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.

项目摘要/摘要 绘制人类基因组功能元素的努力，其中包括诸如绝缘子等元素， 增强子，启动子和转录起始站点历史上将基因组视为线性。但是，它 现在，人们对基因组具有三维（3D）的组织，这对于调解很重要 调节元件与基因编码序列之间的功能关联。线性地图提供 基因组的不完整情况，通常很难或不可能推断功能关联 没有拓扑框架提供背景的监管要素。我们已经开发并提前了 功能强大的高分辨率方法用于提供这种拓扑框架，染色质相互作用分析 使用配对 - 末端标签测序（CHIA-PET）。使用chia-pet，我们证明了特定的DNA基序 受CCTC结合因子（CTCF）约束对于定义拓扑结构域和排列基因至关重要 由RNA聚合酶II（RNAPII）介导的协调转录位置。因此，结合 CTCF和RNAPII CHIA-PET将有效地绘制主要的结构代码，并且 脚手架rnapii相关的转录调节的拓扑组织。我们将贡献chia-pet 编码项目的技术既加强现有的编码数据集并确定新的“结构” 代码”元素及其与基因编码序列的相互作用，这些序列将有助于理解转录 基因组的景观。 我们已经建立了从图书馆生产到人类数据处理的强大的CHIA-PET管道， 小鼠细胞。在这里，我们建议将此平台应用于分析大量的细胞系和主要单元格 代表具有重要生物学性的大范围的细胞空间。根据我们目前的作品 规模和估计的预算分配，我们的目标是从CTCF和RNAPII生产1024个高质量数据集 CHIA-PET实验，每个实验都有两个生物学重复的256个生物样品。该管道容量将 应用于编码财团选择的样本，并将其旨在贡献A的样本池 收集高价值的生物样品，这些样本可能对财团和该财团都具有共同兴趣 更大的研究社区。这些样品包括原发性和体外界定的人类血细胞， 健康诱导的多能干细胞（IPSC），与IPSC区分开的成熟神经元和 健康和疾病模型小鼠的几种主要细胞和组织类型。这些样品被选择为 扩展编码项目探索的“单元格空间”，也是因为CHIA-PET分析将是 与揭示基本生物学特别相关。

项目成果

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

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