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These features may affect the DNA and/or RNA structures, or possibly an RNA/DNA hybrid, which in turn signals for an RDD event as mentioned above. In this work, we examined where RDDs occur and considered the results in the context of known RNA-editing mechanisms. We showed that all 12 types of RDDs are found in RNAs that have recently extruded from the RNA Pol II exit channel. The RDD events occurred in?vivo on transcripts ?35 nt from the exit channel of Pol II. Pol II elongates in mammalian cells at 20�C60 bases per second (Ardehali and Lis, 2009). Therefore, the RDD events found ?35 bases from the exit channel must occur very shortly after nascent RNA synthesis. Thus, our results indicate that RDDs are likely to occur within a few seconds of RNA synthesis and before classic www.selleckchem.com/products/AP24534.html RNA-editing events. RNAs synthesized by RNA Pol II are quickly modified: 5�� caps are added as the RNA end exits the Pol II RNA channel (Rasmussen and Lis, 1993), introns are often spliced cotranscriptionally (Carrillo Oesterreich et?al., 2010?and?Vargas et?al., 2011), and 3�� ends are cleaved and polyadenylated before Pol II terminates transcription (Osheim et?al., 2002). Based on knowledge about cotranscriptional processing events and results from the present study, we suggest that RDDs occur soon after the capping of the transcripts Oxalosuccinic acid and before splicing. Our purpose in examining the timing of RDDs was to narrow the search for the underlying mechanisms that mediate its formation. A cotranscriptional event that coincides temporally with RDD formation is the emergence of the R loop (Broccoli et?al., 2000, Drolet et?al., 1995?and?Mass�� and MI-773 in vivo Drolet, 1999). As a preliminary search for an association between RDDs and the R?loop, we studied RDDs in very nascent RNA of cells from a juvenile ALS patient with a mutation in the senataxin gene (Chen et?al., 2004). The RNA/DNA helicase senataxin interacts with RNA polymerase and mediates the resolution of R loops. We found that the patient had ?50% fewer RDDs in her nascent RNAs. The RDDs seem to be associated with the R loop since there is enrichment in R-loop-forming sequences (Ginno et?al., 2012) around RDD sites and depletion of G-bearing RDD transcripts in the patient. These findings point to a possible coupling of RDDs and R-loop formations, and encourage further studies to uncover the molecular basis. The GRO-seq and PRO-seq assays allowed us to study very nascent RNA for RDD formation. However, these methods also limited our studies to sequences that are covered by or immediately adjacent (