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Series GSE218590 Query DataSets for GSE218590
Status Public on Sep 18, 2023
Title Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5ʹ strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site—a role we postulate is played by DNA-dependent protein kinase (DNA-PK) in mammals. Here we interrogate the sites of MRN-dependent processing by isolating and sequencing DNA-PK-bound DNA fragments that are products of MRN cleavage. These intermediates are generated with highest efficiency when DNA-PK is catalytically blocked, yielding products within 200 bp of the break site, whereas DNA-PK products in the absence of kinase inhibition show much greater dispersal. Use of light-activated Cas9 to induce breaks facilitates temporal resolution of DNA-PK and Mre11 binding, showing that Mre11 and DNA-PK both bind to DNA ends before release of DNA-PK-bound products. These results support a sequential model of double-strand break repair involving collaborative interactions between homologous and non-homologous repair complexes.
Overall design Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for phospho-DNA-PKcs(S2056), GLASS-ChIP DNA sequencing for phospho-DNA-PKcs(S2056), and Mre11 ChIPseq
Contributor(s) Deshpande R, Marin-Gonzalez A, Ha T, Paull T, Barnes H, Woolley P
Citation(s) 37717054
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM138548 DNA end processing by the Mre11/Rad50/Nbs1 complex in human cells UNIVERSITY OF TEXAS AUSTIN TANYA T PAULL
Submission date Nov 22, 2022
Last update date Sep 27, 2023
Contact name Tanya T. Paull
Phone 5122327803
Organization name Univ. of Texas at Austin
Department Molecular Biosciences
Lab Paull
Street address 2500 Speedway MBB 2.448
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (58)
GSM6752995 GC, no 4-OHT, +NU-7441, +antibody, rep1
GSM6752996 GC, no 4-OHT, +NU-7441, -antibody, rep1
GSM6752997 GC, no 4-OHT, +NU-7441, +antibody, rep2
BioProject PRJNA904374

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE218590_CtIP_GC_no_4-OHT_+antibody.bigwig 45.8 Mb (ftp)(http) BIGWIG
GSE218590_CtIP_GC_plus_4-OHT_+antibody.bigwig 40.1 Mb (ftp)(http) BIGWIG
GSE218590_CtIP_PC_no_4-OHT_+antibody.bigwig 656.5 Mb (ftp)(http) BIGWIG
GSE218590_CtIP_PC_plus_4-OHT_+antibody.bigwig 718.3 Mb (ftp)(http) BIGWIG
GSE218590_GC+DNAPKiplus4H1hronly+PFM01+antibody.bigwig 70.0 Mb (ftp)(http) BIGWIG
GSE218590_GC+DNAPKiplus4H1hronly+PFM39+antibody.bigwig 133.9 Mb (ftp)(http) BIGWIG
GSE218590_GC+DNAPKiplus4H1hronly+antibody.bigwig 124.3 Mb (ftp)(http) BIGWIG
GSE218590_GC_+DNA-PKi_15m_post-light_+antibody_R1_and_R2.bigwig 67.2 Mb (ftp)(http) BIGWIG
GSE218590_GC_+DNA-PKi_60m_post-light_+antibody_R1_and_R2.bigwig 74.0 Mb (ftp)(http) BIGWIG
GSE218590_GC_+DNA-PKi_no_light_+antibody_R1_and_R2.bigwig 59.0 Mb (ftp)(http) BIGWIG
GSE218590_GC_+DNAPKi_no_4H_+antibody__R1_and_R2.bigwig 417.0 Mb (ftp)(http) BIGWIG
GSE218590_GC_+DNAPKi_plus_4H_+antibody__R1_and_R2.bigwig 335.2 Mb (ftp)(http) BIGWIG
GSE218590_GC_no_4H_+antibody_R1_and_R2.bigwig 301.8 Mb (ftp)(http) BIGWIG
GSE218590_GC_plus_4H_+antibody_R1_and_R2.bigwig 344.7 Mb (ftp)(http) BIGWIG
GSE218590_Mre11_+DNA-PKi_15m_post-light_+antibody_R1_and_R2.bigwig 176.1 Mb (ftp)(http) BIGWIG
GSE218590_Mre11_+DNA-PKi_60m_post-light_+antibody_R1_and_R2.bigwig 155.1 Mb (ftp)(http) BIGWIG
GSE218590_Mre11_+DNA-PKi_no_light_+antibody_R1_and_R2.bigwig 176.5 Mb (ftp)(http) BIGWIG
GSE218590_PC_+DNA-PKi_15m_post-light_+antibody_R1_and_R2.bigwig 353.9 Mb (ftp)(http) BIGWIG
GSE218590_PC_+DNA-PKi_60m_post-light_+antibody_R1_and_R2.bigwig 343.4 Mb (ftp)(http) BIGWIG
GSE218590_PC_+DNA-PKi_no_light_+antibody_R1_and_R2.bigwig 318.6 Mb (ftp)(http) BIGWIG
GSE218590_PC_+DNAPKi_no_4H_+antibody.bigwig 319.0 Mb (ftp)(http) BIGWIG
GSE218590_PC_+DNAPKi_plus_4H_+antibody.bigwig 264.2 Mb (ftp)(http) BIGWIG
GSE218590_PC_no_4H_+antibody.bigwig 363.0 Mb (ftp)(http) BIGWIG
GSE218590_PC_plus_4H_+antibody.bigwig 383.7 Mb (ftp)(http) BIGWIG
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Raw data are available in SRA
Processed data are available on Series record

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