Three-dimensional interrogation of gene regulation using next generation chromatin conformation capture and super-resolution imaging.

要形成构成我们身体的细胞和组织，需要对我们基因的活动进行精确的控制。基因的蛋白质产物构成了我们细胞的功能和结构成分。基因的表达是由一组称为转录因子的蛋白质控制的，这些蛋白质结合了我们DNA(也称为“基因组”)中的特定序列。如果这种控制被基因组中的序列变化改变，那么我们细胞的正确功能就会受到影响，并可能导致疾病：特定的一种或多种疾病取决于受影响的细胞的类型。科学家们已经非常擅长寻找编码蛋白质的~2%的DNA，然而，很明显，我们基因组的其他部分(称为调节元件)在控制我们的基因方面起着关键作用。调节元件散布在基因组中，识别这些元件的新方法表明，很难理解它们控制哪个基因，因为它们不一定控制附近的基因，但可能影响相当遥远的基因。一种名为染色体构象捕获的技术可以将调控元件与它们控制的基因联系起来，方法是绘制它们的物理相互作用图，这是它们活动所必需的，但这仍然无法解释为什么某些元件可以接触和调节某些特定的基因，而不是其他基因。这是一个重要的问题，因为基因组序列的变化可能会阻止调控元件与正确的基因对话，或者导致它们与错误的基因对话，从而产生非常具破坏性的后果。使这些相互作用具体化的机制尚不清楚，但被认为是由于基因组在细胞核中的三维排列。这项提案中的工作采用了分子生物学家、化学家和计算科学家合作开发的技术，以3D可视化这些相互作用，以了解某些调控元件如何与特定基因一起工作，以及基因组的变化如何改变这一点并导致疾病。

To form the cells and tissues that make up our bodies requires exquisite control of the activity of our genes. The protein products of genes form the functional and structural components of our cells. Gene expression is controlled by a subgroup of proteins called transcription factors which bind specific sequences in our DNA (also called the "genome"). If this control is altered by sequence changes in the genome then the correct function of our cells is affected and can lead to disease: the particular disease or diseases depend on the types of cells affected. Scientists have become very good at finding the ~ 2% of our DNA that encodes for protein, however it has become clear that other parts of our genome (called regulatory elements) play a critical role in controlling our genes.Regulatory elements are scattered throughout the genome and novel methods that identify such elements show that it is very difficult to understand which gene they control as they do not necessarily control nearby genes, but may affect quite distant genes. A technique called chromosome conformation capture can link regulatory elements to the genes they control by mapping their physical interactions, which are necessary for their activity, but this still does not explain why certain elements can contact and regulate some specific genes but not others. This is an important question because changes in the genome sequence can prevent regulatory elements talking to the correct genes or cause them to talk to the wrong genes with very damaging consequences. The mechanism that makes these interactions specific is unknown, but is thought to be due to the three dimensional arrangement of the genome in the nucleus. The work in this proposal adapts technologies developed by a collaboration between molecular biologists, chemists and computational scientists to visualize these interactions in 3D to understand how certain regulatory elements work with specific genes and how changes in the genome can alter this and cause disease.