Biosensing of chromatin packing in live cells

为了将包含生物体遗传密码的两米长的DNA分子装入几微米大小的细胞核中，分子压缩成一种称为染色质的致密结构。染色质的一些部分显示出一种更开放的形式，称为常染色质，这是高基因表达的特征，而其他部分显示出一种更密集的染色质，称为异染色质。目前，还没有能够实时感知从异染色质到常染色质转化并返回的生物传感技术，这是了解细胞如何功能和人类基因组如何调节的一个至关重要的问题。因此，该项目的目标是开发一种在活细胞中对染色质包装进行动态生物传感的方法，并且在不使用可能影响细胞功能和染色质动力学的外部标记的情况下实现这一目标。这将通过利用散射光的特性来实现，散射光携带着被散射物体的信息，即使物体的结构非常微小，以至于普通显微镜无法分辨。该项目的一个重要部分将是教育推广计划，与代表性不足的群体和K-12学生分享技术。这项外展计划旨在帮助来自少数民族学生占主导地位的当地社区的K-12教育弱势学生。在本应用中提出的用于活细胞中染色质包装动态生物传感的新型无标记技术将解决遗传学和表观遗传学中尚未解决的基本问题。它应该有助于回答一个知之甚少的问题，即信号转导途径如何直接与染色质沟通，以改变表观遗传景观。它还可以促进一种新的合成生物学生物传感方法，因为染色质可以作为早期发育过程中代谢变化的传感器。它还应该对公共卫生产生重要影响，包括癌症中的染色质变化或表观遗传学在传染病中的作用。该方法将推进工程和生命科学，并将基于分形传感原理的组合，因为已知活细胞中的染色质是分形的，异染色质和常染色质结构域表现出不同的分形维数，以及相干共聚焦光吸收和散射光谱显微镜。提出的方法的动机是新的基本见解，即染色质分形的自相似特性反映在染色质光散射光谱中，这些光谱可以连续快速地记录，在多种空间和时间尺度上创建染色质的3D动态地图。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

In order to pack a two-meter-long DNA molecule that contains the genetic code of an organism into a several-micron sized nucleus, the molecule compacts into a dense structure called chromatin. Some parts of chromatin display a more open form called euchromatin, which is characteristic of high gene expression, while others exhibit a more densely packed chromatin called heterochromatin. Currently, there is no biosensing technology capable of sensing the conversion from heterochromatin to euchromatin and back in real time, which is a critically important question for understanding how cells function and how the human genome is regulated. Thus, the goal of this project is to develop a method for dynamic biosensing of chromatin packing in live cells and to achieve this without employing external markers that can affect cell function and, as a result, chromatin dynamics. This will be achieved by using properties of scattered light, which carries information about the object it is scattered by, even if the structure of the object is so tiny that regular microscopes cannot resolve it. An important part of this project will be an educational outreach program to share the technology with underrepresented groups and K-12 students. This outreach program is designed to reach K-12 educationally disadvantaged students from local neighborhoods with predominantly ethnic-minority student populations.The novel label-free technology for dynamic biosensing of chromatin packing in live cells, proposed in this application will address fundamental unsolved problems in genetics and epigenetics. It should help to answer a poorly understood question of how signal transduction pathways directly communicate with chromatin to change the epigenetic landscape. It can also facilitate a novel synthetic biology biosensing approach as chromatin can serve as a sensor of metabolic changes during early development. It should also have important implications in public health, including chromatin changes in cancer or the role of epigenetics in infectious diseases. The approach will advance both engineering and life sciences and will be based on a combination of the principles of fractal sensing, since it is known that chromatin in live cells is organized as a fractal with heterochromatin and euchromatin domains exhibiting different fractal dimensions, and coherent confocal light absorption and scattering spectroscopic microscopy. The proposed approach is motivated by the new fundamental insights that self-similar properties of the chromatin fractal are reflected in the chromatin light scattering spectra, and these spectra can be continuously and rapidly recorded creating a 3D dynamic map of chromatin on a multitude of spatial and temporal scales.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.