Reconstruction of 3D Genome Architecture from Chromatin Conformation Capture Data

摘要 我们即将进入构象生物学的新时代。基因组构象对于 许多细胞过程，包括基因调控，具有某些改变（易位，fu- 是致癌的。虽然最近的检测，特别是Hi-C，已经改变了人们对 染色质结构，即使是更新的技术也有可能显着改善 三维（3D）基因组重建的准确性和分辨率。然而，为了充分 实现这一潜力，将需要新的统计方法和算法来操作 由此产生的数据和结构，并整合伴随的生物医学数据。该项目旨在 发展这样的方法。一个具体的例子是目前的调查结果， 绝缘邻近破坏作为一种新的致癌机制的实例。而不是 个别情况下，我们将开发方法来检测，并优先考虑，全基因组的候选人， 建立在我们以前的3D热点引出工作上。特别是，我们将设计原创的 无重建方法，以避免推断架构时的不确定性。 尽管有这些不确定性，重建赋予了几个优点。我们将部署新的 设计的分析，结合最近的算法进步，以提高重建精度 和决心。多重FISH提供了更丰富的染色质构象成像， 改进将Hi-C接触与距离联系起来的传递函数，这是重建的前兆。 以蛋白质为中心的HiChIP提供了信息读取的增益，多读取拯救也是如此。结合 这些进展将产生3D基因组重建的增强方法。 "a" 3D基因组重建的概念一直受到质疑，因为基础Hi-C 测定基于大的细胞群体。多重原位Hi-C使得能够产生 数千个单细胞数据集，我们将结合新的多轨道重建 解剖细胞间结构异质性的算法。我们还将利用这些数据来开发 基于结构差异的分类器，用于细胞类型之间的区分。 Hi-C数据的许多下游解释来自接触的光谱分析 基质，尤其是染色质分隔区的描绘。频谱总结具有局限性 包括在高分辨率下的隔室识别、对标准化的敏感性以及 解释变异。我们将评估接触矩阵的谱分析，重点是 近似对3D重建的影响，通过（i）推断的距离矩阵，（ii） 衍生重建，和（iii）随后的热点检测。

Abstract We are poised to enter a new era of conformational biology. Genome conformation is critical for numerous cellular processes, including gene regulation, with certain alterations (translocations, fu- sions) being oncogenic. While recent assays, notably Hi-C, have already transformed understanding of chromatin architecture, even newer technologies have the potential to dramatically improve accuracy and resolution of three-dimensional (3D) genome reconstructions. However, to fully realize this potential, new statistical methods and algorithms will be required to operate on the resultant data and structures, and to integrate concomitant biomedical data. This project aims at developing such methods. A concrete example is provided by current findings identifying an instance of insulated neighborhood disruption as a novel oncogenic mechanism. Instead of an individual instance, we will develop methods to detect, and prioritize, genome-wide candidates, building on our previous work on 3D hotspot elicitation. In particular, we will devise original reconstruction-free approaches to avert uncertainties in inferring architecture. Despite these uncertainties, reconstructions confer several advantages. We will deploy newly devised assays, in conjunction with recent algorithmic advances, to improve reconstruction accuracy and resolution. Multiplexed FISH provides richer imaging of chromatin conformation, enabling refinement of transfer functions linking Hi-C contacts to distances, a precursor to reconstruction. Protein-centric HiChIP provides gains in informative reads, as does multi-read rescue. Combining these advances will produce enhanced approaches to 3D genome reconstruction. The very notion of ‘a’ 3D genome reconstruction has been questioned since the underlying Hi- C assays are based on large cell populations. Multiplexed in situ Hi-C has enabled generation of thousands of single-cell datasets which we will couple with a new multi-track reconstruction algorithm to dissect inter-cellular structural heterogeneity. We will also use this data to develop classifiers, based on structural differences, for between cell-type discrimination. Much downstream interpretation of Hi-C data has derived from spectral analysis of the contact matrix, especially delineation of chromatin compartments. Spectral summarization has limitations including compartment identification at high resolution, sensitivity to normalization, and extent of explained variation. We will evaluate spectral analysis of contact matrices with emphasis on the impact of approximations on 3D reconstructions, assessed via (i) inferred distance matrices, (ii) derived reconstructions, and (iii) subsequent hotspot detection.