GSE120371
Deregulated expression of mammalian lncRNA through loss of SPT6 induces R-loop formation, replication stress and cellular senescence
Extensive tracts of the mammalian genome that lack protein-coding function are still transcribed into long noncoding RNA. While these lncRNA are generally short-lived, length-restricted and non-polyadenylated, how their expression is distinguished from protein-coding genes remains enigmatic. Surprisingly depletion of the ubiquitous Pol II associated transcription elongation factor SPT6, promotes a redistribution of H3K36me3 histone marks from active protein coding to lncRNA genes which correlates with increased lncRNA transcription. SPT6 knockdown also impairs the recruitment of Integrator complex to chromatin which results in a transcriptional termination defect for lncRNA genes. This leads to the formation of extended, polyadenylated lncRNA that are both chromatin restricted and form increased levels of RNA:DNA hybrid (R-loops) that are associated with DNA damage.  Additionally, these deregulated lncRNA overlap with DNA replication origins leading to localized DNA replication stress and a cellular senescence phenotype. Overall our results underline the importance of restricting lncRNA expression. Overall design: Directional R-loop occupancy was conducted by sequencing the RNA moeity of the R-loop fragments which were immunoprecipitated by mouse monoclonal S9.6 antibody.