猪肺泡巨噬细胞系中等位基因特异性表达调控的生物信息学分析

发布时间：2018-03-10 13:02

本文选题：猪肺泡巨噬细胞　切入点：Poly(I:C)　出处：《华中农业大学》2017年硕士论文　论文类型：学位论文

【摘要】：猪肺泡巨噬细胞(PAM)作为机体重要的免疫细胞,在抵抗病原入侵和免疫应答方面发挥着重要的作用。有研究表明等位基因的特异性表达与某些易感疾病的发生紧密相关,但是在PAM细胞中探究等位基因特异性表达与疾病、免疫相关的进展还不是很多,并且关于等位基因特异性表达的调控机制研究的也不是很透彻。因此,本论文将围绕猪肺泡巨噬细胞系3D4/21在受到Poly(I:C)刺激前后等位基因的特异性表达情况以及可能受到的转录调控因素,如转录因子结合、组蛋白修饰以及单倍型染色质交互差异等方面展开分析,主要结果如下:基于RNA-seq数据,分别鉴定出PAM细胞系3D4/21在受到Poly(I:C)刺激和未刺激情况下具有偏好性表达的等位基因,经过综合比较,发现有一些与病原感染、免疫应答相关的等位基因在刺激后呈现出了不同的表达偏好性并且其总的表达量相比于未刺激的情况下显著升高,我们推测这些基因含有抵抗病原体入侵的相关突变,可作为候选的疾病抗性基因进行下步实验验证。为了进一步理解等位基因不平衡表达的相关调控机制,我们结合ChIP-seq数据进行关联分析,结果表明转录因子结合和组蛋白修饰的单倍型偏好性与等位基因表达的偏好性高度相关。而且我们通过在单倍型水平上观察CTCF,RNAPII介导的染色质交互信息,可以看到单倍型染色质交互的偏好性与等位基因表达的偏好性也具有一致性。我们的研究结果对于探索提高猪抗病能力和免疫能力提供了一些有益的启示,对于理解等位基因的特异性表达及相关调控因素的关系具有一定的参考意义。
[Abstract]:As an important immune cell, porcine alveolar macrophage (PAM) plays an important role in resisting pathogen invasion and immune response. Some studies have shown that the specific expression of allele is closely related to the occurrence of some susceptible diseases. However, there is not much progress in exploring the relationship between allele-specific expression and disease in PAM cells, and the regulation mechanism of allele-specific expression is not very thorough. This paper will focus on the specific expression of alleles in porcine alveolar macrophage cell line 3D4 / 21 before and after stimulation by Polynei: C and the possible transcriptional regulatory factors, such as transcription factor binding. Histone modification and haplotype chromatin interaction were analyzed. The main results were as follows: based on RNA-seq data, the alleles of PAM cell line 3D4 / 21 were identified with preference expression under and without stimulation of PAM cell line 3D4 / 21, respectively. After comprehensive comparison, we found that some alleles associated with pathogen infection and immune response showed different expression preferences after stimulation, and the total expression of these alleles was significantly higher than that without stimulation. We speculate that these genes contain mutations related to resistance to pathogen invasion, which can be used as candidate disease resistance genes for next step experiments. In order to further understand the related regulation mechanism of unbalanced expression of alleles, We use the ChIP-seq data to do the association analysis, The results showed that the haplotype preference of transcription factor binding and histone modification was highly correlated with the preference of allelic expression, and we observed the chromatin interaction mediated by CTCF RNAPII at the haplotype level. It can be seen that the preference of haplotype chromatin interaction is also consistent with that of allelic expression. It has some reference significance for understanding the specific expression of alleles and the relationship between related regulatory factors.
【学位授予单位】：华中农业大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S852.4;Q811.4

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