猪胚胎期五个基因的分离、印记鉴定及甲基化分析
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摘要
印记基因是指来自双亲的两个等位基因的表达具有倾向性,只表达一个亲本的,另一个亲本的不表达或者表达量很低的一类基因。它们对哺乳动物胚胎的生长、发育、胎盘的功能以及繁殖性状等方面起着重要作用。印记基因不但调控一些与质量性状相关的基因的表达,而且还影响许多数量性状的表型方差和表型值。全基因组扫描发现许多QTLs是父本或者母本印记的,它们与生长、背膘厚、胴体组成和繁殖性状相关。与人和鼠中印记基因的研究相比,在猪中对印记的研究很少。因此,在猪中鉴定新的印记基因非常重要,这不但可以完善家畜中印记基因的研究,而且可以加强基因组印记在不同物种中的比较基因组学分析。
本研究利用RT-PCR-RFLP和直接测序的方法,鉴定了5个基因在妊娠30天、65天和100天胚胎中的印记状态。运用RCR-RFLP,检测了4个基因的SNP,以及其在不同品种中的等位基因频率,并且将这些多态位点与大白猪和梅山猪交配的F2代群体的胴体性状和肉质性状进行了关联分析。运用荧光定量和半定量RT-PCR的方法分析了目的基因的组织表达情况。获得4个基因的启动子序列,并对其中2个基因的启动子活性进行分析,且分析了其CpG岛的甲基化情况,具体结果如下：
1.分离克隆了猪DIO3、RTL1、DIRAS3和COPG2基因,都包含完整的开放阅读框(ORF),预测的氨基酸序列与人和鼠具有很高的相似性。
2.利用RT-PCR-RFLP和PCR直接测序的方法,在大白猪与梅山猪正反交产生的30 d、65 d和100 d胚胎中检测了DIO3、RTL1、NNAT、DIRAS3和COPG2基因的印记状态：DIO3、RTL1和DIRAS3基因在30 d胚胎、65 d和100 d胚胎的心脏、肝脏、脾脏、肺脏、肾脏、胃、小肠、肌肉、脑和胎盘组织都表现为父本表达；NNAT基因在65 d和100 d胚胎的脾脏组织中为双表达,其余组中都是父本表达；COPG2基因在各个阶段都是双表达的。
3.用荧光定量PCR方法检测了DIO3基因在二月龄大白母猪不同组织中的表达情况,在脂肪组织中表达量最高。用半定量RT-PCR的方法检测了RTL1基因在大白猪65d胚胎的13个组织中的表达情况,在小肠、股二头肌和半腱肌中表达量较高；利用用荧光定量PCR的方法检测其在两个猪种(梅山猪和大白猪)的4个发育阶段(胚胎60 d,出生后35,60和120天)的三种类型的肌肉(背最长肌、股二头肌和半腱肌)中的表达情况；并且用半定量RT-PCR的方法检测了其随着C2C12细胞分化的表达量降低。检测到猪COPG2基因存在五个不同的转录本,分别命名为COPG2-1、CDPG2-2、COPG2-3、CDPG2-4和COPG2-5,利用半定量RT-PCR的方法分析了不同转录本在猪胚胎期65 d和出生后二月龄各10个组织中的表达情况。
4.利用数据库中已有序列,设计引物PCR扩增获得了猪RTL1、NNAT和DIRAS3基因的启动子序列,利用基因组步移的方法获得了猪LCAT基因的启动子序列。发现RTL1和NNAT基因启动子区存在许多与肌肉发育相关的转录因子结合位点,如MyoD、YY1及NF-kappaB等,并且双荧光素酶报告基因系统检测了RTL1和NNAT基因的启动子活性。对RTL1和NNAT基因的启动子区的CpG岛进行了预测,并且用亚硫酸氢盐测序法对其甲基化状态进行了分析,初步推测NNAT基因的启动子区的两个CpG岛可能是差异甲基化区。
5.利用PCR-RFLP技术,对DIO3、RTL1、NNAT和CoPG2基因中的SNP位点在不同品种猪中进行了基因分型,并在大白猪和梅山杂交产生的F2代群体中进行了性状关联分析。结果表明(1)DIO3基因外显子A687C位点与瘦肥肉比率、肥肉率、瘦肉率、板油重、肩部膘厚、6-7腰椎间膘厚、臀部膘厚、眼肌面积、背最长肌含水量、背最长肌失水率、背最长肌系水力、背最长肌肌肉色值、股二头肌肌肉色值、背最长肌大理石纹、股二头肌大理石纹呈显著相关(P<0.05),与肌内脂肪含量呈极显著相关(P<0.01);(2)RTL1基因外显子G1209A位点与皮率、内脂率、6-7腰椎间膘厚、胸腰椎间膘厚、背最长肌pH、股二头肌肌肉色值呈显著相关(P<0.05),与骨率、肩部膘厚、臀部膘厚、平均背膘厚、背最长肌失水率、背最长肌系水力、背最长肌肌肉色值呈极显著相关(P<0.01);RTL1基因外显子A3929G位点与内脂率、肩部膘厚、眼肌高、眼肌面积、背最长肌含水量、背最长肌肌肉色值、背最长肌肌内脂肪量显著相关(P<0.05),与皮率、背最长肌失水率、背最长肌系水力、股二头肌肌肉色值呈极显著相关(P<0.01);(3)NNAT基因启动子A-107G位点与眼肌高、眼肌宽、眼肌面积、背最长肌含水量、背最长肌大理石纹、股二头肌大理石纹呈显著相关(P<0.05);CDPG2基因3'UTR区G/A突变与肥肉率、胸腰椎间膘厚、臀部膘厚、平均背膘厚、背最长肌pH、股二头肌pH、头半棘肌pH显著相关(P<0.05)
Imprinted genes are the genes whose expression is dependent on parental origin that is only one allele from the father or mother is expressed and the other allele is not expressed or lowly expressed. In mammals, they play an essential role in the regulation of fetal growth, development, placental function and reproduction traits. They not only control the gene expression related to quality traits, but also affect the phenotypic variance of many quantitative traits and the phenotypic values. Studies of genome-wide scanning for QTL revealed that many QTLs are maternally or paternally imprinted, which significantly affect growth, backfat thickness, carcass composition and reproduction. However, comparing to the extensive research of imprinting in human and mouse, there is still a dearth of knowledge about imprinting in swine. Therefore, the identification of new imprinted genes in swine is very important, not only for completing the imprinting study in livestock but also for the comparative genomic analysis of genomic imprinting among different species.
In this study, the RT-PCR-RFLP method were used to detect the imprinting status of five porcine gene at developmental stages of day 30,65 and 100 of gestation. Using PCR-RFLP, we detected SNPs of four genes in different pig breeds and performed associations with carcass and meat quality traits in Large White and Meishan F2 hybrids. Using Real-time PCR and semi-quantitative RT-PCR, we analysed the tissue expression of candidate genes. We obtained promoter sequences of four genes, and analysed the promoter activity of two genes.in addition, we analyzed the methylation status of CpG islands. The main results are as follows:
1. We isolated and cloned the porcine DIO3、RTL1、DIRAS3 and COPG2 genes, which all contain the complete open reading frame (ORF), the deduced amino acid sequences have high similarity with human and mouse.
2. The reciprocal Yorkshire×Meishan F1 hybrid model and the RT-PCR-RFLP method were used to detect the imprinting status of porcine DIO3, RTL1, NNAT, DIRAS3 and COPG2 genes at the developmental stages of day 30,65 and 100 of gestation. Porcine DIO3, RTL1 and DIRAS3 genes were paternally expressed in day 30 fetuses, day 65 and day 100 fetal tissues, including heart, liver, spleen, lung, kidney, stomach, small intestine, skeletal muscle, brain and placenta; NNAT gene escapes imprinting in the day 65 and day 100 fetal spleen, but paternally expressed in the other tissues; COPG2 gene was not imprinted in all developmental stages.
3. We detected the tissue expression profile of DIO3 gene in the two month Yorkshire sow by Real-time PCR, and found that it high expressed in adipose tissue. Semi-quantitative RT-PCR analysis was performed to detect the relative mRNA expression profile of RTL1 gene in 13 different tissuses, which were collected from day 65 fetuses of Yorkshire, the result showed that the RTL1 gene was expressed at a high leveal in the small intestine, biceps femoris and semitendinosus. we used the real-time PCR technique to examine the mRNA expression in two pig breeds (Yorkshire and Meishan) at four stages (fetal 60 days and postnatal 35,60 and 120 days) and three types of muscles (longissimus dorsi muscle, LD; biceps femoris, BF; semitendinosus,ST). Moreover, we found the expression of RTL1 was reduced as the differentiation of C2C12 cells. Five different transcripts were detected in COPG2 gene, named COPG2-1, COPG2-2, COPG2-3, COPG2-4 and COPG2-5 respectively. The expression level of different COPG2 isoforms in different ten tissues of two develepent stages (fetal 65 days and postnatal 60 days) were detected by semi-quantitative RT-PCR.
4. According to the sequences of database, PCR primers were designed to amplify the promoter sequences of porcine RTL1, NNAT and DIRAS3 gene. The promoter regions of porcine LCAT gene were obtained by genomics walking. Several binding sites for MyoD、YY1 and NF-kappaB which are involved in muscle development were observed in RTL1 and NNAT promoter regions. In addition, we analyzed the promoter activety by dual luciferase reporter system. Using the bioinformatics software, we predicted the CpG islands in the RTL1 and NNAT promoter regions, and analyzed the methylation of the CpG islands by Bisulfite Sequencing PCR. We speculated that the two CpG islands in NNAT gene promoter region maybe the differentially methylated region.
5. Using PCR-RFLP, we detected SNPs of DIO3, RTL1, NNAT and COPG2 genes in different pig breeds and performed associations with carcass and meat quality traits in Large White and Meishan F2 hybrids. The results showed:(1) DIO3, A687C-Acy I-RFLP is significant association with ratio of lean to fat (RLF), fat meat percentage (FMP), lean meat percentage (LMP), shoulder fat thickness (SFT),6-7th rib fat thickness (RFT), buttock fat thickness (BFT), loin eye area (LEA), longissimus dorsi drip loss rate (LD DLR), longissimus dorsi water holding capacity (LD WHC), Water Moisture (m. longissimus Dorsi, LD) (WM), meat color value (LD), meat color value (BF), meat marbling (LD) and meat marbling (BF) (P<0.05), is higher significant association with intramuscular fat (LD) (P<0.01); (2) RTL1,G1209A-Sat I-RFLP is significant association with skin percentage (SP), internal fat rate (IFR),6-7 rib fat thickness (RFT), thorax-waist fat thickness (TFT), Meat pH (m.longissimus Dorsi, LD) and meat color value (BF) (P<0.05), is higher significant association with bone percentage (BP), shoulder fat thickness (SFT), buttock fat thickness (BFT), average backfat thickness (ABT), longissimus dorsi drip loss rate (LD DLR), longissimus dorsi water holding capacity (LD WHC) and meat color value (LD) (P<0.01); RTL1, A3929G-Van91 I-RFLP is significant association with internal fat rate (IFR), shoulder fat thickness (SFT), loin eye height (LEH), loin eye area (LEA), Water Moisture (m.longissimus Dorsi, LD) (WM), meat color value (LD) and intramuscular fat (LD) (P<0.05), is higher significant association with skin percentage (SP), longissimus dorsi drip loss rate (LD DLR), longissimus dorsi water holding capacity (LD WHC) meat color value (BF) (P<0.01); (3) A-107G in the promoter of NNAT gene is significant association with loin eye height (LEH), Loin Eye width (LEW), loin eye area (LEA), Water Moisture (m.longissimus Dorsi, LD) (WM), meat marbling (LD) and meat marbling (BF) (P<0.05); (4) G/A polymorphism in the 3'UTR of COPG2 is significant association with fat percentage (FP), thorax-waist fat thickness (TFT), buttock fat thickness (BFT), average backfat thickness (ABT), Meat pH (m.longissimus Dorsi, LD), Meat pH (m.Biceps Femoris, BF) and Meat pH (m.Semispinalis Capitis, SC) (P<0.05).
本研究利用RT-PCR-RFLP和直接测序的方法,鉴定了5个基因在妊娠30天、65天和100天胚胎中的印记状态。运用RCR-RFLP,检测了4个基因的SNP,以及其在不同品种中的等位基因频率,并且将这些多态位点与大白猪和梅山猪交配的F2代群体的胴体性状和肉质性状进行了关联分析。运用荧光定量和半定量RT-PCR的方法分析了目的基因的组织表达情况。获得4个基因的启动子序列,并对其中2个基因的启动子活性进行分析,且分析了其CpG岛的甲基化情况,具体结果如下：
1.分离克隆了猪DIO3、RTL1、DIRAS3和COPG2基因,都包含完整的开放阅读框(ORF),预测的氨基酸序列与人和鼠具有很高的相似性。
2.利用RT-PCR-RFLP和PCR直接测序的方法,在大白猪与梅山猪正反交产生的30 d、65 d和100 d胚胎中检测了DIO3、RTL1、NNAT、DIRAS3和COPG2基因的印记状态：DIO3、RTL1和DIRAS3基因在30 d胚胎、65 d和100 d胚胎的心脏、肝脏、脾脏、肺脏、肾脏、胃、小肠、肌肉、脑和胎盘组织都表现为父本表达；NNAT基因在65 d和100 d胚胎的脾脏组织中为双表达,其余组中都是父本表达；COPG2基因在各个阶段都是双表达的。
3.用荧光定量PCR方法检测了DIO3基因在二月龄大白母猪不同组织中的表达情况,在脂肪组织中表达量最高。用半定量RT-PCR的方法检测了RTL1基因在大白猪65d胚胎的13个组织中的表达情况,在小肠、股二头肌和半腱肌中表达量较高；利用用荧光定量PCR的方法检测其在两个猪种(梅山猪和大白猪)的4个发育阶段(胚胎60 d,出生后35,60和120天)的三种类型的肌肉(背最长肌、股二头肌和半腱肌)中的表达情况；并且用半定量RT-PCR的方法检测了其随着C2C12细胞分化的表达量降低。检测到猪COPG2基因存在五个不同的转录本,分别命名为COPG2-1、CDPG2-2、COPG2-3、CDPG2-4和COPG2-5,利用半定量RT-PCR的方法分析了不同转录本在猪胚胎期65 d和出生后二月龄各10个组织中的表达情况。
4.利用数据库中已有序列,设计引物PCR扩增获得了猪RTL1、NNAT和DIRAS3基因的启动子序列,利用基因组步移的方法获得了猪LCAT基因的启动子序列。发现RTL1和NNAT基因启动子区存在许多与肌肉发育相关的转录因子结合位点,如MyoD、YY1及NF-kappaB等,并且双荧光素酶报告基因系统检测了RTL1和NNAT基因的启动子活性。对RTL1和NNAT基因的启动子区的CpG岛进行了预测,并且用亚硫酸氢盐测序法对其甲基化状态进行了分析,初步推测NNAT基因的启动子区的两个CpG岛可能是差异甲基化区。
5.利用PCR-RFLP技术,对DIO3、RTL1、NNAT和CoPG2基因中的SNP位点在不同品种猪中进行了基因分型,并在大白猪和梅山杂交产生的F2代群体中进行了性状关联分析。结果表明(1)DIO3基因外显子A687C位点与瘦肥肉比率、肥肉率、瘦肉率、板油重、肩部膘厚、6-7腰椎间膘厚、臀部膘厚、眼肌面积、背最长肌含水量、背最长肌失水率、背最长肌系水力、背最长肌肌肉色值、股二头肌肌肉色值、背最长肌大理石纹、股二头肌大理石纹呈显著相关(P<0.05),与肌内脂肪含量呈极显著相关(P<0.01);(2)RTL1基因外显子G1209A位点与皮率、内脂率、6-7腰椎间膘厚、胸腰椎间膘厚、背最长肌pH、股二头肌肌肉色值呈显著相关(P<0.05),与骨率、肩部膘厚、臀部膘厚、平均背膘厚、背最长肌失水率、背最长肌系水力、背最长肌肌肉色值呈极显著相关(P<0.01);RTL1基因外显子A3929G位点与内脂率、肩部膘厚、眼肌高、眼肌面积、背最长肌含水量、背最长肌肌肉色值、背最长肌肌内脂肪量显著相关(P<0.05),与皮率、背最长肌失水率、背最长肌系水力、股二头肌肌肉色值呈极显著相关(P<0.01);(3)NNAT基因启动子A-107G位点与眼肌高、眼肌宽、眼肌面积、背最长肌含水量、背最长肌大理石纹、股二头肌大理石纹呈显著相关(P<0.05);CDPG2基因3'UTR区G/A突变与肥肉率、胸腰椎间膘厚、臀部膘厚、平均背膘厚、背最长肌pH、股二头肌pH、头半棘肌pH显著相关(P<0.05)
Imprinted genes are the genes whose expression is dependent on parental origin that is only one allele from the father or mother is expressed and the other allele is not expressed or lowly expressed. In mammals, they play an essential role in the regulation of fetal growth, development, placental function and reproduction traits. They not only control the gene expression related to quality traits, but also affect the phenotypic variance of many quantitative traits and the phenotypic values. Studies of genome-wide scanning for QTL revealed that many QTLs are maternally or paternally imprinted, which significantly affect growth, backfat thickness, carcass composition and reproduction. However, comparing to the extensive research of imprinting in human and mouse, there is still a dearth of knowledge about imprinting in swine. Therefore, the identification of new imprinted genes in swine is very important, not only for completing the imprinting study in livestock but also for the comparative genomic analysis of genomic imprinting among different species.
In this study, the RT-PCR-RFLP method were used to detect the imprinting status of five porcine gene at developmental stages of day 30,65 and 100 of gestation. Using PCR-RFLP, we detected SNPs of four genes in different pig breeds and performed associations with carcass and meat quality traits in Large White and Meishan F2 hybrids. Using Real-time PCR and semi-quantitative RT-PCR, we analysed the tissue expression of candidate genes. We obtained promoter sequences of four genes, and analysed the promoter activity of two genes.in addition, we analyzed the methylation status of CpG islands. The main results are as follows:
1. We isolated and cloned the porcine DIO3、RTL1、DIRAS3 and COPG2 genes, which all contain the complete open reading frame (ORF), the deduced amino acid sequences have high similarity with human and mouse.
2. The reciprocal Yorkshire×Meishan F1 hybrid model and the RT-PCR-RFLP method were used to detect the imprinting status of porcine DIO3, RTL1, NNAT, DIRAS3 and COPG2 genes at the developmental stages of day 30,65 and 100 of gestation. Porcine DIO3, RTL1 and DIRAS3 genes were paternally expressed in day 30 fetuses, day 65 and day 100 fetal tissues, including heart, liver, spleen, lung, kidney, stomach, small intestine, skeletal muscle, brain and placenta; NNAT gene escapes imprinting in the day 65 and day 100 fetal spleen, but paternally expressed in the other tissues; COPG2 gene was not imprinted in all developmental stages.
3. We detected the tissue expression profile of DIO3 gene in the two month Yorkshire sow by Real-time PCR, and found that it high expressed in adipose tissue. Semi-quantitative RT-PCR analysis was performed to detect the relative mRNA expression profile of RTL1 gene in 13 different tissuses, which were collected from day 65 fetuses of Yorkshire, the result showed that the RTL1 gene was expressed at a high leveal in the small intestine, biceps femoris and semitendinosus. we used the real-time PCR technique to examine the mRNA expression in two pig breeds (Yorkshire and Meishan) at four stages (fetal 60 days and postnatal 35,60 and 120 days) and three types of muscles (longissimus dorsi muscle, LD; biceps femoris, BF; semitendinosus,ST). Moreover, we found the expression of RTL1 was reduced as the differentiation of C2C12 cells. Five different transcripts were detected in COPG2 gene, named COPG2-1, COPG2-2, COPG2-3, COPG2-4 and COPG2-5 respectively. The expression level of different COPG2 isoforms in different ten tissues of two develepent stages (fetal 65 days and postnatal 60 days) were detected by semi-quantitative RT-PCR.
4. According to the sequences of database, PCR primers were designed to amplify the promoter sequences of porcine RTL1, NNAT and DIRAS3 gene. The promoter regions of porcine LCAT gene were obtained by genomics walking. Several binding sites for MyoD、YY1 and NF-kappaB which are involved in muscle development were observed in RTL1 and NNAT promoter regions. In addition, we analyzed the promoter activety by dual luciferase reporter system. Using the bioinformatics software, we predicted the CpG islands in the RTL1 and NNAT promoter regions, and analyzed the methylation of the CpG islands by Bisulfite Sequencing PCR. We speculated that the two CpG islands in NNAT gene promoter region maybe the differentially methylated region.
5. Using PCR-RFLP, we detected SNPs of DIO3, RTL1, NNAT and COPG2 genes in different pig breeds and performed associations with carcass and meat quality traits in Large White and Meishan F2 hybrids. The results showed:(1) DIO3, A687C-Acy I-RFLP is significant association with ratio of lean to fat (RLF), fat meat percentage (FMP), lean meat percentage (LMP), shoulder fat thickness (SFT),6-7th rib fat thickness (RFT), buttock fat thickness (BFT), loin eye area (LEA), longissimus dorsi drip loss rate (LD DLR), longissimus dorsi water holding capacity (LD WHC), Water Moisture (m. longissimus Dorsi, LD) (WM), meat color value (LD), meat color value (BF), meat marbling (LD) and meat marbling (BF) (P<0.05), is higher significant association with intramuscular fat (LD) (P<0.01); (2) RTL1,G1209A-Sat I-RFLP is significant association with skin percentage (SP), internal fat rate (IFR),6-7 rib fat thickness (RFT), thorax-waist fat thickness (TFT), Meat pH (m.longissimus Dorsi, LD) and meat color value (BF) (P<0.05), is higher significant association with bone percentage (BP), shoulder fat thickness (SFT), buttock fat thickness (BFT), average backfat thickness (ABT), longissimus dorsi drip loss rate (LD DLR), longissimus dorsi water holding capacity (LD WHC) and meat color value (LD) (P<0.01); RTL1, A3929G-Van91 I-RFLP is significant association with internal fat rate (IFR), shoulder fat thickness (SFT), loin eye height (LEH), loin eye area (LEA), Water Moisture (m.longissimus Dorsi, LD) (WM), meat color value (LD) and intramuscular fat (LD) (P<0.05), is higher significant association with skin percentage (SP), longissimus dorsi drip loss rate (LD DLR), longissimus dorsi water holding capacity (LD WHC) meat color value (BF) (P<0.01); (3) A-107G in the promoter of NNAT gene is significant association with loin eye height (LEH), Loin Eye width (LEW), loin eye area (LEA), Water Moisture (m.longissimus Dorsi, LD) (WM), meat marbling (LD) and meat marbling (BF) (P<0.05); (4) G/A polymorphism in the 3'UTR of COPG2 is significant association with fat percentage (FP), thorax-waist fat thickness (TFT), buttock fat thickness (BFT), average backfat thickness (ABT), Meat pH (m.longissimus Dorsi, LD), Meat pH (m.Biceps Femoris, BF) and Meat pH (m.Semispinalis Capitis, SC) (P<0.05).
引文
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