Extended Data Fig. 8: INTS12-coordinated Pol II removal is dispensable for TC-DPC repair.

a, INTS12 KO cells reconstituted with stably expressed WT or 3 A INTS12-Flag were either untreated or treated with FA (1 mM, 1 h). Chromatin fractions (Input) and anti-Flag immunoprecipitates (IPs) were analyzed by WB. b, Control or INTS12 KO cells expressing INTS10-Flag or not (-) were untreated or treated with FA (1 mM, 1 h) and analyzed as in a. c, HeLa cells were untreated or treated with Camptothecin (CPT, 1 µM, 30 min, left) or 5-Aza-2’-deoxycytidine (5-aza-dc, 100 µM, 30 min, right) as indicated. Lysates were separated on Phos-tag SDS-PAGE and immunoblotted with the indicated antibodies. d, Lysates from HeLa cells that were untreated or treated with 4ST (4 d) and UVA (recover 30 min) were analyzed as in c. e, Schematic illustrating the potential role of INTS12 and its coordinated Pol II removal in TC-DPC repair. f, Box plots showing the DPC-seq coverage per gene in control, INTS12 KO, or CSB KO cells with or without 4 h recovery after FA treatment (n = 9288). Control, P < 2.2E-16; INTS12 KO, P < 2.2E-16; CSB KO, P = 1.7E-15. g, Heatmaps of DPC-seq data in control, INTS12 KO, or CSB KO cells after FA treatment followed by recovery for the indicated times. Genes were grouped into non, low, medium and high transcriptional activity gene sets as determined by TT-seq. h, i, Metaplots showing the average DPC-seq signal levels of all expressed (h) or non-expressed (i) genes in control, INTS12 KO, or CSB KO cells with or without 4 h recovery after FA treatment. j, Genome browser tracks showing the DPC-seq read distribution across the representative inactive gene in control, INTS12 KO, or CSB KO cells after FA treatment followed by recovery for the indicated times. For f, box plots show the minimum, quartiles and maximum. Statistical analysis was performed using two-tailed unpaired t-tests. All Western blots are representative of three independent experiments.

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