Persistence of backtrackingby human RNA polymerase II

RNA polymerase II (RNA Pol II) can backtrack during transcription elongation, exposing the 30end of nascentRNA. Nascent RNA sequencing can approximate the location of backtracking events that are quicklyresolved; however, the extent and genome-wide distribution of more persistent backtracking are unknown.Consequently, we developed a method to directly sequence the extruded, ''backtracked'' 30RNA. Our datashow that RNA Pol II slides backward more than 20 nt in human cells and can persist in this backtracked state.Persistent backtracking mainly occurs where RNA Pol II pauses near promoters and intron-exon junctionsand is enriched in genes involved in translation, replication, and development, where gene expression isdecreased if these events are unresolved. Histone genes are highly prone to persistent backtracking, andthe resolution of such events is likely required for timely expression during cell division. These results demon-strate that persistent backtracking can potentially affect diverse gene expression programs.