Comprehensive Mapping of Long-Range Chromatin Interactions in Humanand Mouse Genomes

人类和小鼠基因组中长程染色质相互作用的综合图谱

• 批准号: 10241034
• 负责人: CHARLES LEE
• 金额: $ 194.94万
• 依托单位: JACKSON LABORATORY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-02-01 至 2023-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10241034
• 关键词: 3-Dimensional; Affect; Binding; Biological; Biological Assay; Biology; Blood Cells; Budgets; Catalogs; Cell Line; Cells; Chromatin; Code; Collection; Communities; DNA; Data Set; Disease; Disease model; Elements; Enhancers; Gene Order; Genes; Genetic; Genetic Transcription; Genome; Human; Human Genome; In Vitro; Libraries; Maps; Mediating; Methods; Mus; Mutation; Neurons; Production; Public Health; RNA Polymerase II; Regulator Genes; Regulatory Element; Research; Resolution; Sampling; Structure; Technology; Tissues; Transcription Initiation Site; Transcriptional Regulation; base; computerized data processing; experimental study; induced pluripotent stem cell; interest; linear transformation; mouse genome; mouse model; promoter; scaffold

PROJECT SUMMARY/ABSTRACT Efforts to map the functional elements of the human genome, which include elements such as insulators, enhancers, promoters and transcriptional start sites, have historically treated the genome as linear. However, it is now well appreciated that the genome has a three-dimensional (3D) organization that is important for mediating functional associations between regulatory elements and gene-coding sequences. Thus a linear map provides an incomplete picture of the genome, and it is often difficult or impossible to infer functional associations between regulatory elements without a topological framework to provide context. We have developed and advanced a powerful, high-resolution method for providing such a topological framework, Chromatin Interaction Analysis using Paired-End Tag sequencing (ChIA-PET). Using ChIA-PET, we have demonstrated that specific DNA motifs bound by CCTC-binding Factor (CTCF) are critical in defining topological domains and arranging the gene positions for coordinated transcription mediated by RNA Polymerase II (RNAPII). Therefore, the combination of CTCF and RNAPII ChIA-PET will be effective for comprehensively mapping the major structure codes and topological organization that scaffold RNAPII associated transcriptional regulation. We will contribute ChIA-PET technology to the ENCODE Project to both strengthen existing ENCODE datasets and identify new “structure code” elements and their interplays with gene-coding sequences that will aid in understanding the transcriptional landscape of the genome. We have established a robust ChIA-PET pipeline from library production to data processing for human and mouse cells. Here, we propose to apply this platform to assay large numbers of cell lines and primary cells that represent a wide-range of cellular space with important biological significance. Based on our current production scale and estimated budget allocation, we aim to produce 1024 high quality datasets from CTCF and RNAPII ChIA-PET experiments, each with two biological replicates for 256 biological samples. This pipeline capacity will be applied to samples selected by the ENCODE Consortium, and to this sample pool we aim to contribute a collection of high value biological samples that are likely of common interest to both the Consortium and the greater research community. These samples include both primary and in vitro–differentiated human blood cells, healthy and diseased induced pluripotent stem cells (iPSC), mature neurons differentiated from the iPSCs, and several major cell and tissue types from healthy and disease-model mice. These samples were selected to expand the “cell space” explored by the ENCODE Project and also because ChIA-PET analyses will be particularly relevant for revealing fundamental biology.

项目总结/摘要 绘制人类基因组功能元件的努力，包括绝缘体等元件， 增强子、启动子和转录起始位点在历史上将基因组视为线性的。但 现在已经很好地认识到，基因组具有三维（3D）组织，其对于介导 调控元件和基因编码序列之间的功能关联。因此，线性映射提供 这是一个不完整的基因组图片，往往很难或不可能推断出功能之间的联系， 调控元件，而没有拓扑框架来提供背景。我们已经开发和推进了一个 染色质相互作用分析是一种强大的、高分辨率的方法，可以提供这样一个拓扑框架 使用配对末端标签测序（ChIA-PET）。使用ChIA-PET，我们已经证明了特定的DNA基序 在定义拓扑结构域和排列基因中起关键作用 RNA聚合酶II（RNAPII）介导的协调转录的位置。因此， CTCF和RNAPII ChIA-PET将有效地全面绘制主要结构代码， 拓扑组织支架RNAPII相关的转录调控。我们将贡献ChIA-PET 技术应用于ENCODE项目，以加强现有的ENCODE数据集并识别新的“结构 编码”元件及其与基因编码序列的相互作用，这将有助于理解转录 基因组的全景 我们已经建立了一个强大的ChIA-PET管道，从库生产到人类数据处理， 小鼠细胞。在这里，我们建议应用该平台来测定大量的细胞系和原代细胞， 代表了具有重要生物学意义的广泛的细胞空间。根据我们目前的产量 我们的目标是从CTCF和RNAPII中产生1024个高质量的数据集 ChIA-PET实验，每个实验有256个生物样品的两个生物重复。这条管道的容量将 应用于ENCODE联盟选择的样本，我们的目标是为这个样本库贡献一个 收集高价值的生物样本，这些样本可能是财团和 更大的研究社区。这些样品包括原代和体外分化的人血细胞， 健康和患病的诱导多能干细胞（iPSC），从iPSC分化的成熟神经元，和 来自健康和疾病模型小鼠的几种主要细胞和组织类型。这些样本被选中， 扩大了ENCODE项目探索的“细胞空间”，也因为ChIA-PET分析将被 特别是与揭示基础生物学有关。

项目成果

In situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing.

• DOI: 10.1002/cpz1.174
• 发表时间: 2021-08
• 期刊: Current protocols
• 作者: Wang P;Feng Y;Zhu K;Chai H;Chang YT;Yang X;Liu X;Shen C;Gega E;Lee B;Kim M;Ruan X;Ruan Y
• 通讯作者: Ruan Y

Correction to: Spatial chromatin architecture alteration by structural variations in human genomes at the population scale.

更正：人口规模的人类基因组结构变异导致空间染色质结构改变。

• DOI: 10.1186/s13059-019-1780-6
• 发表时间: 2019
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: Sadowski,Michal;Kraft,Agnieszka;Szalaj,Przemyslaw;Wlasnowolski,Michal;Tang,Zhonghui;Ruan,Yijun;Plewczynski,Dariusz
• 通讯作者: Plewczynski,Dariusz