Mutations in several general pre-mRNA splicing factors have been linked to myelodysplastic syndromes (MDSs) and solid tumors. These mutations have generally been assumed to cause disease by the resultant splicing defects， but different mutations appear to induce distinct splicing defects， raising the possibility that an alternative common mechanism is involved. Here we report a chain of events triggered by multiple splicing factor mutations， especially high-risk alleles in SRSF2 and U2AF1， including elevated R-loops， replication stress， and activation of the ataxia telangiectasia and Rad3-related protein (ATR)-Chk1 pathway. We further demonstrate that enhanced R-loops， opposite to the expectation from gained RNA binding with mutant SRSF2， result from impaired transcription pause release because the mutant protein loses its ability to extract the RNA polymerase II (Pol II) C-terminal domain (CTD) kinase-the positive transcription elongation factor complex (P-TEFb)-from the 7SK complex. Enhanced R-loops are linked to compromised proliferation of bone-marrow-derived blood progenitors， which can be partially rescued by RNase H overexpression， suggesting a direct contribution of augmented R-loops to the MDS phenotype.