The nucleotides on both strands at 115 of the 225 sites had undergone RNA editing, which we called symmetrical RNA editing (SRE). Four of six these SRE sites (66.7%) were experimentally confirmed. Re-examination of strand-specific RNA-Seq data from A. thaliana and O. sativa identified 327...
To determine whether R-loops form at PREs, we carried out two biological replicates of strand-specific DNA-RNA Immunoprecipitation followed by next generation sequencing (DRIP-seq) in Drosophila embryos (2–6 and 10–14 hour (H)) and in S2 cells (Fig. 1, Supplementary Fig. 1). DRIP-se...
1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms7002 Massively parallel sequencing of RNA (RNA-seq) has revolutionized our understanding of transcriptomes1–3. Several library preparation methods for strand-specific sequencing of RNA (ssRNA-seq) have been developed in the recent past3–8. ...
Here, we report that plant and animal +ssRNA viruses contain small open reading frames (ORFs) in their −RNA (reverse ORFs [rORFs]). Using turnip mosaic virus (TuMV) as a model for plant +ssRNA viruses, we demonstrate that small proteins encoded by rORFs display specific subcellular ...
As HO-TRCs could result in R-loop accumulation and DNA damage, we then analyzed the DNA damage sites in the chloroplast genome by DEtail-seq (DNA End tailing and sequencing), a method we recently developed that can detect 3′ end damage sites with strand-specific information29. Along with ...
a single-strand-specific cytidine deaminase and an exonuclease to generate a single-stranded DNA substrate for deamination. We demonstrate effective base editing in nuclear, mitochondrial and chloroplast genomes. At certain mitochondrial sites, we show editing efficiencies of 14% and strand specificity of...
RNA-splicing factors such as NONO and THRAP355,56have also been implicated in DNA repair and might represent a sub-family of RNA-processing proteins involved in the DDR.55,56,60In addition, research from the Farnebo lab has identified WRAP53β, the small Cajal body-specific RNA (scaRNA)...
(D277N) in SPO11 abolishes meiotic DSB formation in mice. However, unlike topo VI, which requires ATP for its activity, the mouse SPO11 complex does not depend on ATP for DNA cleavage. This distinction might reflect an evolutionary adaptation in SPO11 function specific to meiotic DSB ...
Furthermore, we also observed decreases in the total absolute indel rates when using the double tap method in ten out of eleven cases (Fig.2c, d). In all cases, introduction rates of the specific indels targeted with secondary gRNAs decreased (Fig.2d). At the same time, certain indel se...