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全基因组调控性变异研究及其在精神分裂症遗传分析中的应用
其他题名Genome Genome -wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its wide regulatory variation study and its application in genetic analysis of schizophrenia application in genetic analysis of schizophrenia application in genetic analysis of schizophrenia application in genetic analysis of schizophrenia application in genetic analysis of schizophrenia application in genetic analysis of schizophrenia application in genetic analysis of schizophrenia application in genetic analysis of schizophreniaapplication in genetic analysis of schizophrenia application in genetic analysis of schizophrenia application in genetic analysis of schizophrenia application in genetic analysis of schizophreniaapplication in genetic analysis of schizophrenia application in genetic analysis of schizophreniaapplication in genetic analysis of schizophrenia application
杜阳
学位类型博士
导师王晶
2016-04
学位授予单位中国科学院研究生院
学位授予地点北京
学位专业心理学
关键词调控性变异 调控元件 遗传易感性 转录因子 精神分裂症 Microrna
摘要近些年,对复杂疾病的遗传学关联研究在全基因组范围内发现了成千上万的疾病相关的遗传易感位点。然而对这些遗传易感位点的功能分析发现,绝大多数复杂疾病相关的易感位点位于基因组非编码区域,提示调控性遗传变异在复杂疾病发病过程中起着重要的作用。已有的调控性变异分析工具为疾病的遗传学研究结果提供了些许线索,然而由于这些工具大多数基于预测源性的调控元件注释遗传变异的调控功能,在可靠性方面略显不足。近年来随着二代测序技术的快速发展,人们对基因组各类功能元件尤其是对非编码区功能元件进行了大量的探索,积累了丰富的数据。如何基于这些种类众多,数量庞大的功能元件来挖掘遗传变异位点的潜在功能,进而探索疾病的遗传机制是本论文所要解决的问题。
在论文的第一部分,我们首先构建了用于遗传变异调控特征分析的数据库工具rSNPBase和rVarBase。rSNPBase从转录调控与转录后调控两个方面,在全基因组范围内依据单核苷酸多态性位点(Single nucleotide polymorphism, SNPs)与调控元件(包括开放染色质区域、转录因子结合区域、组蛋白修饰区域、甲基化岛、染色质交互区域、RNA结合蛋白结合区域和miRNA编码区域)在染色体位置上的重叠性鉴定调控性SNPs(regulatory SNPs,rSNPs),并分析rSNPs潜在的靶基因。rVarBase是rSNPBase数据库的升级版本,它不仅包含了对调控性SNPs的注释,还可以用于新生突变和拷贝数变异(Copy number variation,CNV)等多类型遗传变异(variants)的调控属性注释。rVarBase从三个维度注释变异位点的调控属性,即变异位点的染色质状态、变异位点相关的调控元件以及潜在的靶点基因。rSNPBase与rVarBase使用经实验验证调控元件对遗传变异进行注释与分析,相比于其它基于生物信息预测的遗传变异功能注释工具,更具有可靠性和实验指导性。
在论文的第二部分,我们首先使用rVarBase分析了精神分裂症(Schizophrenia, SZ)遗传易感位点的调控特征,结果表明约77.2%的SZ遗传易感位点具有潜在的调控功能,被鉴定为SZ相关的调控性易感位点。大约36%的SZ相关的调控性易感位点分布在调控元件所在区域中,进一步的调控元件分析表明染色质交互作用区域和转录因子结合区域与SZ的遗传易感性密切相关,转录因子富集分析发现ZNF263、KDM1A等转录因子等在SZ的遗传易感位点中显著富集;其次,我们重点关注了microRNA(miRNA)这一重要的非编码RNA与SZ遗传易感位点的相关性。通过全基因组范围内的miRNAs与SZ遗传关联分析,我们首先发现了12个与疾病显著相关的miRNAs,除了已知的miR-137和miR-let-7g,还包括10个新的与疾病相关的miRNAs,这些新鉴定的miRNAs中,miR-4529、miR-4688以及miR-135a-1可以在大脑中表达。对miRNA区域内SNPs调控功能研究发现,与SZ显著相关的SNPs对miR-4529的表达具有潜在的调控作用。进一步的生物信息学分析提示miR-4529靶基因与SZ遗传易感基因之间密切相关。通路分析发现miR-4529的靶基因显著富集于SZ相关的生物学通路histone deacetylase complex(GO:0000118)和Wnt signaling pathway(hsa04310)。这些证据提示miR-4529及其靶基因在SZ的遗传机制中具有潜在的作用。
综上所述,本论文通过对遗传变异与各类调控元件的分析,在全基因组范围内鉴定了具有潜在调控功能的变异位点。结合调控性变异与SZ的遗传易感位点分析发现,大多数SZ的遗传易感位点具有潜在的调控功能。从miRNA层面对SZ遗传易感位点的分析发现了新的疾病相关的miRNAs。这些结果表明了调控性变异在复杂疾病遗传分析中的重要作用,并为SZ的遗传学研究提供了新的视角,并为后续进一步分子实验指明了方向。
其他摘要In recent years, genetic studies of complex disease have identified thousands of susceptibility loci over the whole genome. However, functional analysis of these susceptibility loci showed the majority of which are located in the noncoding area of human genome, suggesting that regulatory variation play a role in the development of complex disease. Existing annotation tools of regulatory variation have facilitated the genetic research of complex disease. However, they are less reliable since most of these tools annotated variant with reference to predicted regulatory elements. In recent year, benefited from the rapid development of next-generation sequencing technology, researchers have identified various functional elements in the human genome, especially for which within noncoding area. How to integrate the massive various elements and explore the potential function of human variants, and further interpret the genetic mechanisms is the problem we focus in this study.
In the first part, we implemented two database-based tools rSNPBase and rVarBase to provide regulatory annotation for genetic variations in human genome. rSNPBase annotated genome-wide Single nucleotide polymorphism (SNPs) by using regulatory elements involved in both transcription and post-transcription regulation, including open chromatin regions, transcription factor(TF) binding regions, histone modifications region, CpG islands, chromatin interaction region, RNA binding protein binding regions and miRNA coding region, and its potential target genes. rVarBase is an updated version of rSNPBase, it provides annotations on more types of human variants such as known Cope Number Variation (CNV) and novel mutations. rVarBase annotates variants’ regulatory feature in three fields: chromatin state of the region surrounding variant, regulatory elements overlapped with variant, and variant's potential target genes. Both rSNPBase and rVarBase annotated variants with reference to experimentally supported regulatory elements, thus providing more reliable information than those predicted-based tools and could well guide further experiments.
In the second part, we first analyze the regulatory characteristics of schizophrenia (SZ) susceptibility loci based on rVarBase. We found that about 77.2% of the SZ susceptibility loci have potential regulatory functions. Among these regulatory loci, approximately 36% are located within the sequence of regulatory elements. An in-depth analysis of the regulatory elements shows a close relation between chromatin interaction region, transcription factor binding region and SZ susceptibility loci. By using TF enrichment analysis, we found two significantly enriched transcription factors: ZNF263 and KDM1A. Secondly, we focus on the association between microRNA (miRNA) and SZ susceptibility loci. Through a genome wide association study of miRNAs and SZ, we identified 12 miRNAs which were significantly associated to SZ. Two of the 12 miRNAs, miR-137 and miR-let-7g, had been identified in previous studies and the other 10 were newly identified. We analyzed the expression status of the 10 new miRNAs, results showed that miR-4529, miR-4688 and miR-135a-1 are expression in brain tissue. Functional analysis of SNPs flanking miRNAs showed a potential regulatory role of SZ associated SNPs in the expression of miR-4529. Further bioinformatics analysis for miRNA targets genes also implied strong correlations between miR-4529 target gene and SZ susceptibility genes. Pathway analysis found that target genes of miR-4529 significantly enriched in the SZ related biological pathways ‘histone deacetylase complex (GO: 0000118)’ and ‘Wnt signaling pathway (hsa04310)’. These evidences suggest that miR-4529 and its target gene have a potential role in the genetic mechanisms SZ.
In summary, our study identified genome-wide regulatory variants by performing an integrated analysis of various regulatory elements and human variations. A combined analysis of regulatory variants and SZ susceptibility loci showed that the majority of SZ associated loci imply a potential regulatory function. Through the miRNA analysis, we identified new disease-associated miRNAs. Collectively, result from these study suggest that regulatory variation play an important role in the genetic analysis of complex disease, provide new insight for the genetic studies of SZ and could support the molecules experiments in the future.
学科领域健康心理学
语种中文
文献类型学位论文
条目标识符http://ir.psych.ac.cn/handle/311026/19941
专题健康与遗传心理学研究室
作者单位中国科学院心理研究所
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杜阳. 全基因组调控性变异研究及其在精神分裂症遗传分析中的应用[D]. 北京. 中国科学院研究生院,2016.
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