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SummaryR-loops comprise an RNA/DNA hybrid and displaced single-stranded DNA. They play important biological roles and are implicated in pathology. Even so, proteins recognizing these structures are largely undefined. Using affinity purification with the S9.6 antibody coupled to mass spectrometry, we defined the RNA/DNA hybrid interactome in HeLa cells. This consists of known R-loop-associated factors SRSF1, FACT, and Top1, and yet uncharacterized interactors, including helicases, RNA processing, DNA repair, and chromatin factors. We validate specific examples of these interactors and characterize their involvement in R-loop biology. A top candidate DHX9 helicase promotes R-loop suppression and transcriptional termination. DHX9 interacts with PARP1, and both proteins prevent R-loop-associated DNA damage. DHX9 and other interactome helicases are overexpressed in cancer, linking R-loop-mediated DNA damage and disease. Our RNA/DNA hybrid interactome provides a powerful resource to study R-loop biology in health and disease.

Friedreich ataxia (FRDA) and Fragile X syndrome (FXS) are among 40 diseases associated with expansion of repeated sequences (TREDs). Although their molecular pathology is not well understood, formation of repressive chromatin and unusual DNA structures over repeat regions were proposed to play a role. Our study now shows that RNA/DNA hybrids (R-loops) form in patient cells on expanded repeats of endogenous FXN and FMR1 genes, associated with FRDA and FXS. These transcription-dependent R-loops are stable, co-localise with repressive H3K9me2 chromatin mark and impede RNA Polymerase II transcription in patient cells. We investigated the interplay between repressive chromatin marks and R-loops on the FXN gene. We show that decrease in repressive H3K9me2 chromatin mark has no effect on R-loop levels. Importantly, increasing R-loop levels by treatment with DNA topoisomerase inhibitor camptothecin leads to up-regulation of repressive chromatin marks, resulting in FXN transcriptional silencing. This provides a direct molecular link between R-loops and the pathology of TREDs, suggesting that R-loops act as an initial trigger to promote FXN and FMR1 silencing. Thus R-loops represent a common feature of nucleotide expansion disorders and provide a new target for therapeutic interventions.

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.

Silicon monoxide is a promising alternative anode material due to its much higher capacity than graphite, and improved cyclability over other Si anodes. An in-depth analysis of the lithium silicide (Li x Si) phases that form during lithiation/delithiation of SiO is presented here and the results are compared with pure-Si anodes. A series of anode materials is first prepared by heating amorphous silicon monoxide (a-SiO) at different temperatures, X-ray diffraction and 29 Si NMR analysis revealing that they comprise small Si domains that are surrounded by amorphous SiO 2 , the domain size and crystallinity growing with heat treatment. In and ex situ 7 Li and 29 Si solid-state NMR combined with detailed electrochemical analysis reveals that a characteristic metallic Li x Si phase is formed on lithiating a-SiO with a relatively high Li concentration of x = 3.4-3.5, which is formed/decomposed through a continuous structural evolution involving amorphous phases differing in their degree of Si-Si connectivity. This structural evolution differs from that of pure-Si electrodes where the end member, crystalline Li 15 Si 4 , is formed/decomposed through a two-phase reaction. The reaction pathway of SiO depends, however, on the size of the ordered Si domains within the pristine material. When crystalline domains of 5 nm within a SiO 2 matrix are present, a phase resembling Li 15 Si 4 forms, albeit at a higher overpotential. The continuous formation/decomposition of amorphous Li x Si phases without the hysteresis and phase change associated with the formation of c-Li 15 Si 4 , along with a partially electrochemically active SiO 2 /lithium silicate buffer layer, are paramount for the good cyclability of a-SiO.

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Na-ion batteries are promising alternatives to Li-ion systems for electrochemical energy storage because of the higher natural abundance and widespread distribution of Na compared to Li. High capacity anode materials, such as phosphorus, have been explored to realize Na-ion battery technologies that offer comparable performances to their Li-ion counterparts. While P anodes provide unparalleled capacities, the mechanism of sodiation and desodiation is not well-understood, limiting further optimization. Here, we use a combined experimental and theoretical approach to provide molecular-level insight into the (de)sodiation pathways in black P anodes for sodium-ion batteries. A determination of the P binding in these materials was achieved by comparing to structure models created via species swapping, ab initio random structure searching, and a genetic algorithm. During sodiation, analysis of P chemical shift anisotropies in NMR data reveals P helices and P at the end of chains as the primary structural components in amorphous NaP phases. X-ray diffraction data in conjunction with variable field Na magic-angle spinning NMR support the formation of a new NaP crystal structure (predicted using density-functional theory) on sodiation. During desodiation, P helices are re-formed in the amorphous intermediates, albeit with increased disorder, yet emphasizing the pervasive nature of this motif. The pristine material is not re-formed at the end of desodiation and may be linked to the irreversibility observed in the Na-P system.