Fig. 6: Targeting of R-loops by HDACi may change gene expression without modifying the pattern of spliced isoforms. | Nature Communications

Fig. 6: Targeting of R-loops by HDACi may change gene expression without modifying the pattern of spliced isoforms.

From: Accelerated DNA replication fork speed due to loss of R-loops in myelodysplastic syndromes with SF3B1 mutation

Fig. 6

a Violin plots with medians and quartiles representing R-loops as shared peak numbers by DRIP-seq of 3 SF3B1MUT, 3 SF3B1WT (2 SRSF2MUT, 1 TET2/NRASMUT) and 4 control erythroblasts ± HDACi at 0.5 μM for 20 h. Two-sided unpaired t-test. b R-loop annotation to gene features in SF3B1MUT samples. Left panel: Shared peak numbers. Right panel: Fold-increase of peak number between HDACi and DMSO conditions. c R-loop profiles near BCL2L1 and PTPN11 promoter. RPM: reads par million. d Quantification of BCL2L1, NCOA4, PTPN11 and HK1 transcripts by RT-qPCR in 4 SF3B1MUT and 3 control samples. Mean quantities normalized to PPIA ± SD. Two-sided unpaired t-test. e Expression of PPOX, PPM1A, COASY, S100A4, and BCL2L1 transcript isoforms by RT-PCR representative of 4 SF3B1MUT, 6 SF3B1WT and 2 control samples. **** P < 0.0001, *** P < 0.001, ** P < 0.01, * P < 0.05. Source data are provided as a Source Data file.

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