从猪胚胎骨骼肌cDNA文库中分离、定位新基因并分析部分基因的功能
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摘要
随着猪基因组研究工作的不断深入，许多与猪生产性状(生长、胴体与肉质性状)相关的新基因被证实。但相对猪整个基因组来说，仍然还有大量基因没有发现。而猪胚胎期形成的肌纤维数目与猪日增重及生长速度呈正相关，是动物产肉量的重要决定因素。因此，从猪胚胎cDNA文库中分离证实与猪生产性状相关的基因，必将会为分子育种实践提供重要的指导作用。
本文从猪55天胚胎骨骼肌cDNA文库中筛选出15个功能基因，通过功能分析选出CA3和HUMMLC2B基因作进一步研究，并取得了如下结果：
1．通过猪55天胚胎骨骼肌cDNA文库测序并结合猪EST数据库的信息分离出15个猪基因，即K-ALPHA-1、TUBB、MAPRE1、TUBA3、ATP6VOE、RPL6、RPL7、RPL10、HUMMLC2B、BNIP3L、NHP2L1、CA3、CCNT2、PC4和FLJ30294，并分析其cDNA及预测的蛋白质序列(CCNT2和FLJ30294除外)。
2．在猪×仓鼠辐射杂种板中对上述所分离的基因进行染色体定位(HUMMLC2B除外)，定位结果如下：K-ALPHA-1定位于SSC5p，TUBB定位于SSC7p11，TUBA3定位于SSC5p11-p15，MAPRE1定位于SSC17q21-23，RPL6定位于SSC14q22-24，RPL7定位于SSC4q11-14，RPL10定位于SSCXq26，ATP6VOE定位于SSC16q，BNIP3L定位于SSC14q21-22，CCNT2定位于SSC15q12-14，NHP2L1定位于SSC5p12-15，FLJ30294定位于SSC3q11-14，PC4定位于SSC16q11-14，CA3定位于SSC4q11-q14，同时用猪×啮齿类体细胞杂种板对CA3基因进行了区域定位(SSC4q11-q14)。
3．对于CA3基因，通过猪cDNA文库测序和猪ESTs序列拼接分别获得了两个长短不同的cDNA序列，命为CA3b和CA3a，序列分析显示CA3b与CA3a之间存在一gap，预测的蛋白质显示CA3b缺少CA3a的C末端(78aa)。并且荧光共聚焦显微镜的观察结果显示GFP融合的CA3a蛋白位于整个细胞中，而CA3b仅位于细胞质中。
4．获得了猪CA3和HUMMLC2B基因的全长基因组DNA序列，并分析了其基因组结构。结果显示CA3基因是由7个外显子和6内含子组成(相对CA3a的cDNA序列)，约10.5kb。HUMMLC2B基因是由7个外显子和6个内含子组成，约2.9kb，包含多个重复序列。两个基因所有内含子和外显子的拼接位点都符合GT-AG规则。
5．为了研究猪候选基因在骨骼肌发育中可能的作用，应用实时荧光定量PCR技术对候选基因进行了时空表达谱分析。结果显示，CA3基因在通城猪胚胎33天骨骼肌中表达量最低，65天达到最高，然后下降到一定程度并和出生后的表达量保持相对稳定的水平。而在大白猪胚胎骨骼肌中的表达模式和通城猪不同，即在33天表达量最低，但在65天和90天表达量没有明显差异。组织表达谱显示CA3在骨骼肌和肝脏中表达量最高，在肺脏、淋巴结、胃、大肠和小肠中表达量较低，而在心脏和脾脏中没有检测到表达。
6．而HUMMLC2B基因在通城猪胚胎骨骼肌中的表达模式和长白猪相似(胚胎33天、65天、90天)，但在通城猪出生后随年龄的增加其表达量不断降低(出生后2天、28天和成年)。组织表达谱分析显示HUMMLC2B基因仅在所有被检测的骨骼肌中表达，并且表达量较高，而其它组织中除脂肪中有极少量的表达外，都没有检测到表达。
7．亚细胞定位结果显示GFP融合的HUMMLC2B蛋白位于整个细胞中。
8．SNPs的检测结果证实CA3基因有两个可用于PCR-RFLP的SNPs位点，即BsuRI-PCR和Hinfl-PCR，分别位于第五和第六内含子中。而HUMMLC2B基因有23个潜在的SNPs，其中可用于PCR-RFLP的四个SNPs位点，即HinlI-PCR(两个)，MspI-PCR和BglI-PCR，分别位于第三内含子，第四外显子和第五内含子中(MspI-PCR和BglI-PCR位点)；另外四个SNPs位点用DHPLC技术检测，两个SNPs位于第六内含子中，两个SNPs位于第七外显子中。
9．对上述PCR—RFLP多态位点在五指山猪、香猪、巴马香猪三个小型猪品种以及莱芜猪、通城猪、大白猪、长白猪和杜洛克中分析基因型和等位基因频率以及各等位基因在不同猪品种中的分布差异。
10．在我室与通城县畜牧局合作组建的试验群体中(三个纯繁群：通城猪、大白和长白猪及两个三元杂交群：长大通和大长通)，分析猪CA3和HUMMLC2B基因的多态与部分经济性状的关联。结果显示：①对于CA3基因，G8603A位点多态与肌内脂肪含量呈极显著相关(P＜0.01)，且与腿臀比率呈显著相关(P＜0.05)；G8371A位点GG基因型个体与GA基因型个体间大理石纹和肌内脂肪含量差异极显著(P＜0.01)，而与三点平均背膘厚差异显著(P＜0.05)。②对于HUMMLC2B基因，G1094A和T1513C位点没有检测到与性状的关联；G1876A位点GG基因型个体和GA基因型个体间屠宰率和肉色差异显著(P＜0.05)；T2005G位点GG基因型个体与TG基因型个体肉色差异显著(P＜0.05)，且TT基因型个体和TG基因型个体间红细胞数(RBC)、红细胞压积(HCT)、红细胞分布密度(RDW)差异显著(P＜0.05)。
With the development of porcine genomic studies, many genes associated with pig production traits have been identified, however, additional genes need be identified and further characterized. Moreover, the number of porcine muscle fibers, fixed at birth, is an important factor affecting animal meat quality and quantity, which positive associations exist between muscle fiber number and average daily gain and growth rate. Therefore, it will be necessary for isolation and identification of these genes associated with econimic traits from the fetal cDNA library of porcine skeletal muscle.In this present study, porcine 15 genes were isolated from skeletal muscle cDNA library of pig day-55 embryos, and CA3 and HUMMLC2B genes were choosen for further analyses of the potential functions. These main results were as follows:1. Combining sequencing of the cDNA library and porcine EST data, porcine 15 genes were isolated and identified, and these genes were: K-ALPHA-J, TUBB, MAPRE1, TUBA3, ATP6VOE, RPL6, RPL7, RPL10, HUMMLC2B, BNIP3L, NHP2L1, CA3, CCNT2, PC4 and FLJ30294. Sequences of cDNA and predicted proteins of these genes (except for CCNT2 and FLJ30294) were further analyzed.2. These above genes (except for HUMMLC2B) were assigned in pig×hamster hybrids panel, and the results were followed: K-ALPHA-1: SSC5p, TUBB: SSC7p11, MAPRE1: SSC17q21-23, TUBA3: SSC5p11-pl5, RPL6: SSC14q22-24, RPL7: SSC4q11-14, RPL10: SSCXq26, ATP6VOE: SSC16q, BNIP3L: SSC14q21-22, CCNT2: SSC15q12-14, NHP2L1: SSC5pl2-15, FLJ30294: SSC3q11-14, PC4: SSC16q11-14 and CA3: SSC4q11-q14. CA3 was further mapped using porcine somatic cell hybrid panel.3. To the CA3 gene, two different cDNA sequences (namely CA3b and CA3a) were obtained by sequencing of the cDNA library and e-PCR of porcine ESTs sequences, respectively. A gap was shown between the cDNA sequences of CA3b and CA3a by sequence comparison, and the predicted proteins showed that CA3b was the absence of 78 amino acids in the C-terminal domain of CA3a. The fluorescence mapping result using confocal microcopy showed the GFP-fused CA3a protein was distributed throughout the whole cell, but the GFP-fused CA3b protein was only distributed in cytoplasm.4. The full-length DNA sequences of the CA3 and HUMMLC2B genes were obtained and the genomic structures were analyzed. It was identified that the CA3 gene comprised 7 exons and 6 introns (for the cDNA sequence of CA3a), which spaned about 10.5 kb. The HUMMLC2B gene comprised 7 exons and 6 introns, which spaned about 2.9kb. All splice sites of exon/intron of the two genes conformed to the GT/AG rule.
5. In order to study potential functions of target genes, temporal and spatial expression profiles were analyzed using real-time PCR. It was demonstrated that the expression levels of CA3 increased from prenatal 33-day-old to 65-day-old skeletal muscle in Tongcheng pigs. These levels subsequently decreased to similar levels as those seen in prenatal 90-day-old pigs, as well as those in postnatal 2-day-old, 28-day-old, and adult pigs, but the expression patterns of Chinese Tongcheng pig embryos were different from that of Landrace pig embryos. CA3 was expressed at higher levels in skeletal muscle and liver than lung, lymph node, large and small intestine, but was not detected in heart and spleen in an adult Wuzhishan pig.
6. The results revealed HUMMLC2B expression variation in a waveform manner in the skeletal muscle of both Chinese Tongcheng and Western Landrace pig breeds at days 33, 65 and 90 post coitum (p.c). After birth, the expression levels of HUMMLC2B were also found to decrease gradually with age. Our spatial expression analysis showed that HUMMLC2B was highly expressed in the semitendinosus, gastroenemius, biceps femoris and longissimus dorsi muscles. In contrast, only low levels of expression of this gene were evident in fat, and no expression was detectable in brain, heart, kidney, lung, liver, lymph node, spleen, stomach, or in either the large or small intestine.
7. Construction of GFP-fused HUMMLC2B expression vector was transfected into PK15 cells, and the fluorescence mapping result using confocal microcopy showed that the protein was distributed throughout the whole cell containing cytoplasm and nucleus.
8. Single nucleotide polymorphisms (SNPs) in the CA3 and HUMMLC2B genes were detected. It was demonstrated that the CA3 gene included two SNPs for PCR-RFLP (BsuRI-PCR and HinfI-PCR), which were respectively located in the 5th and 6th introns. The HUMMLC2B gene contained four PCR-RFLP sites (two Hin1I-PCR, MspI-PCR and BglI-PCR), which were respectively located in the 3 th intron, 4th exons and 5th introns (for the last two sites) among twenty-three potential polymorphism sites following screening the HUMMLC2B genome DNA sequence. Additional four SNPs, which were respectively located in the 6th intron (two SNPs) and the 7th exon (two SNPs), were detected using denaturing high performance liquid chromatography (DHPLC).
9. Genotypes and allele frequencies of these above six PCR-RFLP sites of the CA3 and HUMMLC2B genes were determined in five Chinese pig breeds, Wuzhishan pigs, Xiang pigs, Bama xiang pigs, Tongcheng pigs and Laiwu pigs, and three introduced pig breeds, Landrace, Yorkshire and Duroc.
10. Associations were analyzed between genotypes of these above polymorphisms of the CA3 and HUMMLC2B genes and phenotypes of economic traits in the experimental population constructed by the cooperation of our lab and animal husbandry bureau of Tongcheng county, which consisted of Tongcheng, Large White, Landrace and and a further pair of three-cross breeds, Landrace×(Large White×Tongcheng) and Large White×(Landrace×Tongcheng). The results were as follows:①For the CA3 gene, highly significant associations in the G8607A site was detected between genotypes with intramuscular fat content (P＜0.01) and significant association between genotypes with percentage of ham (P＜0.05); In the G8371A site, there were highly significant association between the GG genotype of pigs with intramuscular fat content and marbling score and that of the GA genotype (P＜0.01), and significant association with average backfat thickness (P＜0.05).②For the HUMMLC2B gene, no significant association in the G1094A and T1513C sites was detected between genotypes and traits; In the G1876A site, there was significant association between the GG genotype of pigs with dressing percent and meat color and that of the GA genotype (P＜0.05); In the T2005G site, there was significant association between the GG genotype of pigs with meat color and that of the TG genotype (P＜0.05), and between the TT genotype of pigs with total erythrocytes (RBC), hematocrit (HCT) and red cell distribution width and that of the TG genotype (P＜0.05).
本文从猪55天胚胎骨骼肌cDNA文库中筛选出15个功能基因，通过功能分析选出CA3和HUMMLC2B基因作进一步研究，并取得了如下结果：
1．通过猪55天胚胎骨骼肌cDNA文库测序并结合猪EST数据库的信息分离出15个猪基因，即K-ALPHA-1、TUBB、MAPRE1、TUBA3、ATP6VOE、RPL6、RPL7、RPL10、HUMMLC2B、BNIP3L、NHP2L1、CA3、CCNT2、PC4和FLJ30294，并分析其cDNA及预测的蛋白质序列(CCNT2和FLJ30294除外)。
2．在猪×仓鼠辐射杂种板中对上述所分离的基因进行染色体定位(HUMMLC2B除外)，定位结果如下：K-ALPHA-1定位于SSC5p，TUBB定位于SSC7p11，TUBA3定位于SSC5p11-p15，MAPRE1定位于SSC17q21-23，RPL6定位于SSC14q22-24，RPL7定位于SSC4q11-14，RPL10定位于SSCXq26，ATP6VOE定位于SSC16q，BNIP3L定位于SSC14q21-22，CCNT2定位于SSC15q12-14，NHP2L1定位于SSC5p12-15，FLJ30294定位于SSC3q11-14，PC4定位于SSC16q11-14，CA3定位于SSC4q11-q14，同时用猪×啮齿类体细胞杂种板对CA3基因进行了区域定位(SSC4q11-q14)。
3．对于CA3基因，通过猪cDNA文库测序和猪ESTs序列拼接分别获得了两个长短不同的cDNA序列，命为CA3b和CA3a，序列分析显示CA3b与CA3a之间存在一gap，预测的蛋白质显示CA3b缺少CA3a的C末端(78aa)。并且荧光共聚焦显微镜的观察结果显示GFP融合的CA3a蛋白位于整个细胞中，而CA3b仅位于细胞质中。
4．获得了猪CA3和HUMMLC2B基因的全长基因组DNA序列，并分析了其基因组结构。结果显示CA3基因是由7个外显子和6内含子组成(相对CA3a的cDNA序列)，约10.5kb。HUMMLC2B基因是由7个外显子和6个内含子组成，约2.9kb，包含多个重复序列。两个基因所有内含子和外显子的拼接位点都符合GT-AG规则。
5．为了研究猪候选基因在骨骼肌发育中可能的作用，应用实时荧光定量PCR技术对候选基因进行了时空表达谱分析。结果显示，CA3基因在通城猪胚胎33天骨骼肌中表达量最低，65天达到最高，然后下降到一定程度并和出生后的表达量保持相对稳定的水平。而在大白猪胚胎骨骼肌中的表达模式和通城猪不同，即在33天表达量最低，但在65天和90天表达量没有明显差异。组织表达谱显示CA3在骨骼肌和肝脏中表达量最高，在肺脏、淋巴结、胃、大肠和小肠中表达量较低，而在心脏和脾脏中没有检测到表达。
6．而HUMMLC2B基因在通城猪胚胎骨骼肌中的表达模式和长白猪相似(胚胎33天、65天、90天)，但在通城猪出生后随年龄的增加其表达量不断降低(出生后2天、28天和成年)。组织表达谱分析显示HUMMLC2B基因仅在所有被检测的骨骼肌中表达，并且表达量较高，而其它组织中除脂肪中有极少量的表达外，都没有检测到表达。
7．亚细胞定位结果显示GFP融合的HUMMLC2B蛋白位于整个细胞中。
8．SNPs的检测结果证实CA3基因有两个可用于PCR-RFLP的SNPs位点，即BsuRI-PCR和Hinfl-PCR，分别位于第五和第六内含子中。而HUMMLC2B基因有23个潜在的SNPs，其中可用于PCR-RFLP的四个SNPs位点，即HinlI-PCR(两个)，MspI-PCR和BglI-PCR，分别位于第三内含子，第四外显子和第五内含子中(MspI-PCR和BglI-PCR位点)；另外四个SNPs位点用DHPLC技术检测，两个SNPs位于第六内含子中，两个SNPs位于第七外显子中。
9．对上述PCR—RFLP多态位点在五指山猪、香猪、巴马香猪三个小型猪品种以及莱芜猪、通城猪、大白猪、长白猪和杜洛克中分析基因型和等位基因频率以及各等位基因在不同猪品种中的分布差异。
10．在我室与通城县畜牧局合作组建的试验群体中(三个纯繁群：通城猪、大白和长白猪及两个三元杂交群：长大通和大长通)，分析猪CA3和HUMMLC2B基因的多态与部分经济性状的关联。结果显示：①对于CA3基因，G8603A位点多态与肌内脂肪含量呈极显著相关(P＜0.01)，且与腿臀比率呈显著相关(P＜0.05)；G8371A位点GG基因型个体与GA基因型个体间大理石纹和肌内脂肪含量差异极显著(P＜0.01)，而与三点平均背膘厚差异显著(P＜0.05)。②对于HUMMLC2B基因，G1094A和T1513C位点没有检测到与性状的关联；G1876A位点GG基因型个体和GA基因型个体间屠宰率和肉色差异显著(P＜0.05)；T2005G位点GG基因型个体与TG基因型个体肉色差异显著(P＜0.05)，且TT基因型个体和TG基因型个体间红细胞数(RBC)、红细胞压积(HCT)、红细胞分布密度(RDW)差异显著(P＜0.05)。
With the development of porcine genomic studies, many genes associated with pig production traits have been identified, however, additional genes need be identified and further characterized. Moreover, the number of porcine muscle fibers, fixed at birth, is an important factor affecting animal meat quality and quantity, which positive associations exist between muscle fiber number and average daily gain and growth rate. Therefore, it will be necessary for isolation and identification of these genes associated with econimic traits from the fetal cDNA library of porcine skeletal muscle.In this present study, porcine 15 genes were isolated from skeletal muscle cDNA library of pig day-55 embryos, and CA3 and HUMMLC2B genes were choosen for further analyses of the potential functions. These main results were as follows:1. Combining sequencing of the cDNA library and porcine EST data, porcine 15 genes were isolated and identified, and these genes were: K-ALPHA-J, TUBB, MAPRE1, TUBA3, ATP6VOE, RPL6, RPL7, RPL10, HUMMLC2B, BNIP3L, NHP2L1, CA3, CCNT2, PC4 and FLJ30294. Sequences of cDNA and predicted proteins of these genes (except for CCNT2 and FLJ30294) were further analyzed.2. These above genes (except for HUMMLC2B) were assigned in pig×hamster hybrids panel, and the results were followed: K-ALPHA-1: SSC5p, TUBB: SSC7p11, MAPRE1: SSC17q21-23, TUBA3: SSC5p11-pl5, RPL6: SSC14q22-24, RPL7: SSC4q11-14, RPL10: SSCXq26, ATP6VOE: SSC16q, BNIP3L: SSC14q21-22, CCNT2: SSC15q12-14, NHP2L1: SSC5pl2-15, FLJ30294: SSC3q11-14, PC4: SSC16q11-14 and CA3: SSC4q11-q14. CA3 was further mapped using porcine somatic cell hybrid panel.3. To the CA3 gene, two different cDNA sequences (namely CA3b and CA3a) were obtained by sequencing of the cDNA library and e-PCR of porcine ESTs sequences, respectively. A gap was shown between the cDNA sequences of CA3b and CA3a by sequence comparison, and the predicted proteins showed that CA3b was the absence of 78 amino acids in the C-terminal domain of CA3a. The fluorescence mapping result using confocal microcopy showed the GFP-fused CA3a protein was distributed throughout the whole cell, but the GFP-fused CA3b protein was only distributed in cytoplasm.4. The full-length DNA sequences of the CA3 and HUMMLC2B genes were obtained and the genomic structures were analyzed. It was identified that the CA3 gene comprised 7 exons and 6 introns (for the cDNA sequence of CA3a), which spaned about 10.5 kb. The HUMMLC2B gene comprised 7 exons and 6 introns, which spaned about 2.9kb. All splice sites of exon/intron of the two genes conformed to the GT/AG rule.
5. In order to study potential functions of target genes, temporal and spatial expression profiles were analyzed using real-time PCR. It was demonstrated that the expression levels of CA3 increased from prenatal 33-day-old to 65-day-old skeletal muscle in Tongcheng pigs. These levels subsequently decreased to similar levels as those seen in prenatal 90-day-old pigs, as well as those in postnatal 2-day-old, 28-day-old, and adult pigs, but the expression patterns of Chinese Tongcheng pig embryos were different from that of Landrace pig embryos. CA3 was expressed at higher levels in skeletal muscle and liver than lung, lymph node, large and small intestine, but was not detected in heart and spleen in an adult Wuzhishan pig.
6. The results revealed HUMMLC2B expression variation in a waveform manner in the skeletal muscle of both Chinese Tongcheng and Western Landrace pig breeds at days 33, 65 and 90 post coitum (p.c). After birth, the expression levels of HUMMLC2B were also found to decrease gradually with age. Our spatial expression analysis showed that HUMMLC2B was highly expressed in the semitendinosus, gastroenemius, biceps femoris and longissimus dorsi muscles. In contrast, only low levels of expression of this gene were evident in fat, and no expression was detectable in brain, heart, kidney, lung, liver, lymph node, spleen, stomach, or in either the large or small intestine.
7. Construction of GFP-fused HUMMLC2B expression vector was transfected into PK15 cells, and the fluorescence mapping result using confocal microcopy showed that the protein was distributed throughout the whole cell containing cytoplasm and nucleus.
8. Single nucleotide polymorphisms (SNPs) in the CA3 and HUMMLC2B genes were detected. It was demonstrated that the CA3 gene included two SNPs for PCR-RFLP (BsuRI-PCR and HinfI-PCR), which were respectively located in the 5th and 6th introns. The HUMMLC2B gene contained four PCR-RFLP sites (two Hin1I-PCR, MspI-PCR and BglI-PCR), which were respectively located in the 3 th intron, 4th exons and 5th introns (for the last two sites) among twenty-three potential polymorphism sites following screening the HUMMLC2B genome DNA sequence. Additional four SNPs, which were respectively located in the 6th intron (two SNPs) and the 7th exon (two SNPs), were detected using denaturing high performance liquid chromatography (DHPLC).
9. Genotypes and allele frequencies of these above six PCR-RFLP sites of the CA3 and HUMMLC2B genes were determined in five Chinese pig breeds, Wuzhishan pigs, Xiang pigs, Bama xiang pigs, Tongcheng pigs and Laiwu pigs, and three introduced pig breeds, Landrace, Yorkshire and Duroc.
10. Associations were analyzed between genotypes of these above polymorphisms of the CA3 and HUMMLC2B genes and phenotypes of economic traits in the experimental population constructed by the cooperation of our lab and animal husbandry bureau of Tongcheng county, which consisted of Tongcheng, Large White, Landrace and and a further pair of three-cross breeds, Landrace×(Large White×Tongcheng) and Large White×(Landrace×Tongcheng). The results were as follows:①For the CA3 gene, highly significant associations in the G8607A site was detected between genotypes with intramuscular fat content (P＜0.01) and significant association between genotypes with percentage of ham (P＜0.05); In the G8371A site, there were highly significant association between the GG genotype of pigs with intramuscular fat content and marbling score and that of the GA genotype (P＜0.01), and significant association with average backfat thickness (P＜0.05).②For the HUMMLC2B gene, no significant association in the G1094A and T1513C sites was detected between genotypes and traits; In the G1876A site, there was significant association between the GG genotype of pigs with dressing percent and meat color and that of the GA genotype (P＜0.05); In the T2005G site, there was significant association between the GG genotype of pigs with meat color and that of the TG genotype (P＜0.05), and between the TT genotype of pigs with total erythrocytes (RBC), hematocrit (HCT) and red cell distribution width and that of the TG genotype (P＜0.05).
引文
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