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. 2024 Apr 10;26(5):784–796. doi: 10.1038/s41556-024-01401-2

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a, Volcano plot of MS analyses illustrating the interacting proteins with elongating RNAPII following formaldehyde treatment compared to UV irradiation. The plot displays the log₂(fold change) and significance (−log₁₀(P value)). Unpaired two-sided t-test. Permutation-based FDR < 0.05 (n = 3). Supplementary Table 2 provides the full results. b, Chromatin fractions of HeLa cells after formaldehyde treatment or UV irradiation were subjected to immunoprecipitation with anti-RPB1 CTD phospho-Ser2 antibodies, followed by immunoblotting with the indicated antibodies. Experiments were independently replicated twice with consistent results. c, Metagene profile from DPC-seq within or near transcribed regions of genes with TPM ≥ 30 at 0 and 4 h after formaldehyde washout in cells treated with VCP/p97 inhibitors. Data represent the average of two replicates. d, DPC residual ratios in cells treated with VCP/p97 inhibitors, shown in seven gene-length bins with TPM ≥ 100. Means (±s.e.m.) from three independent experiments are shown. Two-sided unpaired t-test. e, Metagene profile from DPC-seq within or near transcribed regions of genes with TPM ≥ 30 at 0 and 4 h after formaldehyde washout in HeLa cells treated with proteasome inhibitors. Data represent the average of three replicates. f, DPC residual ratios in cells treated with proteasome inhibitors are shown in seven gene-length bins with TPM ≥ 100. Means (±s.e.m.) from three independent experiments are shown. Two-sided unpaired t-test. g, Metagene profile from DPC-seq within or near transcribed regions of genes with TPM ≥ 30 at 0 and 4 h after formaldehyde washout in ΔCSB HeLa cells treated with the indicated inhibitors. Data represent the average of three replicates. h, DPC residual ratios in ΔCSB HeLa cells treated with the indicated inhibitors, shown in seven gene-length bins with TPM ≥ 100. Means (±s.e.m.) from three independent experiments are shown. Two-sided unpaired t-test. Source numerical data and unprocessed blots are available in the source data.

Source data