Sanborn Adrian L, Rao Suhas S P, Huang Su-Chen, Durand Neva C, Huntley Miriam H, Jewett Andrew I, Bochkov Ivan D, Chinnappan Dharmaraj, Cutkosky Ashok, Li Jian, Geeting Kristopher P, Gnirke Andreas, Melnikov Alexandre, McKenna Doug, Stamenova Elena K, Lander Eric S, Aiden Erez Lieberman
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030; Department of Computer Science, Stanford University, Stanford, CA 94305;
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; School of Medicine, Stanford University, Stanford, CA 94305;
Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6456-65. doi: 10.1073/pnas.1518552112. Epub 2015 Oct 23.
We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic "tension globule." In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops. However, the extrusion model explains a far wider array of observations, such as why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.
我们最近使用原位Hi-C技术创建了哺乳动物基因组的千碱基分辨率三维图谱。在此，我们将这些图谱与新的Hi-C、显微镜及基因组编辑实验相结合，以研究染色质纤维、结构域和环的物理结构。我们发现，观察到的接触结构域与普通凝聚态聚合物的平衡状态不一致。结合Hi-C数据和新的数学定理，我们表明接触结构域也不符合分形球状体模型。相反，我们使用物理模拟来研究两种基因组折叠模型。在一种模型中，聚合物凝聚过程中的单体间吸引力导致形成各向异性的“张力球状体”。在另一种模型中，CCCTC结合因子（CTCF）和黏连蛋白在间期共同作用挤出无结环。两种模型都与观察到的接触结构域以及接触结构域倾向于在环内形成的观察结果一致。然而，挤压模型解释了更广泛的一系列观察结果，例如为什么环往往不重叠以及为什么环锚对处的CTCF结合基序呈汇聚方向。最后，我们进行了13项基因组编辑实验，研究改变CTCF结合位点对染色质折叠的影响。汇聚规则在每种情况下都能正确预测受影响的环。此外，挤压模型仅使用野生型中CTCF结合位点的位置就能在计算机上准确预测每个实验产生的三维图谱。因此，我们表明使用小至单个碱基对的靶向突变来破坏、恢复和移动环及结构域是可行的。
