Computational Methods for Predicting Changes in 3-D Chromosome Re- arrangement and Gene Deregulation in Human Diseases

该项目的目的是开发计算模型，以预测三维染色质组织。这可以从HiP-HoP模型开始实现，HiP-HoP模型允许复制通过3C和FISH实验获得的Pax6位点的构象。HiP-HoP模拟的基本思想是将染色质纤维表示为一个珠子弹簧聚合物，其中每个珠子对应1kb。为了理解基因组基因座如何折叠，有必要包括蛋白质（即转录因子），它们可以结合沿染色质链形成分子桥的特定位点。聚合物是由不同类型的珠子组成的，这些珠子与转录因子的相互作用或强或弱。ENCODE项目的数据允许为每个头分配特定类型，因为它们提供了有关表观遗传标记（例如H3K27ac区域）的信息，但也关于染色质可及性（例如通过使用ATAC-seq）。该模型还通过将转录因子视为可以在结合和非结合状态之间来回切换的珠子，嵌入了可能的翻译后修饰或活性蛋白质降解。染色质纤维折叠也受到CTCF/内聚蛋白环的影响：为了包括这种环挤压（LE）机制，在HiP-HoP模型中引入了非相邻珠之间的附加弹簧。在模拟过程中，弹簧运动形成循环，它们可以与灯丝结合或分离。最后一种机制旨在重现黏合蛋白和CTCF结合位点之间的相互作用，因为黏合蛋白驱动的LE过程在遇到具有面向挤出机方向的基序的CTCF位点时停止。最后，重要的是将染色质描述为异型纤维，以便准确预测具有不同转录活性水平的细胞内的3-D位点折叠。异型染色质是通过在没有乙酰化标记的珠粒之间加入额外的弹簧而获得的，这使得H3K27ac区域不那么紧密。HiP-HoP模型的所有先前的特征都可以正确地再现Pax6基因座的折叠，也可以再现珠蛋白基因座的折叠，而不需要对实验数据（例如HiC数据）进行任何拟合。因此，这个博士项目的目的是从这个模型开始预测其他细胞类型和不同生物体中基因座的结构。

The aim of this project is to develop computational models in order to predict the 3-D chromatin organization. This could be achieved by starting from the HiP-HoP model which allowed to reproduce the conformation of the Pax6 locus obtained through 3C and FISH experiments. The basic idea of HiP-HoP simulations is to represent the chromatin fibre as a bead- spring polymer where each bead corresponds to 1 kb. To understand how genomic loci fold, it is necessary to include proteins (i.e. transcription factors) which can bind particular sites along the chromatin chain forming molecular bridges. The polymer is so composed by beads of different types having a stronger or weaker interaction with transcription factors. Data from the ENCODE project allow to assign a specific type to each bead as they give information about epigenetic marks (e.g. H3K27ac regions), but also about chromatin accessibility (e.g. by using ATAC-seq). This model embeds also possible post-translational modifications or active protein degradation by considering transcription factors as beads which can switch back and forth between a binding and a non-binding state.Chromatin fibre folding is influenced by CTCF/cohesin loops too: to include this loop-extrusion (LE) mechanism, additional springs between non-adjacent beads are introduced in the HiP-HoP model. The springs move during simulations forming loops, and they can bind and unbind to the filament. This last mechanism intends to reproduce interactions between cohesin and CTCF binding sites, since the LE process driven by cohesin stops when this encounters a CTCF site with a motif oriented towards the direction of the extruder. Lastly it is important to depict chromatin as a heteromorphic fibre in order to accu- rately predict the 3-D loci folding within cells with different levels of transcriptional activity. The heteromorphic chromatin is obtained by including additional springs between beads without acetylation mark, leaving H3K27ac regions less compact. All previous features characterize the HiP-HoP model which correctly reproduces the folding of the Pax6 locus, but also of the globin loci, without requiring any fitting to experimental data (e.g. HiC data). The aim of this PhD project is therefore to start from this model to predict confor- mations of loci in other cell types and different organisms.