大白猪和二花脸猪妊娠后期胎盘转录谱比较及印记基因鉴定研究
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摘要
中国猪高产仔优良种质特性的遗传机制一直是国内外有关研究人员关心的热点。研究表明,在胚胎着床以前中国梅山猪与大白猪的子宫中胚胎数目没有差异,但怀孕结束后的产仔数却存在显著差异。已经证明这种现象与不同猪种妊娠后期胎盘效率(胎儿与胎盘的重量比)有着一定的关系。在梅山猪的妊娠后期,胎盘血管密度增加,重量不再有明显的变化,而大白猪的胎盘则仍然有一次大幅度的增殖,两者在胎盘效率上出现明显的不同。因此,研究胎盘效率相关候选基因可揭示猪的高产机制并为育种工作提供理论和实践指导。
     印记基因是指父本或母本的等位基因表达而另一等位基因不表达或很少表达的一类基因。对哺乳动物的研究表明,印记基因在胎儿、胎盘的生长发育、母性行为及胎儿出生后的生长等方面发挥着重要的调节作用。另外,胎盘的进化和基因组印记是同时出现的,且大部分的印记基因在胎盘组织高表达且印记。目前,对基因组印记的研究主要集中在人和小鼠中,对家畜特别是猪中的研究很少。因此,在猪胎盘组织中鉴定印记基因对于研究基因组印记在物种间的保守性和印记基因的功能具有重要意义。
     本研究以12头彼此无相关的纯种大白猪和二花脸猪(太湖猪的一个类群)后备母猪为材料,在妊娠75天和90天屠宰后收集胎儿胎盘样品(每品种每阶段3个生物学重复)。每头母猪后代中随机挑选2个雌性胎儿的胎盘,在提取RNA后等量混合与猪Affymetrix芯片杂交,数据校正后应用GLM(SAS)模型进行了差异表达基因筛选,并进一步对差异表达基因进行了基因本体(GO)功能注释、聚类及生物学通路分析。利用采集的胎盘组织,通过RT-PCR-RFLP分析和PCR产物直接测序法检测候选印记基因的SNP表达情况,鉴定了11个候选印记基因在猪胎盘组织中的印记状态。主要结果如下:
     1.通过结合Affymetrix芯片杂交与生物信息及DNA序列比对分析发现芯片上20201个转录本中11849个转录本在胎盘组织中表达;统计发现226个转录本在二花脸猪和大白猪妊娠75天胎盘差异表达,577个转录本在二花脸猪和大白猪妊娠90天胎盘差异表达。
     2.GO(Gene Ontology)分析显示上述差异表达基因主要是参与能量代谢,胎儿胎盘发育,血管发育和免疫相关等生物学过程。聚类分析发现二花脸猪妊娠75天和90天,大白猪妊娠75天和90天分别有着更相近的基因表达模式。
     3.从芯片检测到的不同品种胎盘差异表达基因中选出8个基因(ALDH1A1、DIO3、DIRAS3、PLAGL1、PON2、ASCL2、WIF1和SLC38A4)进行Real-time PCR验证,其中5个为候选印记基因(DIRAS3,PON2,PLAGL1,DIO和ASCL2)。结果显示这些基因表达趋势和芯片结果相吻合。
     4.利用Real-time PCR方法,研究了VEGF通路主要基因(VEGF,VEGFR-1,VEGFR-2,VE-cadherin和β-arrestin2)在二花脸猪和大白猪妊娠75天和90天胎盘的表达情况,发现其中4个基因在品种或时期间存在差异表达。
     5.根据人和小鼠印记基因的印记状况及生理功能,结合本研究芯片检测到的表达情况,筛选了PEG1、PEG3、PEG5、PEG10、GATM、INPP5F、PON2、DCN、PLAGL1、SLC38A4、DIRAS3和ASCL2等12个基因作为猪候选印记基因。利用电子克隆和比较基因组学方法获得了2个候选印记基因(PEG1和GATM)的cDNA序列,均包括完整的开放阅读框。
     6.通过RT-PCR-RFLP分析和直接测序法,鉴定了11个候选印记基因在猪胎盘组织中的印记情况。其中,7个基因(PEG1、PEG3、PEG5、PEG10、PLAGL1、SLC38A4和DIRAS3)在胎盘组织中为印记表达基因,4个基因(PON2、DCN、INPP5F和GATM)在胎盘组织中为双等位基因表达基因(非印记基因)。
     7.利用辐射杂种板对PEG1、PEG3、PEG10、GATM和INPP5F等5个基因进行了染色体精细定位,分别将其定位在SSC18q13-21、6q22—q23、9p13-21、q12-21和14q29区域。
     8.利用PCR-RFLP技术,对PEG1、PEG3、PEG10、GATM和INPP5F基因中的SNP位点在9个品种中进行了基因分型,并对INPP5F基因HincⅡ多态位点在大白猪群中进行了性状关联分析,结果表明该位点多态性与生长性状30-100kg平均日增重和出生至100Kg平均日增重相关。
     9.发现PEG5基因在二花脸和大白猪妊娠75天和90天胎盘组织存在差异表达。扩增获得其启动子序列1722 bp。应用生物信息学方法对它的结构和转录因子结合位点进行了预测,发现了许多CTCF结合位点。对其中一个CpG岛进行了甲基化检测,发现在二花脸和大白妊娠75天和90天胎盘组织中均表现为高甲基化水平。
Chinese indigenous pigs are the most prolific breed of swine in the world.In fact, Large White pigs had no significant difference in number of live embryos with the Meishan pigs between 6-10 days after mating,but had significant lower litter size.One important reason of this phenomenon is associated with the placental efficiency difference in different breeds.During the later gestation stages,the Meishan pigs increased the vascular density,while the Large White pigs have the second increase in the area of placenta instead of vascular density,e.g,the placental efficiency between the two breeds are different.Thus,it is very important to identify molecular machenisms affecting placental efficiency to offer new ideas to improve reproduction traits in the pig.
     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.They play important roles in the fetal and placental development,maternal behavior and the postnatal growth.Most of the imprinted genes are expressed highly and imprinted in the placenta.At present,most studies on genomic imprinting are in human and mouse but little in livestock,especially in the pig.Therefore, it is of interest to identify more imprinted genes in pig placentas for analyzing the conservation of genomic imprinting among different species.
     In this study,twelve Erhualian(sub-population of the Taihu pigs) and Large White pregnant sows were necropsied at two ages respectively(75-and 90-d fetal,3 sows at each stage).The uteruses were removed immediately and the placentas were collected. Two female placentas from each sow were used to extract RNA and then pooled in equal quantity.The RNAs were sent to a commercial service for hybridization to the porcine Affymetrix GeneChip.Normalized data was used to analysis by GLM(SAS) model. Differentially expressed genes were identified and used to do GO(Gene Ontology) analysis,cluster and pathway analysis.Employing the RT-PCR-RFLP and product sequencing,we detected the allelic expression of eleven potential imprinted genes,and determined the imprinting status of these genes in the porcine placenta.The main results are as follows:
     1.The transcriptome analysis indicated that 11,849 probesets were expressed in the placenta;921(p<0.05) transcripts that were differentially expressed between E75 and L75;1145(p<0.05) transcripts that were differentially expressed between E90 and L90.
     2.GO analysis indicated that the proteins encoded by these differentially expressed genes are associated with metabolism,fetal and placental development,blood vessel development and immunity processes.Cluster analysis showed that L75 and L90 were initially clustered together because their expression profiles were similar,E75 and E90 were clustered in another class.
     3.We selected eight genes(ALDH1A1,DIO3,DIRAS3,PLAGL1,PON2,ASCL2,WIF1 and SLC38A4) to confirm the microarray data using real-time RT-PCR.Among these genes,DIRAS3,PON2,PLAGL1,DIO and ASCL2 genes are candidate imprinted genes.The results indicated that the expression patterns of eight genes are consistent with the microarray data.
     4.Employing the Real-time PCR,we identified the expression of genes of VEGF pathway(VEGF,VEGFR-1,VEGFR-2,VE-cadherin andβ-arrestin 2) in E75,L75, E90 and L90.The results indicated that four genes(VEGFR-1,VEGFR-2, VE-cadherin andβ-arrestin 2) are differentially expressed in placentas between breeds.
     5.We chose PEG1,PEG3,PEG5,PEG10,GATM,INPP5F,PON2,DCN,PLAGL1, SLC38A4,DIRAS3 and ASCL2 genes as candidate imprinted genes in pigs according to the imprinting status in human and mouse and their biological functions.We obtained the complete open reading frame(ORF) of PEG1 and GATM genes with electronic cloning and sequencing.
     6.Using the RT-PCR-RFLP and sequencing,we detected the imprinting status of eleven genes in the porcine placentas.Seven genes(PEG1、PEG3、PEG5、PEG10、PLAGL1、SLC38A4 and DIRAS3) were imprinted and four genes(PON2,DCN,INPP5F and GATM) were not imprinted in the placenta.
     7.Using RH panel,we assigned PEG1,PEG3,PEG10,GATM and INPP5F genes to porcine 18q13-21,6q22-q23,9p13-21,1q12-21 and 14q29.
     8.Using PCR-RFLP,we detected the allele frequencies of five SNPs in PEG1、PEG3、PEGIO,GATM and INPP5F genes among different populations.The different genotypes of HincⅡ-RFLP for INPP5F gene showed significant difference on the ADG from birth to 100Kg and ADG from 30 to 100Kg in the Large White pigs.
     9.Using Real-time PCR,we found that PEG5 gene is differentially expressed between E75 and L75,E90 and L90.The 1722 bp promoter sequence was successfully cloned.We predicated the structure and probable transcriptional factor sites of the promoter sequence and found some CTCF binding sites.The methylation of the CpG island in E75,L75,E90 and L90 were all high.
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