Liu Pengyu, Lusk Jacob, Jonoska Nataša, Vázquez Mariel
Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, United States of America.
Department of Mathematics and Statistics, University of South Florida, Tampa, Florida, United States of America.
PLoS Comput Biol. 2024 Dec 13;20(12):e1012669. doi: 10.1371/journal.pcbi.1012669. eCollection 2024 Dec.
R-loops are a class of non-canonical nucleic acid structures that typically form during transcription when the nascent RNA hybridizes the DNA template strand, leaving the non-template DNA strand unpaired. These structures are abundant in nature and play important physiological and pathological roles. Recent research shows that DNA sequence and topology affect R-loops, yet it remains unclear how these and other factors contribute to R-loop formation. In this work, we investigate the link between nascent RNA folding and the formation of R-loops. We introduce tree-polynomials, a new class of representations of RNA secondary structures. A tree-polynomial representation consists of a rooted tree associated with an RNA secondary structure together with a polynomial that is uniquely identified with the rooted tree. Tree-polynomials enable accurate, interpretable and efficient data analysis of RNA secondary structures without pseudoknots. We develop a computational pipeline for investigating and predicting R-loop formation from a genomic sequence. The pipeline obtains nascent RNA secondary structures from a co-transcriptional RNA folding software, and computes the tree-polynomial representations of the structures. By applying this pipeline to plasmid sequences that contain R-loop forming genes, we establish a strong correlation between the coefficient sums of tree-polynomials and the experimental probability of R-loop formation. Such strong correlation indicates that the pipeline can be used for accurate R-loop prediction. Furthermore, the interpretability of tree-polynomials allows us to characterize the features of RNA secondary structure associated with R-loop formation. In particular, we identify that branches with short stems separated by bulges and interior loops are associated with R-loops.
R环是一类非经典核酸结构，通常在转录过程中形成，此时新生RNA与DNA模板链杂交，使非模板DNA链未配对。这些结构在自然界中大量存在，并发挥着重要的生理和病理作用。最近的研究表明，DNA序列和拓扑结构会影响R环，但目前尚不清楚这些因素以及其他因素如何促成R环的形成。在这项工作中，我们研究了新生RNA折叠与R环形成之间的联系。我们引入了树多项式，这是一类新的RNA二级结构表示方法。树多项式表示由与RNA二级结构相关联的有根树以及与该有根树唯一确定的多项式组成。树多项式能够对无假结的RNA二级结构进行准确、可解释且高效的数据分析。我们开发了一种计算流程，用于从基因组序列研究和预测R环的形成。该流程从共转录RNA折叠软件中获取新生RNA二级结构，并计算这些结构的树多项式表示。通过将此流程应用于包含R环形成基因的质粒序列，我们建立了树多项式系数和与R环形成的实验概率之间的强相关性。这种强相关性表明该流程可用于准确的R环预测。此外，树多项式的可解释性使我们能够表征与R环形成相关的RNA二级结构特征。特别是，我们发现由凸起和内环隔开的短茎分支与R环相关。
