三个地方品种鸡肌肉组织基因组DNA甲基化分析
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摘要
DNA甲基化是在DNA甲基转移酶的催化下，将S-硫代腺苷甲硫氨酸中的甲基基团转移到胞嘧啶的第五个碳原子上，使DNA分子中碱基结合甲基的过程。DNA甲基化在基因表达、X染色体的失活、遗传印记、细胞分化、染色质结构维持、胚胎发育、癌症的发生和胚胎发育中扮演着重要角色。DNA甲基化作为一种重要的表观遗传修饰，其功能主要是通过基因表达抑制来实现。显著的甲基化水平差异已经在不同组织中发现，并且在相同组织具有不同的功能。很多研究表明不同的甲基化水平可能与组织特异性转录和某些性状有关，并且对正常的分化和发育以及一些性状起到至关重要的作用。肉质性状是个复杂的性状，由多基因控制，因此控制肉质性状基因的甲基化水平的改变必然影响其表达，进而对肉质性状产生效应。
DNA甲基化水平受到品种、性别、年龄、环境、饲养管理水平等诸多因素的影响，并且在时间和空间上存在差异表达。本研究采用荧光标记的甲基化敏感性扩增多态性技术对汶上芦花鸡9种组织基因组DNA甲基化水平进行了检测，共计检测到19,795个片段，其中非甲基化片段8,935个；半甲基化片段5,668个，全甲基化片段5,192个。半甲基化比率胸肌显著高于其他组织（P<0.05），全甲基化比率肺脏极显著高于其他组织（P<0.01），甲基化比率胸肌和肺脏显著高于其他组织（P<0.05）。
利用所建立的F-MSAP方法检测了汶上芦花鸡、仙居三黄鸡和淮北麻鸡胸肌组织基因组DNA甲基化水平，并与肉质性状进行相关性分析。半甲基化比率3个品种间差异不显著（P>0.05）；全甲基化比率仙居三黄鸡极显著高于淮北麻鸡，淮北麻鸡又极显著高于汶上芦花鸡（P<0.01）；甲基化比率仙居三黄鸡极显著高于淮北麻鸡和汶上芦花鸡（P<0.01），而淮北麻鸡和汶上芦花鸡差异不显著（P>0.05）。基因组DNA甲基化水平与肉质性状相关性分析结果表明，甲基化水平与汶上芦花鸡肌纤维密度和剪切力相关性差异极显著（P<0.01），与仙居三黄鸡肌纤维密度和滴水损失相关性差异极显著（P<0.01），与淮北麻鸡滴水损失相关性差异显著（P<0.05），甲基化水平与三个品种的其他肉质性状相关性差异不显著。
最后对甲基化差异基因FABP4mRNA表达水平与汶上芦花鸡肉质性状相关性进行了分析，结果表明甲基化差异基因FABP4mRNA表达水平与汶上芦花鸡剪切力相关性差异显著（P<0.05），而与其它肉质性状相关性差异不显著（P>0.05）。
DNA methylation is catalyzed by DNA methyltransferases (Mtases) which transfer a methylgroup from S-adenosine-L-methionine to the5th carbon of cytosine. DNA methylation plays acrucial role in many biological processes, including gene expression regulation, X chromosomeinactivation, genomic imprinting, cell differentiation, chromatin modification, cancer developmentand embryo development. The main function of DNA methylation, which mostly occurs at CpGislands, is to inhibit gene expression. Significant differences in methylation levels have been foundin different tissues and in different individuals within the same organization. Many studies haveshown that different methylation levels may be associated with tissue-specific transcription orcertain traits and can play a crucial role in normal differentiation, development and some traits.TheMeat quality traits are complicated traits traits are controlled by many genes, some of which mayplay a major role. Changes in the methylation levels of certain genes controlling meat quality traitswill inevitably affect their expression levels, thereby affecting meat quality traits.
DNA methylation levels were affected by breed, sex, age, environment, feeding andmanagement, and there are differences in the temporal and spatial expression. In the present study,we used the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP)method to investigate the differences of genome DNA methylation levels in pectoral muscletissues of male Wenshang Barred chicken, a total of19,795fragments were obtained including8935unmethylated bands,5668hemimethylated bands and5192fully methylated bands.Hemimethylation ratio of pectoral muscle was higher than that of other tissues(P<0.05), fullymethylation ratio of lung was significantly higher than that of other tissues(P<0.01), andmethylation ratios of pectoral muscle and lung were higher than that of other tissues(P<0.05).
We also used the F-MSAP which we founded to investigate the DNA methylation leveldifferences in pectoral muscle tissues and their relationships with meat quality traits of male Wenshang Barred chicken, Xianju chicken and Huaibei Partridge chicken. There was nosignificant different of hemimethylated ratio among three breeds(P>0.05); The fully methylationratio of Xianju chicken was significantly higher than that of Huaibei Partridge chicken, andHuaibei Partridge chicken was significantly higher than that of Wenshang Barred chicken(P<0.01);For the methylation ratio, Xianju chicken was significantly higher than that of Huaibei Partridgechicken and Wenshang Barred chicken, but there was no significant different between WenshangBarred chicken and Huaibei Partridge chicken. The correlation analysis between the methylationlevels and the meat quality traits were also done, The results showed that different methylationlevels were highly significant correlations with muscle fiber density and shear force in WenshangBarred chicken (P<0.01), and for Xianju chicken different methylation levels were highlysignificant correlations with muscle fiber density and drip loss (P<0.01), but for Huaibei Partridgechicken methylation levels were significant correlations with drip loss(P<0.05). However, nosignificant correlations were found with other traits in three breeds (P>0.05).
The association of the specific methylation FABP4with the meat quality traits were detected,The results showed that the levels of FABP4mRNA were highly significant correlations withshear force of pectoral muscle in Wenshang Barred chicken(P<0.05), However, no significantcorrelations were found with other meat quality traits (P>0.05).
DNA甲基化水平受到品种、性别、年龄、环境、饲养管理水平等诸多因素的影响，并且在时间和空间上存在差异表达。本研究采用荧光标记的甲基化敏感性扩增多态性技术对汶上芦花鸡9种组织基因组DNA甲基化水平进行了检测，共计检测到19,795个片段，其中非甲基化片段8,935个；半甲基化片段5,668个，全甲基化片段5,192个。半甲基化比率胸肌显著高于其他组织（P<0.05），全甲基化比率肺脏极显著高于其他组织（P<0.01），甲基化比率胸肌和肺脏显著高于其他组织（P<0.05）。
利用所建立的F-MSAP方法检测了汶上芦花鸡、仙居三黄鸡和淮北麻鸡胸肌组织基因组DNA甲基化水平，并与肉质性状进行相关性分析。半甲基化比率3个品种间差异不显著（P>0.05）；全甲基化比率仙居三黄鸡极显著高于淮北麻鸡，淮北麻鸡又极显著高于汶上芦花鸡（P<0.01）；甲基化比率仙居三黄鸡极显著高于淮北麻鸡和汶上芦花鸡（P<0.01），而淮北麻鸡和汶上芦花鸡差异不显著（P>0.05）。基因组DNA甲基化水平与肉质性状相关性分析结果表明，甲基化水平与汶上芦花鸡肌纤维密度和剪切力相关性差异极显著（P<0.01），与仙居三黄鸡肌纤维密度和滴水损失相关性差异极显著（P<0.01），与淮北麻鸡滴水损失相关性差异显著（P<0.05），甲基化水平与三个品种的其他肉质性状相关性差异不显著。
最后对甲基化差异基因FABP4mRNA表达水平与汶上芦花鸡肉质性状相关性进行了分析，结果表明甲基化差异基因FABP4mRNA表达水平与汶上芦花鸡剪切力相关性差异显著（P<0.05），而与其它肉质性状相关性差异不显著（P>0.05）。
DNA methylation is catalyzed by DNA methyltransferases (Mtases) which transfer a methylgroup from S-adenosine-L-methionine to the5th carbon of cytosine. DNA methylation plays acrucial role in many biological processes, including gene expression regulation, X chromosomeinactivation, genomic imprinting, cell differentiation, chromatin modification, cancer developmentand embryo development. The main function of DNA methylation, which mostly occurs at CpGislands, is to inhibit gene expression. Significant differences in methylation levels have been foundin different tissues and in different individuals within the same organization. Many studies haveshown that different methylation levels may be associated with tissue-specific transcription orcertain traits and can play a crucial role in normal differentiation, development and some traits.TheMeat quality traits are complicated traits traits are controlled by many genes, some of which mayplay a major role. Changes in the methylation levels of certain genes controlling meat quality traitswill inevitably affect their expression levels, thereby affecting meat quality traits.
DNA methylation levels were affected by breed, sex, age, environment, feeding andmanagement, and there are differences in the temporal and spatial expression. In the present study,we used the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP)method to investigate the differences of genome DNA methylation levels in pectoral muscletissues of male Wenshang Barred chicken, a total of19,795fragments were obtained including8935unmethylated bands,5668hemimethylated bands and5192fully methylated bands.Hemimethylation ratio of pectoral muscle was higher than that of other tissues(P<0.05), fullymethylation ratio of lung was significantly higher than that of other tissues(P<0.01), andmethylation ratios of pectoral muscle and lung were higher than that of other tissues(P<0.05).
We also used the F-MSAP which we founded to investigate the DNA methylation leveldifferences in pectoral muscle tissues and their relationships with meat quality traits of male Wenshang Barred chicken, Xianju chicken and Huaibei Partridge chicken. There was nosignificant different of hemimethylated ratio among three breeds(P>0.05); The fully methylationratio of Xianju chicken was significantly higher than that of Huaibei Partridge chicken, andHuaibei Partridge chicken was significantly higher than that of Wenshang Barred chicken(P<0.01);For the methylation ratio, Xianju chicken was significantly higher than that of Huaibei Partridgechicken and Wenshang Barred chicken, but there was no significant different between WenshangBarred chicken and Huaibei Partridge chicken. The correlation analysis between the methylationlevels and the meat quality traits were also done, The results showed that different methylationlevels were highly significant correlations with muscle fiber density and shear force in WenshangBarred chicken (P<0.01), and for Xianju chicken different methylation levels were highlysignificant correlations with muscle fiber density and drip loss (P<0.01), but for Huaibei Partridgechicken methylation levels were significant correlations with drip loss(P<0.05). However, nosignificant correlations were found with other traits in three breeds (P>0.05).
The association of the specific methylation FABP4with the meat quality traits were detected,The results showed that the levels of FABP4mRNA were highly significant correlations withshear force of pectoral muscle in Wenshang Barred chicken(P<0.05), However, no significantcorrelations were found with other meat quality traits (P>0.05).
引文
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