MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (ChIP-Seq)

MePCE is a multifunctional protein that regulates the Positive Transcription Elongation Factor b (P-TEFb) partitioning between the nucleosol and chromatin. While the role of MePCE in sequestering P-TEFb in the nucleoplasm through the 7SK ribonuclear protein complex (RNPc) is well understood, its functions on chromatin remain obscure. In order to address this gap in our knowledge, we performed mass spectrometry of MePCE interactors on chromatin. Our analysis revealed that chromatin-associated-MePCE mainly interacts with factors involved in R-loop processing and DNA repair factors. Consistent with this initial finding, MePCE is rapidly recruited to laser-mediated DNA damage and AsiSI-mediated DNA double stranded breaks (DSBs). Moreover, MePCE depletion specifically impairs DSB repair by homologous recombination (HR). To explore the molecular mechanism behind the observed HR defect, we took advantage of an inducible AsiSI system to analyze the effect of MePCE depletion in DSB repair factor recruitment and R-loop levels at over 100 genomic site-specific DSBs. Consistent with impaired HR, MePCE depletion decreases RAD51 loading and enhances R-loop levels specifically at DSBs. Analysis of R-loop protein complexes by mass spectrometry revealed that in addition to decreasing specific R-loop processing factors and chromatin remodelers, MePCE depletion increased the interaction with R-loops of the other constitutive member of the 7SK RNPc, LARP7, which is degraded by BRCA1/BARD1 upon DSB. Overall, our results uncover dynamic regulation of the 7SK RNPc at DSBs during the repair process and explain the recently observed synthetic lethality of MePCE and BRCA1 deficiency. Overall design: Chromatin Immunoprecipitation of GFP (control), MePCE in U2OS-Flp-In-TREx siNC or siMePCE cells.