Out of Balance: R-loops in Human Disease

R-loops are cellular structures composed of an RNA/DNA hybrid, which is formed when the RNA hybridises to a complementary DNA strand and a displaced single-stranded DNA. R-loops have been detected in various organisms from bacteria to mammals and play crucial roles in regulating gene expression, DNA and histone modifications, immunoglobulin class switch recombination, DNA replication, and genome stability. Recent evidence suggests that R-loops are also involved in molecular mechanisms of neurological diseases and cancer. In addition, mutations in factors implicated in R-loop biology, such as RNase H and SETX (senataxin), lead to devastating human neurodegenerative disorders, highlighting the importance of correctly regulating the level of R-loops in human cells. In this review we summarise current advances in this field, with a particular focus on diseases associated with dysregulation of R-loop structures. We also discuss potential therapeutic approaches for such diseases and highlight future research directions.     

TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution

R-loops, which consist of a DNA/RNA hybrid and a displaced single-stranded DNA (ssDNA), are increasingly recognized as critical regulators of chromatin biology. R-loops are particularly enriched at gene promoters, where they play important roles in regulating gene expression. However, the molecular mechanisms that control promoter-associated R-loops remain unclear. The epigenetic ‘reader’ Tudor domain-containing protein 3 (TDRD3), which recognizes methylarginine marks on histones and on the C-terminal domain of RNA polymerase II, was previously shown to recruit DNA topoisomerase 3B (TOP3B) to relax negatively supercoiled DNA and prevent R-loop formation. Here, we further characterize the function of TDRD3 in R-loop metabolism and introduce the DExH-box helicase 9 (DHX9) as a novel interaction partner of the TDRD3/TOP3B complex. TDRD3 directly interacts with DHX9 via its Tudor domain. This interaction is important for recruiting DHX9 to target gene promoters, where it resolves R-loops in a helicase activity-dependent manner to facilitate gene expression. Additionally, TDRD3 also stimulates the helicase activity of DHX9. This stimulation relies on the OB-fold of TDRD3, which likely binds the ssDNA in the R-loop structure. Thus, DHX9 functions together with TOP3B to suppress promoter-associated R-loops. Collectively, these findings reveal new functions of TDRD3 and provide important mechanistic insights into the regulation of R-loop metabolism.     

Arrangement of the rRNA sequences in the rDNA of Lytechinus variegatus

The arrangement of the 26S RNA and 18S RNA sequences of the ribosomal DNA (rDNA) from the sea urchin Lytechinus variegatus was investigated by an electron microscopic analysis of R-loops formed between the ribosomal RNA genes and the mature ribosomal RNAs. Ninety-eight percent of observed molecules contained R-loops clearly seen as a three-stranded complex. The size of DNA complementary to mature cytoplasmic 18S and 26S ribosomal RNA (rRNA) was calculated by measuring the double-strand (ds) and single-strand (ss) part of the R-loops separately. The values for the 18S R-loop are 1.75±0.24 kb¹ (ss) and 1.56±0.23 kb (ds). The 26S R-loop is 3.34±0.39 kb (ss) and 3.33±0.33 kb (ds). These measurements agree fairly well with the rRNA sizes measured on denaturing sucrose density gradients: 3.23±0.22 kb for the 26S and 1.93±0.10 kb for 18S. The short spacer between the 18S and 26S R-loops is 1.03±0.24 kb and the longer spacer is 5.36±0.53 kb. In long molecules a repeating pattern was observed. The average length of an rDNA repeat unit is 11.33±0.64 kb when computed using double-strand R-loop measurements and 11.50±0.72 when computed using R-loop single-strand lengths.Abbreviations kb kilobases, 1000 bases of RNA or single-strand DNA, and kilobase pairs, 1000 base pairs of duplex DNA or DNA/RNA hybrid - EDTA ethylenediaminetetraacetate - SSC 0.15 M NaCl, 0.015 M sodium citrate - PIPES piperazine-N,N-bis (2-ethanesulfonic acid)-Na_1.4     

R-loop stability as a function of RNA structure and size.

The sequence-specific formation of R-loops can be assayed using RNAs which overlap a HindIII cleavage site in a 3.5 kb plasmid. Chemical modification of the displaced DNA strand has permitted stabilization of these R-loops and allowed a systematic investigation of the dependence of these triple-stranded structures on the chain length and structure of the input RNA. RNAs as short as 50 nt form stable R-loops if 5-allylamine uridines (Uaa-RNA) are used in place of normal uridines; normal RNAs must be 100 nt long to form R-loops quantitatively. Since acetic anhydride decreases the hybridization efficiency of Uaa-RNAs, the positive charge of the RNAs must diminish the electrostatic repulsion of the three negatively charged phosphodiester backbones. The dependence of R-loop stability on the length of RNA can be stimulated with a random walk model, which also applies to strand migration within Holiday junctions. R-loop hybridization provides a versatile method to generate single-stranded DNA in a sequence-selective manner.     

毛果杨固有无序蛋白质基因克隆及胁迫响应分析

为了解毛果杨中固有无序蛋白PtrIDP1（Potri.010G161200.1）基因的相关信息，探究该基因在毛果杨的不同组织、不同逆境胁迫下的表达特性，本研究根据Phytozome数据库中得到的基因全长序列设计引物，克隆得到该基因的目的片段。该基因完整的CDs区序列长度为423 bp，共编码140个氨基酸。构建亚细胞定位表达载体，瞬时转化洋葱表皮细胞，在激光共聚焦显微镜下观察显示，PtrIDP1定位在细胞核内。利用实时定量RT-PCR技术分析了PtrIDP1基因在毛果杨不同组织中的表达特异性和应对非生物胁迫的表达特性。结果表明：PtrIDP1基因在毛果杨的根、茎、叶中均有表达，其中在根部表达量最低，在茎和叶中相对表达量较高。PtrIDP1基因在高盐和干旱胁迫诱导时其表达量的变化模式不同，初步分析认为PtrIDP1基因参与了毛果杨非生物逆境胁迫的响应过程。     

Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions

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.     

PtrWRKY51基因的克隆及抗旱表达特性分析

为明确毛果杨WRKY家族成员PtrWRKY51基因功能,以Nisqually-1株系毛果杨为模板,克隆得到PtrWRKY51基因CDS序列。通过生物信息学分析,结合酵母自激活验证、亚细胞定位及模拟干旱胁迫下的实时荧光定量PCR(qRT-PCR)对PtrWRKY51基因功能进行初步研究。结果表明：PtrWRKY51全长579 bp,编码192 aa。生物信息学分析及亚细胞定位试验结果表明,PtrWRKY51蛋白为非跨膜碱性不稳定亲水蛋白,定位于细胞核,含有WRKY家族特有的保守结构域,是第IIc类WRKY转录因子;酵母自激活验证试验表明PtrWRKY51基因具有自激活活性;qRT-PCR分析表明,8%PEG6000模拟干旱胁迫下,该基因在胁迫12 h后茎部与叶部相对表达量达到最大值,根部则出现在24 h,研究可为PtrWRKY51抗逆及生物学功能进一步研究提供参考。     

意大利蜜蜂工蜂中肠的环状RNA及其调控网络分析

【目的】环状RNA(circRNA)在可变剪接、转录调控和来源基因的表达调控等方面具有重要功能。本研究旨在分析意大利蜜蜂Apis mellifera ligustica工蜂中肠circRNA的数量、种类、结构特征和作用,并通过构建和分析circRNA的调控网络探索circRNA的调控功能。【方法】在实验室条件下人工饲养意大利蜜蜂工蜂,利用circRNA-seq技术对意大利蜜蜂7和10日龄成年工蜂中肠样品进行深度测序。利用find_circ软件从质控后的数据中预测circRNA。通过BLAST比对GO和KEGG数据库,对circRNA的来源基因进行功能和代谢通路注释。利用TargetFinder软件预测circRNA靶向结合的miRNA及miRNA靶向结合的mRNA,通过Cytoscape v.3.2.1软件对circRNA-miRNA和circRNA-miRNA-mRNA调控网络进行构建及可视化。通过设计背靠背引物和线性扩增引物RT-PCR对预测出的circRNA进行验证。【结果】意大利蜜蜂工蜂中肠样品的测序平均得到136 463 071条clean reads,去除rRNA后各样品的anchor reads均在136 779 122条及以上。共预测出10 833个circRNA,长度主要介于15~1 000 nt;上述circRNA的类型丰富,其中已注释的外显子circRNA数量最多,分布在西方蜜蜂1号染色体的circRNA数量最多,其次为8号染色体。CircRNA的来源基因可注释到包括结合、细胞进程和细胞在内的45个GO条目,以及包括内吞作用、内质网蛋白加工及核糖体在内的121条KEGG代谢通路,表明circRNA在意大利蜜蜂工蜂中肠的生长、发育、新陈代谢和细胞生命活动等生物学过程中发挥重要作用。进一步构建circRNA-miRNA和circRNA-miRNA-mRNA调控网络,分析结果显示部分circRNA可能作为竞争性内源RNA吸附结合microRNA,从而调控基因的表达水平。最后,对随机选择的3个circRNA的RT-PCR结果验证了其真实存在。【结论】本研究对意大利蜜蜂工蜂中肠中的circRNA进行预测、分析及鉴定。研究结果提供了中肠circRNA的数量、种类、结构特征、作用和调控网络的信息,揭示了circRNA可能通过作用于来源基因和作为竞争性内源RNA在意大利蜜蜂工蜂中肠的生长发育和免疫防御中发挥作用,为深入研究circRNA在意大利蜜蜂中肠发育及胁迫响应过程中的功能奠定了基础。