Knoch Tobias A
Biophysical Genomics, Department of Cell Biology & Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
Curr Protoc Hum Genet. 2018 Oct;99(1):e55. doi: 10.1002/cphg.55. Epub 2018 Sep 10.
After now more than 170 years of research the dynamic three-dimensional chromatin architecture of genomes and the co-evolved interaction networks of regulatory elements which create genome function - i.e. the storage, expression, and finally replication of genetic information - involves ever more investigative efforts in respect to not only the pure understanding of living organisms, but also diagnosis, treatment, and even future genome engineering. To study genomic interactions, we developed a novel and superior high-quality selective high-resolution, high-throughput chromosome interaction capture method - T2C (targeted chromatin capture) - which allows to arbitrarily balance resolution, frequency range of interactions, and the investigated general genetic region or single interactions in a highly cost-effective manner in respect to the obtainable result and compared to other techniques. Beyond, T2C has such a high signal-to-noise ratio at high resolution that the "genomic" statistical mechanics level can be reached. With the guided T2C protocol described here, we were already able to finally determine the chromatin quasi-fiber conformation and its folding into stable multi-loop aggregates/rosettes connected by a linker. Actually, this guided T2C protocol provides the means for architectural genome sequencing from the level of the single base pair to the entire cell nucleus and thus to analyze genetic interactions in respect to genome function in a systems biological manner in general as well as in settings ranging from basic research, via diagnostics and treatment, to genome engineering. © 2018 by John Wiley & Sons, Inc.
经过170多年的研究，基因组动态三维染色质结构以及共同进化的调控元件相互作用网络（这些网络创造了基因组功能，即遗传信息的存储、表达以及最终的复制），不仅对于纯粹理解生物体，而且对于诊断、治疗乃至未来的基因组工程，都需要投入越来越多的研究精力。为了研究基因组相互作用，我们开发了一种新颖且卓越的高质量选择性高分辨率、高通量染色体相互作用捕获方法——T2C（靶向染色质捕获），与其他技术相比，该方法能够以高度经济高效的方式，根据可获得的结果，任意平衡分辨率、相互作用频率范围以及所研究的一般遗传区域或单个相互作用。此外，T2C在高分辨率下具有如此高的信噪比，以至于能够达到“基因组”统计力学水平。通过本文所述的引导式T2C方案，我们最终已经能够确定染色质准纤维构象及其折叠成由连接体连接的稳定多环聚集体/玫瑰花结。实际上，这种引导式T2C方案为从单碱基对水平到整个细胞核的基因组结构测序提供了手段，从而能够以系统生物学的方式，在从基础研究到诊断、治疗再到基因组工程的各种环境中，分析与基因组功能相关的遗传相互作用。© 2018 John Wiley & Sons, Inc.
