Targeted high-resolution chromosome conformation capture at genome-wide scale-猫眼课题宝

DOI：

10.1101/2020.03.02.953745

发表时间：

2020-03

期刊：

bioRxiv

影响因子：

通讯作者：

中科院分区：

其他

文献类型：

作者：

D. Downes;M. Gosden;Jelena M. Telenius;Stephanie J. Carpenter;L. Nussbaum;Sara de Ornellas;M. Sergeant;Chris Eijsbouts;R. Schwessinger;J. Kerry;N. Roberts;Arun Shivalingam;A. El-Sagheer;A. M. Oudelaar;T. Brown;Veronica J. Buckle;James O J Davies;J. Hughes

染色体构象捕获（3C）为研究各种生物学问题提供了一种适应性强的工具。目前的3C方法提供了整个基因组的低分辨率相互作用谱，或高达几百个基因座的高分辨率相互作用谱。所有3C方法都不同程度地受到低效率、偏差和噪声的影响。因此，尚未大规模实现可再现的高分辨率相互作用曲线的生成。为了克服这一障碍，我们系统地测试和改进了现有的方法。我们表明，从完整的细胞核中分离3C文库，以及在高分辨率方法中使用的富集寡核苷酸的缩短和滴定，降低了噪音，增加了靶向测序。我们将这些技术修改组合到一种新方法Nuclear-Titrated（NuTi）Capture-C中，其提供了比当前Capture-C方案多3倍的信息测序内容。使用NuTi Capture-C，我们一式三份靶向8，061个启动子，证明该方法可大规模生成可重复的高分辨率全基因组3C相互作用谱。

Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at up to several hundred loci. All 3C methods are affected to varying degrees by inefficiency, bias and noise. As such, generation of reproducible high-resolution interaction profiles has not been achieved at scale. To overcome this barrier, we systematically tested and improved upon current methods. We show that isolation of 3C libraries from intact nuclei, as well as shortening and titration of enrichment oligonucleotides used in high-resolution methods reduces noise and increases on-target sequencing. We combined these technical modifications into a new method Nuclear-Titrated (NuTi) Capture-C, which provides a >3-fold increase in informative sequencing content over current Capture-C protocols. Using NuTi Capture-C we target 8,061 promoters in triplicate, demonstrating that this method generates reproducible high-resolution genome-wide 3C interaction profiles at scale.

Targeted high-resolution chromosome conformation capture at genome-wide scale

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