Extended Data Fig. 7: ATM, NELF-E, the PAF complex participate in DSB-induced transcriptional repression in cis.
From: Transcriptional repression facilitates RNA:DNA hybrid accumulation at DNA double-strand breaks
(a) RT–qPCR quantifying cDNA levels normalized to RPLP0 at 4 damaged genes (RBMXL1, MIS12, KLF7 and TRIM37) before and after DSB upon ATMi treatment. Mean and s.e.m. for n = 4 biological replicates are shown. P values are calculated with paired two-sided t-tests. (b) Levels of NELF-E and Myosin measured by Western blot after depletion of NELF-E. A representative experiment is shown (out of n = 2) (c) same as (a) for siRNA NELF-E-transfected cells. (d) Waves of elongation on all genes measured with DRB/TTchem-seq in -DSB and +DSB conditions. (e) Genomic track (hg19) example of a (+) orientated long gene (PKN2) and a (-) orientated short gene (GTF2B) showing waves of elongation measured by DRB/TTchem-seq on both Watson and Crick strands in -DSB and +DSB conditions. (f) Level of repression measured by RT–qPCR for RBMXL1 following DSB induction upon transfection of cells with different siRNAs (indicated on the y axis). The red dotted line represents the baseline of repression detected with siCtrl. (g) Levels of PAF1 and Tubulin (left panel) and SKI8 and Myosin (right panel) measured by Western blot after depletion of either PAF1 or SKI8 (n = 1). (h) Average profile and heatmap of PAF1 ChIP-seq signal on all genes −/+ 2 kb (normalized read count). (i) Genomic tracks (hg19) of PAF1 ChIP-seq before and after DSB induction as well as the Log2 fold change ratio (+DSB/-DSB) at a TC-DSB (DSB 765). Source numerical data and unprocessed blots are available in source data.
