Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.
Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA.
Nucleic Acids Res. 2022 Jul 22;50(13):7260-7286. doi: 10.1093/nar/gkac537.
R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. While the pathological consequences of R-loops have been well-studied to date, the locations, classes, and dynamics of physiological R-loops remain poorly understood. R-loop mapping studies provide insight into R-loop dynamics, but their findings are challenging to generalize. This is due to the narrow biological scope of individual studies, the limitations of each mapping modality, and, in some cases, poor data quality. In this study, we reprocessed 810 R-loop mapping datasets from a wide array of biological conditions and mapping modalities. From this data resource, we developed an accurate R-loop data quality control method, and we reveal the extent of poor-quality data within previously published studies. We then identified a set of high-confidence R-loop mapping samples and used them to define consensus R-loop sites called 'R-loop regions' (RL regions). In the process, we identified a stark divergence between RL regions detected by S9.6 and dRNH-based mapping methods, particularly with respect to R-loop size, location, and colocalization with RNA binding factors. Taken together, this work provides a much-needed method to assess R-loop data quality and offers novel context regarding the differences between dRNH- and S9.6-based R-loop mapping approaches.
R 环是由 RNA 和 DNA 杂交形成的三链核酸结构。尽管迄今为止已经对 R 环的病理后果进行了深入研究，但生理 R 环的位置、种类和动态仍知之甚少。R 环作图研究提供了对 R 环动力学的深入了解，但它们的发现难以推广。这是由于单个研究的生物学范围狭窄、每种作图方式的局限性，以及在某些情况下数据质量较差。在这项研究中，我们重新处理了来自广泛生物学条件和作图方式的 810 个 R 环作图数据集。从这个数据资源中，我们开发了一种准确的 R 环数据质量控制方法，并揭示了先前发表的研究中存在的低质量数据的程度。然后，我们确定了一组高可信度的 R 环作图样本，并使用它们来定义称为“R 环区域”（RL 区域）的一组共识 R 环位点。在此过程中，我们发现 S9.6 和基于 dRNH 的作图方法检测到的 RL 区域之间存在明显差异，尤其是在 R 环大小、位置和与 RNA 结合因子的共定位方面。总之，这项工作提供了一种急需的方法来评估 R 环数据质量，并提供了关于基于 dRNH 和 S9.6 的 R 环作图方法之间差异的新背景。
