转座因子（Transposable Elements，TEs）在人或小鼠细胞内作为最常见的DNA元件类型，具有增强子元件、新型剪接点、mRNAs嵌合和一系列其他基因组元件的功能。之前我们发表的研究中已经揭示染色质状态和相应标记地TEs之间复杂关联，这也暗示着TEs可能在染色质高级三维结构中的存在重要作用。在本项目中，我们将系统地探讨TEs在三维染色质结构中扮演的角色和功能。目前我们已经开发了一种用于分析TEs的新计算框架，分析表明TEs至少占染色质三维结构的50％。随后我们将使用两个示例系统探讨TEs对染色质结构的影响：首先，我们将在小鼠多能干细胞中探讨RLTR13B2（一种内源性逆转录病毒TEs）如何通过改变染色质三维结构来调控目的控转录因子NR5A2的激活。其次我们通过检测转座子的偏好整合位点结合Hi-C技术来分析TEs对染色质三级结构的影响。

The most common types of DNA element inside a human or mouse cell are not genes, but transposable elements (TEs). TEs are a complex mixture of ~1200 distinct types of duplicating DNA, including ancient retroviruses. Only a few are still active, but they can copy themselves into other places in the genome, potentially disrupting oncogenes and tumor suppressors and have been known to directly lead to cancer. ..However, in addition to these deleterious roles, TEs can also function as enhancer elements, novel splice junctions, chimeric mRNAs, and a range of other genomic elements. It is increasingly clear that TEs are playing critical roles in a range of biological functions, and should not be considered as just junk or selfish DNA. We have previously revealed the complex pattern of chromatin that marks TEs, this insight led us to consider the role of TEs in higher order structure. DNA does not exist inside a cell as a long string. It is tightly packaged to fit inside a space just a few micrometers in diameter. The DNA is wrapped around histones which are looped and wrapped to form higher 3D structures of chromatin. We reasoned that, considering that most of the cells’ DNA actually consists of TEs, then the TEs should be a major factor to influence the large-scale 3D structure of chromatin. Our preliminary evidence suggests that this is indeed the case. ..In this project we propose to explore the role of TEs in 3D chromatin organization. We have developed a new computational framework for the analysis of TEs. This suggests that TEs are responsible for at least 50% of the 3D structure of chromatin. We will explore the consequences of TEs on chromatin structure using two example systems:..First, we will explore the role of RLTR13B2 (an endogenous retrovirus TE) in two types of pluripotent stem cells: embryonic stem cells (ESCs) and Epiblast stem cells (EpiSCs). ESCs and EpiSCs represent the early preimplantation epiblast (ESCs) and the later post implantation epiblast (EpiSCs), respectively. ESCs and EpiSCs show many differences, but a key difference is the activity of the transcription factor NR5A2, which is only active in ESCs. We have shown that NR5A2 binds to RLTR13B2, and can open chromatin to make it active, only in ESCs. In EpiSCs NR5A2 is absent, RLTR13B2 is inactive and chromatin is closed. Using a variety of computational and experimental approaches we will demonstrate that when NR5A2 is bound to RTLTR13B2 it alters chromatin architecture to cause the RLTR13B2 to act as an enhancer element for nearby gene expression...Secondly, we will look at the role that TEs play on 3D structure. To achieve this, we must first understand the integration biases of TEs. TEs do not integrate randomly, but instead target specific features. However, these biases are very poorly explored, which is surprising considering the role of TEs in tumorigenesis. We will explore this by introducing ectoptic TEs into the mouse cells (e.g. SVA-type TEs from human), activating retrotransposition, then sequencing the TE integrations using hundreds of cell lines and multiplexed barcoding. We will then use these lines to look at the changes in 3D chromatin. The current state-of the-art technique to measure 3D chromatin is ‘Hi-C’. However, Hi-C suffers from a very low resolution, whilst TEs are typically small, and their effects are poorly captured by Hi-C. We will use our TE lines with ectopic TEs, to see how the introduction of ectopic TEs influences Hi-C data. Despite the low resolution of Hi-C data, as we will know the integration sites for new TEs, we will be able to attribute changes in Hi-C data to the introduction of new TEs, and so define the rules for how TEs impact on 3D chromatin organization...Overall, this project will bring much needed insight into the role of TEs in chromatin architecture. The project will have consequences for a range of biological research areas, from embryology, neurology and the development of human disease.