CAREER: Conservation of cohesin-containing cis regulatory modules in the human and mouse lineages

职业：人类和小鼠谱系中含有粘连蛋白的顺式调节模块的保护

• 批准号: 1651614
• 负责人: Alan Boyle
• 金额: $ 98万
• 依托单位: Regents of the University of Michigan - Ann Arbor
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-04-15 至 2022-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1651614&HistoricalAwards=false
• 关键词: CAREER; Conservation; cohesin; containing; cis

The mouse has been used as a flexible genetic system for exploring how diseases occur, including in humans. However, the treatments that work for mice having a condition almost never work in other animals with that condition. This apparently occurs because, even when gene pathways seem similar across species, their regulation, or network wiring, is different. Some of these changes may be caused by retrotransposon elements, whose presence has been shown to be correlated with changes in the cohesin-associated regulatory modules of human and mouse cells. Modifying sequencing technologies with special reagents has allowed us to start mapping regulatory regions in both human and mouse; results show that there is a high rate of change at regulatory sites, with only about half of the sites showing conserved sequence between human and mouse cell lines and, even where conservation is found, the expected transcription factors don't bind under similar conditions. A further complication is that most gene networks are regulated by multiple transcription factors (TFs) that must bind in a particular order and combination; often this binding is at sites quite distant from the genes. Looping of the DNA at distant sites back around to bring it close, and 'locking' it in place with a regulatory protein, is one of the factors this research aims to dissect. Understanding what these regulatory element TF combinations are, what mechanisms lead to change, and how their regulatory actions can be modulated will have important applications in such areas as the treatment of disease, including better targeted therapies. This research requires strong computational skills as well as understanding the biological states of cells and the technical details of the assays; in addition to mentoring the graduate students who will take leading roles in carrying out the research, high school students will be recruited to participate in computational summer boot camps and undergraduates will be recruited to paid summer internships for immersion in the research methods and questions, with a strong emphasis on bringing more women and under-served minorities into active research experiences. In this project the PI will use recently developed methods to explore the co-binding of transcription factors with CTCF and the cohesin complex in matched human and mouse cells. These sites represent anchor regions for 3D interactions in the genome. Initial work suggests that there is extensive turnover of these sites beyond the already high turnover of cis-regulatory modules in the two genomes. This finding stands in sharp contrast to previously published work showing, at low resolution, there is a high level of conservation of the physical 3D structure between the two species. The PI has previously developed computational methods demonstrating a complex co-localization of transcription factors and shown that these patterns are conserved in mouse. These patterns were shown to maintain similar regulatory properties even with underlying sequence divergence. Here the PI will explore these conserved patterns in terms of conservation at cohesin sites in the two species. As an extension of this, the project will focus on the effect of retrotransposons in the expansion of cohesin sites in the two lineages. Finally, the project will integrate 3D structural information from ChIA-PET and HiC data to determine the effects of the gains and losses of cohesin sites on the conservation of specific loops and topological domains. This work extends from a new way of considering conservation, that of conservation of regulatory patterns instead of considering only sequence context. Because of this, the PI is able to study the entire mouse and human genomes in comparison instead of only the small fraction of the genomes comparable by sequence. As a result, the project will provide new insights into the regulatory structure of the two genomes and shed light on the aspects of gene regulatory control through looping and domain structure that would previously have been impossible to consider. Progress from this project will be available at http://boylelab.org/.

老鼠已被用作一种灵活的遗传系统，用于探索包括人类在内的疾病是如何发生的。然而，对患有这种疾病的老鼠有效的治疗方法几乎对患有这种疾病的其他动物不起作用。这显然是因为，即使基因通路在物种之间看起来相似，它们的调节或网络连接是不同的。其中一些变化可能是由反转录转座子元件引起的，其存在已被证明与人类和小鼠细胞内聚蛋白相关调节模块的变化相关。使用特殊试剂修改测序技术使我们能够开始绘制人类和小鼠的调控区域；结果表明，在调节位点上有很高的变化率，只有大约一半的位点在人和小鼠细胞系之间显示保守序列，即使在发现保守的地方，预期的转录因子在类似的条件下也不会结合。更复杂的是，大多数基因网络是由多个转录因子（TFs）调控的，这些转录因子必须以特定的顺序和组合结合；这种结合通常发生在离基因相当远的地方。将远处的DNA环回以使其靠近，并用一种调节蛋白将其“锁定”在适当的位置，是这项研究的目的之一。了解这些调节元件TF组合是什么，导致变化的机制是什么，以及它们的调节作用如何被调节，将在诸如疾病治疗等领域具有重要的应用，包括更好的靶向治疗。这项研究需要很强的计算能力，以及理解细胞的生物状态和分析的技术细节；除了指导将在研究中发挥主导作用的研究生外，还将招募高中生参加计算夏令营，招募本科生参加带薪暑期实习，沉浸在研究方法和问题中，重点是让更多的女性和服务不足的少数民族参与到积极的研究经验中来。在这个项目中，PI将使用最近开发的方法来探索转录因子与CTCF和内聚蛋白复合物在匹配的人和小鼠细胞中的共结合。这些位点代表了基因组中三维相互作用的锚定区域。最初的研究表明，除了两个基因组中已经很高的顺式调控模块的更替之外，这些位点还存在广泛的更替。这一发现与之前发表的研究结果形成鲜明对比，在低分辨率下，这两个物种之间的物理三维结构保持得很高。PI先前开发了计算方法，证明了转录因子的复杂共定位，并表明这些模式在小鼠中是保守的。这些模式被证明保持相似的调控特性，即使潜在的序列分歧。在这里，PI将在两个物种的粘接位点的保护方面探索这些保守模式。作为该研究的延伸，该项目将重点关注反转录转座子在两个谱系中内聚蛋白位点扩展中的作用。最后，该项目将整合来自china - pet和HiC数据的三维结构信息，以确定黏结位点的增益和损失对特定环和拓扑域的保护的影响。这项工作扩展了一种新的考虑保护的方式，即调节模式的保护，而不是只考虑序列上下文。正因为如此，PI能够研究整个小鼠和人类基因组的比较，而不是只有一小部分基因组的序列可比较。因此，该项目将为两个基因组的调控结构提供新的见解，并通过环和结构域结构阐明基因调控控制的各个方面，这在以前是不可能考虑的。该项目的进展将在http://boylelab.org/上提供。

项目成果

CGIMP: Real-time exploration and covariate projection for self-organizing map datasets

CGIMP：自组织地图数据集的实时探索和协变量投影

• DOI: 10.21105/joss.01520
• 发表时间: 2019
• 期刊: Journal of Open Source Software
• 作者: Diehl, Adam;Boyle, Alan
• 通讯作者: Boyle, Alan

Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes

• DOI: 10.1038/s41467-020-15520-5
• 发表时间: 2020-04-14
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Diehl, Adam G.;Ouyang, Ningxin;Boyle, Alan P.
• 通讯作者: Boyle, Alan P.