通讯作者: 张亚冉，女，博士，助理研究员，研究方向：奶牛分子育种；E-mail: zhang_ya_ran@126.com；
王洪程，男，博士，副教授，研究方向：动物遗传育种与繁殖；E-mail: wanghc@gznu.edu.cn
作者简介:张清兰，女，硕士研究生，研究方向：奶牛分子育种；E-mail: 1400304672@qq.com
基金资助:
国家自然科学基金项目(32202648);山东省重点研发计划（竞争性创新平台）项目(2022CXPT010);山东省农业科学院农业科技创新工程(CXGC2023F10);山东省农业科学院农业科技创新工程(CXGC2023A23)

Identification and Transcriptional Regulation Analysis of Core Promoter in Bovine TARDBP Gene

ZHANG Qing-lan¹^,²(), ZHANG Ya-ran²^,³(), JU Zhi-hua²^,³, WANG Xiu-ge²^,³, XIAO Yao²^,³, WANG Jin-peng²^,³, WEI Xiao-chao²^,³, GAO Ya-ping²^,³, BAI Fu-heng⁴, WANG Hong-cheng¹()

1. School of Life Sciences, Guizhou Normal University, Guiyang 550025
2. Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100
3. Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan 250100
4. Shandong Lurun Animal Products Co., Ltd, Dezhou 250523

Received:2023-11-09 Published:2024-04-26 Online:2024-04-30

摘要/Abstract

摘要：

【目的】为了解牛TARDBP基因结构、功能及启动子活性区域，分析该基因的转录调控机制。【方法】通过PCR技术克隆牛TARDBP基因编码区全长序列。应用生物信息学软件对牛TARDBP蛋白性质和结构进行分析。通过实时荧光定量PCR（RT-qPCR）技术检测TARDBP基因在泌乳期荷斯坦奶牛不同组织中的表达情况。应用5' RACE技术确定牛TARDBP基因的转录起始位点，PCR技术克隆牛TARDBP基因启动子区和5'端系列缺失片段，并运用生物信息学软件对牛TARDBP基因启动子区域CpG岛和潜在转录因子结合位点进行预测，双荧光素酶报告系统确定该基因的核心启动子区域。【结果】牛TARDBP基因在包括乳腺在内的多个组织中均有表达。TARDBP蛋白是一种水溶性非分泌蛋白，存在RNA识别结构域和DNA结合位点。TARDBP基因启动子区存在2个CpG岛和大量转录因子结合位点包括SP1、PPARA、PPARD、PPARG、SREBF1等。双荧光素酶活性分析结果显示牛TARDBP的核心启动子区位于-476 - -149之间，该区域包含Sp1、PPARG、PPARD、SREBF1结合元件，但不存在TATA-box。【结论】牛TARDBP基因在奶牛多个组织中均有表达。-476 - -149片段为牛TARDBP基因的核心启动子区，且该区域中存在与乳脂合成和分泌相关的转录因子结合位点。

关键词: 荷斯坦奶牛, TARDBP基因, 生物信息学, 启动子

Abstract:

【Objective】 The aim of this study is to analyze the transcriptional regulation mechanism of bovine TARDBP gene, as well as its structure, function and promoter active region. 【Method】The complete coding region of bovine TARDBP gene was cloned by PCR. Bioinformatics software was applied to analyze the properties and the structure of bovine TARDBP protein. The expression of TARDBP gene was profiled in different tissues of lactating Holstein cows by real-time fluorescence quantitative PCR（RT-qPCR）. The transcriptional initiation site of TARDBP gene was determined by 5' RACE technique, and the promoter region and 5' terminal deletion fragment of this gene were cloned by PCR. The CpG island and potential transcription factor binding site within the promoter region were predicted by bioinformatics software. The core promoter region was then confirmed by the dual-luciferase reporter system.【Result】Bovine TARDBP gene was expressed in multiple tested tissues including mammary gland. TARDBP protein was water-soluble, and it contained RNA recognition motifs and DNA binding sites. There were two CpG islands and a large number of transcription factor binding sites including SP1, PPARA, PPARD, PPARG, SREBF1 and so on in the promoter region. The results of dual-luciferase activity analysis showed that the core promoter region of bovine TARDBP was between -476 and -149, and Sp1, PPARG, PPARD and SREBF1 binding sites were found in the core promoter, but there was no TATA-box. 【Conclusion】 Bovine TARDBP gene is distributed in various tissues of dairy cows. The core promoter region of bovine TARDBP gene is positioned at -476 to -149, and there are transcription factor binding sites related to milk fat synthesis and secretion in this region.

Key words: Holstein dairy cows, TARDBP gene, bioinformatics, promoter

张清兰, 张亚冉, 鞠志花, 王秀革, 肖遥, 王金鹏, 魏晓超, 高亚平, 白福恒, 王洪程. 牛TARDBP基因核心启动子鉴定与转录调控分析[J]. 生物技术通报, 2024, 40(4): 306-318.

ZHANG Qing-lan, ZHANG Ya-ran, JU Zhi-hua, WANG Xiu-ge, XIAO Yao, WANG Jin-peng, WEI Xiao-chao, GAO Ya-ping, BAI Fu-heng, WANG Hong-cheng. Identification and Transcriptional Regulation Analysis of Core Promoter in Bovine TARDBP Gene[J]. Biotechnology Bulletin, 2024, 40(4): 306-318.

图/表 15

表1 牛TARDBP基因引物序列信息

Table 1 Sequence information of bovine TARDBP gene primer

引物名称 Primer name	引物序列 Primer sequence（5'-3'）	产物大小 Product length/bp	退火温度 Annealing temperature/℃	用途 Usage
TARDBP-F	ATGTCTGAATATATTCGGGTAACCG	1 245	64.4	CDS区扩增
TARDBP-R	CTACATTCCCCAGCCAGAAGATTTA	1 245	64.4
TARDBP-GSP	CCGTGAAGCGAACGAAGCCAAACC	496	68	5'RACE第一轮PCR
TARDBP -NGSP	AGATTCCCCCAGCCAGCATCGG	230	68	5'RACE第二轮PCR
pTARDBP-F	GCAAAGGGATAGAGGGAA	1 954	55	启动子区扩增
pTARDBP-R	CAGGGCGTCCTTAGTGAG	1 954	55
pGL3-P1	CGG GGTACCGCAAAGGGATAGAGGGAA	1 954	55	不同缺失片段扩增
pGL3-P2	CGG GGTACCGTTCAAACTACCGCACAATG	1 498
pGL3-P3	CGG GGTACCTAGGGTGGCAAAGAGTTGG	1 179
pGL3-P4	CGG GGTACCGAGAAGGAAATGGCAACCC	854
pGL3-P5	CGG GGTACCAATGGCTTGGGCTCAACAG	615
pGL3-P6	CGG GGTACCTATAGCCTTCAAGTTCACTCCC	288
pGL3-R1	CCC AAGCTTCAGGGCGTCCTTAGTGAG
TARDBP-q-F	GTTTGGCTTCGTTCGCTTCA	164	60	RT-qPCR
TARDBP-q-R	CCTCTGTACAACGCCCAACA	164
β-actin-q-F	CATCGGCAATGAGCGGTTCC	147
β-actin-q-R	ACCGTGTTGGCGTAGAGGTC	147

表2 生物信息学分析用软件

Table 2 Software for bioinformatics analysis

软件名Software name	网址 Website	用途 Purpose
NCBI	https://www.ncbi.nlm.nih.gov/	氨基酸序列
NCBI	https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi	保守结构域分析
DNAMAN9.0软件		同源性比对
MEGA11.0软件		构建基因系统进化树
ExPASy	https://web.expasy.org/protscale/	理化性质分析
TMHMM	https://services.healthtech.dtu.dk/service.php?TMHMM-2.0	蛋白跨膜结构域预测
SignalP5.0	https://services.healthtech.dtu.dk/service.php?Signal P-5.0	蛋白信号肽预测
NetPhos-3.1	http://www.cbs.dtu.dk/services/NetPhos/	蛋白磷酸化位点分析
NPS@SOPMA	https://npsa-prabi.ibcp.fr/cgi-bin/secpred_sopma.pl	蛋白质二级结构预测
SWISS-MODEL	https://swissmodel.expasy.org/	蛋白质三级结构预测
Meth Primer	http://www.urogene.org/methprimer/	CpG岛预测
AnimalTFDB4	bioinfo.life.hust.edu.cn/AnimalTFDB4	转录因子结合位点预测
TRANSFAC2.0	https://genexplain.com/transfac-2-0/	转录因子结合位点预测

图1 牛TARDBP基因CDS区PCR产物 M：DL5000 DNA marker；1：牛TARDBP基因CDS区

Fig. 1 PCR product of the bovine TARDBP gene CDS region M: DL5000 DNA marker. 1: CDS region of bovine TARDBP gene

表3 牛与不同物种TARDBP氨基酸序列比对

Table 3 Amino acid sequence comparison of TARDBP between cattle and different species

物种 Species	登录号 GenBank No.	氨基酸序列相似性Similarity/%
牛 Bos taurus	NP_001039950.2
山羊 Capra hircus	XP_005690745.1	100
绵羊 Ovis aries	XP_027831445.1	100
犬 Canis lupus familiaris	XP_038516303.1	99.76
猪 Sus scrofa	XP_020950991.1	99.52
家猫 Felis catus	XP_003989534.1	99.03
人 Homo sapiens	NP_031401.1	97.58
苏门答腊猩猩Pongo abelii	NP_001127597.1	97.34
原鸡 Gallus gallus	NP_001026049.2	96.86
热带爪蟾 Xenopus tropicalis	NP_001231687.1	74.10
小鼠 Mus musculus	NP_001003898.1	67.39
大鼠 Rattus norvegicus	NP_001011979.1	66.67

图2 TARDBP基因系统进化树树枝上方数字是>50 ％的自展值（1 000次重复）

Fig. 2 Phylogenetic tree of TARDBP gene The number on the branch is >50% of the self-explanatory value（1 000 repetitions）

表4 牛TARDBP蛋白氨基酸组成

Table 4 Amino acid composition of bovine TARDBP protein

氨基酸 Amino acid	数目 Number	比例Perc-entage/%	氨基酸 Amino acid	数目 Number	比例Perc- entage/%
Ala（A）	27	6.5%	Leu（L）	20	4.8%
Arg（R）	20	4.8%	Lys（K）	20	4.8%
Asn（N）	27	6.5%	Met（M）	17	4.1%
Asp（D）	22	5.3%	Phe（F）	22	5.3%
Cys（C）	7	1.7%	Pro（P）	17	4.1%
Gln（Q）	24	5.8%	Ser（S）	41	9.9%
Glu（E）	20	4.8%	Thr（T）	15	3.6%
Gly（G）	55	13.3%	Trp（W）	6	1.4%
His（H）	5	1.2%	Tyr（Y）	6	1.9%
Ile（I）	14	3.4%	Val（V）	8	6.5%

图3 TARDBP蛋白结构分析 A：牛TARDBP蛋白保守结构域预测；B：牛TARDBP蛋白疏水性预测；C：牛TARDBP蛋白跨膜结构预测；D：牛TARDBP蛋白信号肽预测；E：牛TARDBP蛋白二级结构预测；F：牛TARDBP蛋白三级结构预测；G：牛TARDBP蛋白磷酸化位点预测

Fig. 3 Analysis of TARDBP protein structure A: Prediction of bovine TARDBP protein conserved domain. B: Prediction of bovine TARDBP protein hydrophobicity. C: Prediction of bovine TARDBP protein transmembrane structure. D: Prediction of bovine TARDBP protein signal peptide. E: Prediction of secondary structure of bovine TARDBP protein. F: Tertiary structure prediction of bovine TARDBP protein. G: Prediction of phosphorylation site of bovine TARDBP protein

图4 牛TARDBP基因在不同组织的表达分析相同大写字母表示差异不显著（P>0.05），不同大写字母表示差异极显著（P<0.01）

Fig. 4 Analysis of bovine TARDBP gene expression in different tissues The same capital letter indicates that the difference is not significant（P>0.05）, different capital letters indicate significant differences（P<0.01）

图5 牛TARDBP基因5' RACE扩增电泳图 M：DL5000 DNA marker；1：第一轮PCR产物；2：第二轮PCR产物

Fig. 5 5' RACE amplification electrophoresis of bovine TARDBP gene M: DL5000 DNA marker. 1: First round PCR products. 2: Second round PCR product

图6 牛TARDBP基因转录起始位点

Fig. 6 Transcription start site of bovine TARDBP gene

图7 牛TARDBP基因启动子区PCR产物 M：DL5000 DNA marker；1：牛TARDBP基因 5'侧翼区-1815/+139 片段

Fig. 7 PCR products from the promoter region of bovine TARDBP gene M: DL5000 DNA marker. 1: The 5' flanking region（-1815/+139）of bovine TARDBP gene

图8 牛TARDBP基因5'调控区CpG island 预测结果 A：MethPrimer 软件预测结果；B：CpG islands 在序列中的定位

Fig. 8 Prediction results of CpG island in the 5' regulatory region of bovine TARDBP gene A: The predict result by MethPrimer software. B: The specific location of CpG islands

图9 牛TARDBP基因启动子潜在的转录因子结合位点预测结果 +1表示转录起始位点；方框表示转录因子结合位点；重叠的转录因子结合位点区域用不同颜色的框表示

Fig. 9 Prediction of potential transcription factor binding sites of bovine TARDBP gene promoter +1 indicates transcription initiation site; letters in in box indicates transcription factor binding sites. Overlapping regions of transcription factor binding sites are represented by different colored boxes

图10 牛TARDBP基因启动子不同缺失片段的扩增与载体构建 A：牛TARDBP基因启动子逐段缺失片段扩增电泳图，M：DL5000 DNA marker，1-6：加双酶切位点牛TARDBP基因启动子逐段缺失片段；B：牛TARDBP基因启动子双荧光素报告重组质粒双酶切鉴定电泳图，M：DL5000 DNA marker，1-6：重组质粒

Fig. 10 Amplification and vector construction of different deletion fragments of bovine TARDBP gene promoter A: Electrophoretic amplification of bovine TARDBP gene promoter fragment by fragment deletion, M: DL5000 DNA marker, 1-6: add the missing fragments of bovine TARDBP gene promoter at double restriction sites. B: Electrophoresis of bovine TARDBP gene promoter double fluorescein reporter recombinant plasmid double enzyme digestion identification， M: DL5000 DNA marker, 1-6: recombinant plasmid

图11 牛TARDBP基因启动子在牛乳腺上皮细胞中的活性分析不同字母表示差异显著（P<0.05）

Fig. 11 Activity analysis of bovine TARDBP gene promoter in bovine mammary epithelial cells Different letters indicate significant differences（P<0.05）

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牛TARDBP基因核心启动子鉴定与转录调控分析

Identification and Transcriptional Regulation Analysis of Core Promoter in Bovine TARDBP Gene

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