Transposable Elements Mediate 3D Genome Structure

Transposable elements (TEs) make up nearly half of the human genome and play a role in genetic innovation. Mounting evidence indicates that TEs harbor transcription factor (TF) binding sites and serve as a potent repertoire of cis regulatory elements. Many TEs have been found to be bound by cell-type-specific TFs and have been co-opted to contribute to the regulatory network and maintain cell identity. Proper gene expression requires precise regulatory information to be correctly transmitted through physical chromatin contacts, and the dynamics of which was found driven by transcription factors and epigenetic factors in a context-specific manner. Studies have shown TEs play an important role in shaping genome organization. However, the majority of them have focused on TEs in topologically associated domain boundaries or loop anchors from a more or less CTCF-centric perspective, precluding broader participation of TEs in mediating 3D genome structure through other factors. Furthermore, a full description of TE-bound TFs modulating 3D genome structure has not been elucidated, which can provide new insights into TEs underlying chromatin organization through their associated TFs.

To fill this gap, we used publicly available TF-DNA binding data and deeply sequenced Hi-C data in human pluripotent stem cells to examine the role of TEs in shaping 3D genome structure. We utilized specialized toolsets to include TE sequences in Hi-C data processing and build separate Hi-C matrices with and without TE reads, enabling the direct comparisons of different levels of 3D genome structure. Our data suggest that TEs play an essential role in dominating the 3D organization of the genome by supplying a narrow majority of 3D structure and are particularly responsible for finer-scale contacts. We also categorized TFs regarding their association with chromatin folding and discovered that contact-forming ability of a TF is positively correlated with the TE proportion. We identified that "contact-former" TFs tend to display insulating potential over nearby genes of their binding sites and bind to enhancer-like TEs. Furthermore, we selected four candidate TFs as examples to further support our observation. Taken together, our findings revealed a previously undermined role of TEs in dominating the 3D organization of the genome by in silico modeling and paved the ground for further exploration over TEs' broader function on the dark side of the genome organization.

转座子（transposable elements, TEs）占人类基因组的近一半，在遗传创新中发挥着关键作用。越来越多的证据表明，TEs 序列中含有转录因子（transcription factors, TFs）的结合位点，是一种有效的顺式调控元件。研究发现 TEs 与细胞类型特异性转录因子结合，参与调控网络并维持细胞特性。正确的基因表达需通过染色质的物理接触以传递精确的调控信息，前人研究表明，众多转录因子和表观遗传因子可能在这一动态过程中发挥精确作用。同时，TEs也在塑造基因组结构方面发挥着重要作用。然而，大部分研究关注于拓扑相关域或染色质环的边界中TEs的功能，即以CTCF为中心，从而忽略了TEs通过其他因子介导三维基因组结构中的作用。此外，关于结合TEs的TFs（TE-bound TFs）如何调节三维基因组结构尚未被完整描述，即TEs相关的TFs对染色质结构的影响，而这可为该领域提供新的见解。

为了填补这一空白，本研究整合了大量人类多能干细胞的TF-DNA结合数据与深度测序的Hi-C数据，来探究TEs在塑造三维基因组结构中的作用。本研究利用特殊工具将TE序列纳入Hi-C数据处理，并分别建立包括及不包括TE序列的Hi-C矩阵，从而对不同层次的三维基因组结构进行直接比较。本研究数据表明，TEs是绝大多数的三维染色质结构的基础，特别是更精细级别的结构，因此TEs在三维基因组中发挥着至关重要的作用。本研究进一步通过TFs与染色质折叠的相关程度将其分类，发现TF促进染色质互作结构形成的能力与互作位点中的TE比例呈正相关关系。分析结果表明被分类为可促进染色质互作结构的TFs (contact-former)可能对其结合位点临近基因发挥绝缘作用并偏好与具有增强子特性的TEs结合。此外，本研究筛选了出四个候选TFs作为例子进行下一步探究。综上所述，本研究通过计算机模拟揭示了TEs在构建三维基因组结构中的主导作用，并为进一步探索TEs在基因组结构的广泛功能奠定了基础。

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