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| Status |
Public on Feb 22, 2024 |
| Title |
Dbf4-dependent kinase promotes cell-cycle controlled resection of DNA double strand breaks and repair by homologous recombination |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
DNA double-strand breaks (DSBs) can be repaired by several pathways. In eukaryotes, repair pathway choice – the cellular decision making underlying DSB repair – occurs at the level of DSB resection and is controlled by the cell cycle. Upon cell cycle-dependent activation, cyclin-dependent kinases (CDKs) phosphorylate resection proteins and thereby stimulate DSB resection and repair by homologous recombination (HR). Here, we identify Dbf4-dependent kinase (DDK) as a second major cell cycle regulator of DNA end resection. Using inducible genetic and chemical inhibition of DDK in budding yeast and human cells, we show that DNA resection and HR require activation by DDK. Mechanistically, DDK catalyzes phosphorylation of at least two resection nucleases. Via phosphorylation of the Mre11 activator Sae2 it promotes activation of resection initiation, via phosphorylation of the Dna2 nuclease it promotes long-range resection. Notably, synthetic activiation of DDK allows limited resection and HR in G1 cells, suggesting that DDK is a key component of DSB repair decision making.
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| Overall design |
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Replication Protein A (RPA) in different Saccharomyces cerevisiae strains: WT, dbf4-3AID, sae2-S267E, GAL-DDK, sae2-S267E GAL-DDK. N ≥ 2 replicates
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| Contributor(s) |
Galanti L, Peritore M, Gnügge R, Cannavó E, Palumbieri M, Steigenberger B, Symington LS, Cejka P, Pfander B |
| Citation(s) |
38570537 |
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| Submission date |
May 26, 2023 |
| Last update date |
Apr 17, 2024 |
| Contact name |
Martina Peritore |
| E-mail(s) |
peritore@biochem.mpg.de
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| Phone |
+49 8985783049
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| Organization name |
MPIB
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| Lab |
Pfander
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| Street address |
Am Klopferspitz 18
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| City |
Planegg-Martinsried |
| State/province |
Bayern |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platforms (2) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
| GPL27812 |
Illumina NovaSeq 6000 (Saccharomyces cerevisiae) |
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| Samples (96)
|
| GSM7430069 |
YLG135, mock, input, 0h, rep1 |
| GSM7430070 |
YLG135, mock, input, 2h, rep1 |
| GSM7430071 |
YLG135, mock, input, 4h, rep1 |
| GSM7430072 |
YLG135, IAA, input, 0h, rep1 |
| GSM7430073 |
YLG135, IAA, input, 2h, rep1 |
| GSM7430074 |
YLG135, IAA, input, 4h, rep1 |
| GSM7430075 |
YLG135, mock, RPA ChIP, 0h, rep1 |
| GSM7430076 |
YLG135, mock, RPA ChIP, 2h, rep1 |
| GSM7430077 |
YLG135, mock, RPA ChIP, 4h, rep1 |
| GSM7430078 |
YLG135, IAA, RPA ChIP, 0h, rep1 |
| GSM7430079 |
YLG135, IAA, RPA ChIP, 2h, rep1 |
| GSM7430080 |
YLG135, IAA, RPA ChIP, 4h, rep1 |
| GSM7430081 |
YLG136, mock, input, 0h, rep1 |
| GSM7430082 |
YLG136, mock, input, 2h, rep1 |
| GSM7430083 |
YLG136, mock, input, 4h, rep1 |
| GSM7430084 |
YLG136, IAA, input, 0h, rep1 |
| GSM7430085 |
YLG136, IAA, input, 2h, rep1 |
| GSM7430086 |
YLG136, IAA, input, 4h, rep1 |
| GSM7430087 |
YLG136, mock, RPA ChIP, 0h, rep1 |
| GSM7430088 |
YLG136, mock, RPA ChIP, 2h, rep1 |
| GSM7430089 |
YLG136, mock, RPA ChIP, 4h, rep1 |
| GSM7430090 |
YLG136, IAA, RPA ChIP, 0h, rep1 |
| GSM7430091 |
YLG136, IAA, RPA ChIP, 2h, rep1 |
| GSM7430092 |
YLG136, IAA, RPA ChIP, 4h, rep1 |
| GSM7430093 |
YLG135, mock, input, 0h, rep2 |
| GSM7430094 |
YLG135, mock, input, 2h, rep2 |
| GSM7430095 |
YLG135, mock, input, 4h, rep2 |
| GSM7430096 |
YLG135, IAA, input, 0h, rep2 |
| GSM7430097 |
YLG135, IAA, input, 2h, rep2 |
| GSM7430098 |
YLG135, IAA, input, 4h, rep2 |
| GSM7430099 |
YLG136, mock, input, 0h, rep2 |
| GSM7430100 |
YLG136, mock, input, 2h, rep2 |
| GSM7430101 |
YLG136, mock, input, 4h, rep2 |
| GSM7430102 |
YLG136, IAA, input, 0h, rep2 |
| GSM7430103 |
YLG136, IAA, input, 2h, rep2 |
| GSM7430104 |
YLG136, IAA, input, 4h, rep2 |
| GSM7430105 |
YLG135, mock, RPA ChIP, 0h, rep2 |
| GSM7430106 |
YLG135, mock, RPA ChIP, 2h, rep2 |
| GSM7430107 |
YLG135, mock, RPA ChIP, 4h, rep2 |
| GSM7430108 |
YLG135, IAA, RPA ChIP, 0h, rep2 |
| GSM7430109 |
YLG135, IAA, RPA ChIP, 2h, rep2 |
| GSM7430110 |
YLG135, IAA, RPA ChIP, 4h, rep2 |
| GSM7430111 |
YLG136, mock, RPA ChIP, 0h, rep2 |
| GSM7430112 |
YLG136, mock, RPA ChIP, 2h, rep2 |
| GSM7430113 |
YLG136, mock, RPA ChIP, 4h, rep2 |
| GSM7430114 |
YLG136, IAA, RPA ChIP, 0h, rep2 |
| GSM7430115 |
YLG136, IAA, RPA ChIP, 2h, rep2 |
| GSM7430116 |
YLG136, IAA, RPA ChIP, 4h, rep2 |
| GSM7430117 |
YLG137, input, 0h, rep1 |
| GSM7430118 |
YLG137, input, 2h, rep1 |
| GSM7430119 |
YLG137, input, 4h, rep1 |
| GSM7430120 |
YLG142, input, 0h, rep1 |
| GSM7430121 |
YLG142, input, 2h, rep1 |
| GSM7430122 |
YLG142, input, 4h, rep1 |
| GSM7430123 |
YSB517, input, 0h, rep1 |
| GSM7430124 |
YSB517, input, 2h, rep1 |
| GSM7430125 |
YSB517, input, 4h, rep1 |
| GSM7430126 |
YSB802, input, 0h, rep1 |
| GSM7430127 |
YSB802, input, 2h, rep1 |
| GSM7430128 |
YSB802, input, 4h, rep1 |
| GSM7430129 |
YLG137, RPA ChIP, 0h, rep1 |
| GSM7430130 |
YLG137, RPA ChIP, 2h, rep1 |
| GSM7430131 |
YLG137, RPA ChIP, 4h, rep1 |
| GSM7430132 |
YLG142, RPA ChIP, 0h, rep1 |
| GSM7430133 |
YLG142, RPA ChIP, 2h, rep1 |
| GSM7430134 |
YLG142, RPA ChIP, 4h, rep1 |
| GSM7430135 |
YSB517, RPA ChIP, 0h, rep1 |
| GSM7430136 |
YSB517, RPA ChIP, 2h, rep1 |
| GSM7430137 |
YSB517, RPA ChIP, 4h, rep1 |
| GSM7430138 |
YSB802, RPA ChIP, 0h, rep1 |
| GSM7430139 |
YSB802, RPA ChIP, 2h, rep1 |
| GSM7430140 |
YSB802, RPA ChIP, 4h, rep1 |
| GSM7430141 |
YLG137, input, 0h, rep2 |
| GSM7430142 |
YLG137, input, 2h, rep2 |
| GSM7430143 |
YLG137, input, 4h, rep2 |
| GSM7430144 |
YLG142, input, 0h, rep2 |
| GSM7430145 |
YLG142, input, 2h, rep2 |
| GSM7430146 |
YLG142, input, 4h, rep2 |
| GSM7430147 |
YSB517, input, 0h, rep2 |
| GSM7430148 |
YSB517, input, 2h, rep2 |
| GSM7430149 |
YSB517, input, 4h, rep2 |
| GSM7430150 |
YSB802, input, 0h, rep2 |
| GSM7430151 |
YSB802, input, 2h, rep2 |
| GSM7430152 |
YSB802, input, 4h, rep2 |
| GSM7430153 |
YLG137, RPA ChIP, 0h, rep2 |
| GSM7430154 |
YLG137, RPA ChIP, 2h, rep2 |
| GSM7430155 |
YLG137, RPA ChIP, 4h, rep2 |
| GSM7430156 |
YLG142, RPA ChIP, 0h, rep2 |
| GSM7430157 |
YLG142, RPA ChIP, 2h, rep2 |
| GSM7430158 |
YLG142, RPA ChIP, 4h, rep2 |
| GSM7430159 |
YSB517, RPA ChIP, 0h, rep2 |
| GSM7430160 |
YSB517, RPA ChIP, 2h, rep2 |
| GSM7430161 |
YSB517, RPA ChIP, 4h, rep2 |
| GSM7430162 |
YSB802, RPA ChIP, 0h, rep2 |
| GSM7430163 |
YSB802, RPA ChIP, 2h, rep2 |
| GSM7430164 |
YSB802, RPA ChIP, 4h, rep2 |
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| Relations |
| BioProject |
PRJNA976649 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE233549_RAW.tar |
3.1 Gb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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