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Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability

Nature Cell Biology volume 23, pages 608–619 (2021)Cite this article

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A Publisher Correction to this article was published on 23 June 2021

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Abstract

Correct transcription is crucial for life. However, DNA damage severely impedes elongating RNA polymerase II, causing transcription inhibition and transcription-replication conflicts. Cells are equipped with intricate mechanisms to counteract the severe consequence of these transcription-blocking lesions. However, the exact mechanism and factors involved remain largely unknown. Here, using a genome-wide CRISPR–Cas9 screen, we identified the elongation factor ELOF1 as an important factor in the transcription stress response following DNA damage. We show that ELOF1 has an evolutionarily conserved role in transcription-coupled nucleotide excision repair (TC-NER), where it promotes recruitment of the TC-NER factors UVSSA and TFIIH to efficiently repair transcription-blocking lesions and resume transcription. Additionally, ELOF1 modulates transcription to protect cells against transcription-mediated replication stress, thereby preserving genome stability. Thus, ELOF1 protects the transcription machinery from DNA damage via two distinct mechanisms.

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Fig. 1: Genome-wide CRISPR–Cas9 screen identifies ELOF1 as a factor involved in the UV-induced DNA-damage response.
Fig. 2: ELOF1 is part of the elongating Pol II complex.
Fig. 3: ELOF1 is important for functional TC-NER.
Fig. 4: ELOF1 is an evolutionarily conserved TC-NER factor.
Fig. 5: Prolonged stalling of Pol II at TBLs in the absence of ELOF1.
Fig. 6: ELOF1 is crucial for proper TC-NER complex assembly.
Fig. 7: ELOF1 has an additional function apart from TC-NER.
Fig. 8: ELOF1 is important for preventing genome instability.

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Data availability

All the DRB/TTchem-seq data used in this study are available under GEO accession number GSE148844. All the CPD-seq data are available under GEO accession number GSE149082. The SILAC-based quantitative interaction proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD025304. Source data are provided with this paper. Any other data are available from the corresponding author upon reasonable request.

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Acknowledgements

We thank the Optical Imaging Center and the Proteomics Center of the Erasmus Medical Center for support with microscopes and mass spectrometry analysis. We thank the Advanced Sequencing Facility of the Francis Crick Institute for technical assistance with DRB/TTchem-seq. We acknowledge infrastructural support from the Josephine Nefkens Precision Cancer Treatment Program. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society and was funded by a grant from the Dutch Cancer Society (KWF grant 10506). This work was further funded by the Dutch organization for Scientific Research (NWO-ALW), which awarded a VIDI (864.13.004) and VICI (VI.C.182.025) grant to J.A.M. A.R.C. is supported by the Dutch Cancer Society (KWF grant 11008) and NWO VIDI (193.131). S.L. is funded by the National Science Foundation (MCB-1615550). J.J.W. is funded by the National Institute of Environmental Health Sciences (grants R01ES028698, R21ES029655 and R21ES029302). M.A.T.M.v.V. is funded by a grant from the European Research Council (ERC CoS grant 682421). H.L. is funded by The Netherlands Organization for Scientific Research (project number 711.018.007) and Cancergenomics.nl. W.V. was funded by a grant from the European Research Council (agreement 340988). J.Q.S. was supported by the Francis Crick Institute (which receives funding from Cancer Research UK (FC001166), the UK Medical Research Council (FC001166) and the Wellcome Trust (FC001166)) and by a grant from the European Research Council (agreement 693327).

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Author notes

  1. These authors contributed equally: Di Zhou, Kathiresan Selvam, Barbara Steurer, Chirantani Mukherjee, Bastiaan Evers, Simona Cugusi.

Authors and Affiliations

  1. Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands

    Marit E. Geijer, Di Zhou, Barbara Steurer, Chirantani Mukherjee, Marvin van Toorn, Melanie van der Woude, Roel C. Janssens, Anja Raams, Calvin S. Y. Lo, Joyce H. G. Lebbink, Arjan F. Theil, Wim Vermeulen, Hannes Lans, Arnab Ray Chaudhuri & Jurgen A. Marteijn

  2. School of Molecular Biosciences, Washington State University, Pullman, WA, USA

    Kathiresan Selvam, Dalton A. Plummer & John J. Wyrick

  3. Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands

    Bastiaan Evers & René Bernards

  4. Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK

    Simona Cugusi & Jesper Q. Svejstrup

  5. Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands

    Yannick P. Kok & Marcel A. T. M. van Vugt

  6. Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA

    Wenzhi Gong & Shisheng Li

  7. Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands

    Joyce H. G. Lebbink

  8. Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands

    Bart Geverts & Adriaan B. Houtsmuller

  9. Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands

    Karel Bezstarosti & Jeroen A. A. Demmers

  10. Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK

    Richard Mitter

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  1. Marit E. Geijer
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Contributions

M.E.G. performed the majority of the experiments and generated the ELOF1 and CSB KO cell lines and the ELOF1 and RPB1 KI cell lines. D.Z. generated the CSB and UVSSA KI cells and performed live-cell imaging experiments and the TCR UDS. K.S., D.A.P., W.G., S.L. and J.J.W. performed and supervised all the S. cerevisiae experiments. B.S. and M.E.G. performed the CRISPR–Cas9 screen, and B.E. and R.B. analysed and supervised the screen. C.M., C.L. and A.R.C. performed and supervised the metaphase spread, DNA fibre analysis and 53BP1 cell cycle analysis. S.C., R.M. and J.Q.S. performed and supervised the DRB/TTchem-seq. M.v.T. performed the AlamarBlue cell-viability assay. M.v.d.W. and H.L. performed and supervised the C. elegans experiments. R.C.J. provided experimental support. Y.P.K. performed the EdU and FANCD2 foci analysis, supervised by M.A.T.M.v.V. J.H.G.L. generated images of the Pol II structure. B.G. performed the Monte-Carlo-based modelling and was supervised by A.B.H. K.B. and J.A.A.D. performed and supervised the mass spectrometry analysis. A.R. performed the UDS experiments and A.F.T. performed FACS sorting, both supervised by W.V. J.A.M. conceived and supervised the project and together with M.E.G. wrote the manuscript with input from all authors.

Corresponding author

Correspondence to Jurgen A. Marteijn.

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The authors declare no competing interests.

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Peer review Information Nature Cell Biology thanks the anonymous reviewers for their contribution to the peer review of this work.

Extended data

Extended Data Fig. 1 Generation of ELOF1 knock-in and knock-out cells.

a, Brightfield images of MRC-5 cells irradiated with indicated doses of UV-C for 10 consecutive days. Images were taken every other day. Scale bar: 60 µm. b, Top 10 enriched GO terms (biological process) identified using g:Profiler of UV-sensitive genes with FDR<0.1 (n = 49). c, Schematic of the genomic ELOF1 locus. Scissors indicate target regions of the sgRNAs used to generated ELOF1 KO (−/−) cells, half arrows indicate primers used for genotyping as shown in (c). Red arrows indicate location of the qPCR primers as shown in (e). d,e, Genotyping of ELOF1 KO (−/−) cells, both originating from a single cell clone. d, Genotyping PCR of loss of exon 2 in ELOF1 −/−A cells. Assays in d, i, j and g have been performed two times with similar results. e, Top panel: Sequencing results showing frameshift mutations in the targeted genomic locus of ELOF1 −/−B. Bottom panel: Amino acid sequence of ELOF1 in ELOF1 −/−B cells. f, Relative ELOF1 levels in indicated HCT116 Wt and ELOF1 KO (−/−) cells, with ELOF1 re-expression where indicated, as determined by RT-qPCR. Relative ELOF1 mRNA expression was normalized to GAPDH signal and levels in Wt cells were set to 1. ND=not detected. Data shown in represent average ± SEM (n = 3 independent experiments. g, Immunoblot of indicated HCT116 cell lines showing CSB or ELOF1-GFP expression. Tubulin was used as loading control. h, Relative ELOF1 levels in HCT116 cells transfected with indicated siRNAs as determined by RT-qPCR. Relative ELOF1 expression was normalized to GAPDH signal and siCTRL levels were set to 1. Data shown represent average from 2 independent experiments. i, Immunoblot showing endogenous ELOF1 and XPF levels in ELOF1-mScarletI-HA KI cells (Extended Data Fig. 2a) transfected with indicated siRNAs. Tubulin was used as loading control. j, Immunoblot showing expression of Flag-tagged Wt or indicated ELOF1 mutants in HCT116 ELOF1 −/−A cells. k, Relative colony survival of CPD photolyase cells transfected with indicated siRNAs. PR indicates CPD removal by photoreactivation. Plotted curves represent averages of 2 independent experiments. Numerical data and uncropped blots are provided in source data.

Source data

Extended Data Fig. 2 ELOF1 is part of the Pol II complex.

a, Left panel: Schematic of the genomic locus of ELOF1 for generating ELOF1-mScarletI-HA KI cell line. Half arrows indicate primer locations. Right panel: Genotyping PCR and immunoblot for ELOF1-KI cell line (top). LaminB1 was used as loading control (bottom). b, Immunoblot of HCT116 GFP-RPB1 KI. Tubulin was used as loading control. Immunoblots have been performed two times with similar results. c, Histograms showing intensities of GFP and mScarletI measured over the indicated dotted line in HCT116 double KI cells. d, Native immunoprecipitation of P-Ser2-modified Pol II in HCT116 cells followed by immunoblotting for indicated proteins. Cells were harvested 1 hour after mock treatement or irradiation with 16 J/m2 UV-C. IgG was used as binding control. IP has been performed two times with similar results. e, Interaction heat map based on the SILAC ratios of MRC-5 GFP-RPB1-interacting proteins as determined by quantitative interaction proteomics. Average SILAC ratios of duplicate experiments are plotted and represent RPB1-interactors relative to empty beads. SILAC ratio >1 indicates increase in interaction. * indicates proteins quantified in one experiment. f, Top 10 enriched GO terms (biological processes) identified using g:Profiler of 55 proteins identified as ELOF1 interactor with an average SILAC ratio of 2.5 or higher. Uncropped blots are provided in source data.

Extended Data Fig. 3 ELOF1 stimulates transcription elongation.

a, Browser tracks from DRB/TTchem-seq experiment at ATM, DAP and SCAF4. Results are shown 10, 20, 30 or 40 minutes after DRB release. b, Metagene profiles of DRB/TTchem-seq in HCT116 Wt or indicated KO (−/−) cells, with ELOF1 re-expression where indicated, 10, 20, 30, or 40 minutes after DRB release for 50-100Kb long genes. c, Transcription levels as determined by relative EU incorporation in HCT116 cells transfected with indicated siRNAs. Red lines indicate average integrated density ± SEM. siCTRL n = 247, siSPT4 n = 272, siSPT5 n = 288, siCSB n = 286, siELOF1 #1 n = 285 cells analyzed across 3 (siELOF1 and siCSB) and 4 (siCTRL) independent experiments. d, Representative images of EU incorporation in HCT116 cells transfected with indicated siRNAs. Scale bar: 20 µm. e, Immunoblot for indicated proteins in HCT116 cells transfected with indicated siRNAs. Tubulin was used as loading control. Experiment has has been performed two times with similar results. f, Images of HCT116 Wt and ELOF1 −/−A cells transfected with indicated siRNAs, stained with coomassie blue 10 days after transfection. Cell growth experiment has been executed two times with similar results. Numerical data and uncropped blots are provided in source data.

Source data

Extended Data Fig. 4 Role of ELOF1 during TC-NER and protection against different DNA damaging agents.

a,b, Representative immunofluorescence images of EU incorporation in (a) indicated HCT116 cells, or b, HCT116 cells transfected with indicated siRNAs, 2 or 18 hours after 8 J/m2 UV-C or mock treatment (NT). Scale bar: 20 µm. c, Transcription restart after UV damage as determined by relative EU incorporation in HCT116 cells transfected with indicated siRNAs, 2 or 18 hours after 8 J/m2 UV-C or mock treatment (NT). Relative integrated density of UV-irradiated samples are normalized to mock-treated and set to 100%. Red lines indicate average integrated density of, respectively n = 492, 485, 435, 487, 461, 395, 352, 399, 380, 644, 575, 512 cells collected from three independent experiments. d, Representative immunofluorescence images of amplified EdU signal in XP186LV fibroblasts (XP-C) transfected with indicated siRNAs, 7 hours after exposure to 8 J/m2 UV-C. Scale bar: 20 µm. TCR-UDS has been performed three times with similar results. e, Relative ELOF1 mRNA levels in XP186LV fibroblasts (XP-C) following transfection with indicated siRNAs determined by RT-qPCR. ELOF1 expression was normalized to GAPDH expression and siCTRL levels were set to 1. Data shown represent average of 2 independent experiments. f, Representative fluorescence images of EdU incorporation 3 hours after irradiation with 16 J/m2 UV-C in C5RO (hTert) cells transfected with indicated siRNAs. Scale bar: 20 µm. (g) as in (f) in C5RO (hTert) cells. Data shown represent average of 2 independent experiments. h–k, Relative colony survival of indicated HCT116 Wt and KO (−/−) cells, with ELOF1 re-expression where indicated, continuously exposed to indicated concentrations of (h) camptothecin (CPT) or (i) potassium bromate (KBrO3), or irradiated with indicated doses of (j) ionizing radiation (IR), or exposed to indicated concentrations of (k) hydroxyurea (HU) or (l) aphidicolin. Plotted curves represent averages ± SEM. CPT: n = 2; KBrO3: n = 3; IR: n = 5; HU: n = 3, others n = 4 independent experiments. m, Relative colony survival of HCT116 cells transfected with indicated siRNAs following exposure to indicated doses of UV-C. Plotted curves represent averages ± SEM. siCTRL, siSPT4 and siSPT5 n = 4, siELOF1 #1, siCSB, siXPF n = 2 independent experiments. *P ≤ 0.05, ****p ≤ 0.0001 analyzed by two-sided unpaired T-test in (c) and one-sided unpaired T-test in (h-m). Numerical data are provided in source data.

Source data

Extended Data Fig. 5 Role of yeast elf1 in TC-NER.

a, Indicated mutant yeast strains were serially tenfold diluted, spotted, and exposed to indicated UV-C doses. Spot assay has been performed three times with similar results. b, Schematic showing the CPD-seq method. Isolated DNA is sonicated and adaptors are ligated. CPDs are cleaved by T4 endonuclease V and APE1 nuclease to generate 3’ ends. Following denaturing of the DNA, ends are ligated to a second adaptor that allows CPD sequencing. c, Gene plot analysis of CPD-seq data for ~4500 yeast genes, ordered by transcription frequency66. Plots depict unrepaired CPDs following 2-hour repair relative to no repair for both the transcribed strand (TS) and non-transcribed strand (NTS). Each row represents approximately 10 genes. TSS=transcription start site, TTS=transcription termination site. d, Left panel: Representative gel of bulk repair of UV-induced CPD lesions in Wt and elf1∆ mutant yeast measured by T4 endonuclease V digestion and alkaline gel electrophoresis of genomic DNA isolated from UV-irradiated yeast (100 J/m2 UV-C light) after the indicated time. Right panel: Quantification of CPD repair from n = 3 WT and n = 4 elf1∆ experiments ±SEM. *P ≤ 0.05 analyzed by unpaired two-sided t-test. e, Single nucleotide resolution analysis of CPD-seq data downstream of the TSS of ~5200 yeast genes. Plots depict fraction of unrepaired CPDs following 2-hour repair relative to no repair for both TS and NTS. Nucleosome positioning data51 is shown for reference. f, Controls for UV spotting assays shown in Fig. 4d. g, Image showing repair of CPDs in the TS of the RPB2 gene for indicated yeast strains. The image was generated by converting sequencing reads aligned to RPB2 into bands. U: unirradiated cells. Nucleotide positions relative to TSS (+1) are indicated on the left. h, Left: Relative percentage of CPDs remaining within 54 bp downstream of the TSS of the RPB2 gene. Right: Relative percentage of CPDs remaining in the downstream region (69-353 bp) of the RPB2 gene. Data are presented as mean values from all CPD sites within the indicated regions (0-54 and 69-353 bp) of the RPB2 gene ±SD from one single experiment, error bars are shown for most relevant strains. n = 8 sites (left panel), and n = 73 (right panel). i, Representation of the C. elegans elof-1 genomic organization, depicting the 180 bp emc203 deletion allele generated with CRISPR-Cas9. Shaded boxes: exons, black: coding sequences. Numerical data are provided in source data .

Source data

Extended Data Fig. 6 Effects of ELOF1 deficiency on Pol II elongation speed and complex composition.

a, Relative ELOF1 mRNA levels in GFP-RPB1 KI cells transfected with indicated siRNAs as determined by RT-qPCR. ELOF1 expression was normalized to GAPDH signal and levels of control cells were set to 1. Data shown represent average of 2 independent experiments. b, FRAP analysis of GFP-RPB1 mobility after depletion of indicated factors. Mock-treated curves corresponding to Fig. 4a. siCTRL n = 28, siELOF1 #1 n = 20, siCSB NT n = 14 cells analyzed across 4, 3 and 3 independent experiments respectively. c, Left panel: Residence time of elongating Pol II or right panel: relative fraction size of promoter-bound or elongating Pol II as determined by Monte-Carlo-based modeling of RPB1 mobility as shown in (a). d, Native immunoprecipitation of Pol II in Wt and ELOF −/−A cells followed by immunoblotting for indicated proteins. Cells were harvested 1 hour after mock treatment or irradiation with 16 J/m2 UV-C. MG132: treatment with 50 µM proteasome inhibitor MG132, 1 hour before UV irradiation. e, Native immunoprecipitation of Pol II in Wt and ELOF −/−A cells followed by immunoblotting for indicated proteins. Cells were harvested 1 hour after mock treatment or irradiation with 16 J/m2 UV-C. IP experiments depicted in d and e were executed two times with similar results. Numerical data and uncropped blots are provided in source data.

Source data

Extended Data Fig. 7 ELOF1 KO impairs recruitment of UVSSA but not CSB.

a, Left panel: Schematic of the genomic locus of CSB and used strategy for generating the homozygous CSB-mScarletI-HA KI cell line. Half arrows indicate primer locations. Middle and right panel: Genotyping PCR and immunoblot for CSB-KI cell line. b, Left panel: Schematic of the genomic locus of UVSSA and used strategy for generating the homozygous UVSSA- mScarletI-HA KI cell line. Half arrows indicate primer locations. Middle and right panel: Genotyping PCR and immunoblot for UVSSA-KI cell line. Experiments depicted in a and b were performed two times with similar results. c, Left panel: CSB mobility was determined by FRAP analysis of CSB-mScarletI after the indicated treatments. THZ1: 1 hour treatment (2 µM) before UV-C irradiation (4 J/m2) or mock treatment. Right panel: Relative immobile fraction of CSB as determined by FRAP analysis. Plotted values represent mean ± SEM and are normalized to mock treated. NT n = 32; UV n = 28; THZ1 n = 15; THZ1+UV n = 18 cells analyzed across 2 independent experiments. d, Same as C but for UVSSA-mScarletI. NT n = 10; UV n = 16; THZ1 n = 16; THZ1+UV n = 17 cells analyzed across 2 independent experiments. e,f, FRAP analyses of CSB-mScarletI (e) or UVSSA-mScarletI (f) mobility after transfection with indicated siRNAs in individual graphs. Cells were mock treated (NT) or analyzed directly (UV) or 5 hours (5hr UV) after irradiation with 4 J/m2 UV-C. g, Relative fluorescence intensity of UVSSA in UVSSA-KI cells transfected with indicated siRNAs as determined by live-cell imaging. Plotted values represent mean ± SEM. siCTRL NT n = 30, UV+5h UV n = 21; siELOF1 #1 NT n = 38, UV n = 34, 5h UV n = 16; siELOF1 #2 NT+UV n = 19, 5h UV n = 16 cells analyzed across 4 independent experiments for siCTRL and 3 for siELOF1 and siCSB. h, FRAP analysis of CSB in CSB-KI cells transfected with indicated siRNAs 2 hours after UV. VCPi: VCP inhibitor (5 µM) was directly added after UV-C (4 J/m2). i, Immunoblot of chromatin fraction of indicated cell lines 1 hour after 12 J/m2 UV-C or mock treatment. NAEi = 1 hour treatment with NEDDylation inhibitor (10 µM). SSRP1 is shown as loading control. j, Immunoblot of chromatin fraction of HCT116 cells transfected with indicated siRNAs 1 hour after 12 J/m2 UV-C or mock treatment. SSRP1 is shown as loading control. Immunoblots depicted in i and j were executed two times with similar results. Numerical data and uncropped blots are provided in source data.

Source data

Extended Data Fig. 8 The additional role of ELOF1 in preventing transcription-mediated replication hindrance.

a, Left panel: Representative immunofluorescence images of EU incorporation in indicated HCT116 cells, untreated, or 2 or 22 hours after a 2-hour exposure to 10 µg/ml mitomycin C. Scale bar: 20 µm. Right panel: Transcription restart after mitomycin C as determined by relative EU incorporation in the indicated HCT116 cells. Mitomycin C-treated samples are normalized to mock treated levels and set to 100%. Red lines indicate average integrated density ± SEM of, respectively, n = 1008, 1008, 727, 938, 960, 715, 1133, 1162, 784, 884, 616, 461, 978, 1013, 693, 221, 220, 206 cells collected from four independent experiments. b, Relative colony survival of indicated cell lines with siRNA transfection following exposure to indicated doses of UV-C. Plotted curves represent averages ± SEM, n = 3 independent experiments. c, Percentage of RNA synthesis in untreated HCT116 cells and cells treated with 0.1 µM flavopiridol for 2 hours as determined by FACS-based quantification of EU pulse labeling. Experiment has been performed two times with similar results. d, Fork progression measured by tract lengths of CldU (red) in μm is depicted for indicated HCT116 cells, untreated or after 15 minutes 0.1 µM flavopiridol treatment. Tracts of respectively n = 300, 300, 304 cells collected from two independent experiments. e, As (d) but after treatment for 1 hour with 25 nM MMC. Tracts of, respectively n = 406, 422, 408, 406 cells collected from two independent experiments. f, Representative immunofluorescence images of 53BP1 foci in indicated HCT116 cells, untreated or 6, 24 or 48 hours after exposure to 8 J/m2 UV-C. Scale bar: 20 µm. g, Number of 53BP1 foci as determined in (f) quantified by Cellprofiler and plotted against normalized integrated intensity of DAPI, respectively, n = 10494, 7870, 13916, 16647, 9539, 8313, 8610, 8817, 11253, 10950, 10314, 10494 cells collected from two independent experiments. h, Number of FANCD2 foci per mitosis in prometaphase (left) or anaphase (right) in indicated HCT116 cells in untreated conditions or 48 hours after 4J/m2 UV-C. n = 90 cells collected from 3 independent experiments for all conditions. *p ≤ 0.05, ***p ≤ 0.001, ****p ≤ 0.0001 analyzed by two-sided unpaired T-test (a), one-sided unpaired T-test (b), Kruskal-Wallis test for multiple comparisons (d,e), and two-sided unpaired t-test (Mann-Whitney) (h). Numerical data are provided in source data.

Source data

Extended Data Fig. 9 Pol II-ELOF1 complex structure together with CSB.

a, S.cerevisiae Pol II (5vvr.pdb) with Rpb1 in green, Rpb2 in cyan, DNA in orange and Rad26 (CSB) in pink. The P.pastoris Pol II in complex with elongation factors (5xog.pdb) was superimposed onto this structure (Rpb1 subunits aligned onto each other), and all subunits except Elf1 (ELOF1; purple) were omitted for clarity. Conserved lysine K1246 (K1268 in mammalian Pol II) is indicated in dark red. b, Close up of Elf1 (ELOF1) binding region.

Supplementary information

Peer Review Information

Reporting Summary

Supplementary Table 1

Table showing negatively regulated genes from the CRISPR–Cas9 screen resulting from MaGecK analysis of the change in abundance of sgRNAs in UV-treated over mock-treated samples.

Supplementary Table 2

Table with SILAC ratios and peptide numbers as determined using quantitative interaction proteomics. Each tab represents a different experiment as indicated.

Supplementary Table 3

Table with information on used antibodies.

Supplementary Table 4

Table with primer information.

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Geijer, M.E., Zhou, D., Selvam, K. et al. Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability. Nat Cell Biol 23, 608–619 (2021). https://doi.org/10.1038/s41556-021-00692-z

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