Role of 53BP1 in End Protection and DNA synthesis at DNA breaks [ChIP-seq]
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ABSTRACT:
PROVIDER: PRJNA752902 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15369965.fastq.gz | Fastqsanger.gz | |||
| SRR15369966.fastq.gz | Fastqsanger.gz | |||
| SRR15369967.fastq.gz | Fastqsanger.gz | |||
| SRR15369968.fastq.gz | Fastqsanger.gz | |||
| SRR15369969.fastq.gz | Fastqsanger.gz |
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Project description:Double-strand break (DSB) repair choice is greatly influenced by the initial processing of DNA ends. 53BP1 limits the formation of recombinogenic single strand DNA (ssDNA) in BRCA1-deficient cells leading to defects in homologous recombination (HR). However, the exact mechanisms by which 53BP1 inhibits DSB resection remain unclear. Previous studies have identified two potential pathways: protection against exonucleases presumably through the Shieldin (SHLD) complex binding to ssDNA, and localized DNA synthesis through the (CTC1-STN1-TEN1) CST and DNA polymerase alpha (Polα) to counteract resection. We present evidence here that 53BP1-mediated exonuclease protection plays a more significant role than CST/Polα synthesis in countering hyper-resection at DSBs in G1 phase. Using a combinatorial approach of END-seq, SAR-seq, and RPA ChIP-seq, we directly assessed the extent of resection, DNA synthesis, and ssDNA, respectively, at AsiSI-induced DSBs. We show that in the presence of 53BP1, Polα-dependent DNA synthesis reduces the fraction of resected DSBs and the resection lengths. However, in the absence of 53BP1, Polα activity is sustained on ssDNA yet does not substantially counter resection. In contrast, Exo1 nuclease activity is essential for hyperresection in the absence of 53BP1. Thus, 53BP1 inhibits resection mainly through end-protection rather than by promoting fill-in.
2021-09-10 | GSE181669 | GEO
Project description:Double-strand break (DSB) repair choice is greatly influenced by the initial processing of DNA ends. 53BP1 limits the formation of recombinogenic single strand DNA (ssDNA) in BRCA1-deficient cells leading to defects in homologous recombination (HR). However, the exact mechanisms by which 53BP1 inhibits DSB resection remain unclear. Previous studies have identified two potential pathways: protection against exonucleases presumably through the Shieldin (SHLD) complex binding to ssDNA, and localized DNA synthesis through the (CTC1-STN1-TEN1) CST and DNA polymerase alpha (Polα) to counteract resection. We present evidence here that 53BP1-mediated exonuclease protection plays a more significant role than CST/Polα synthesis in countering hyper-resection at DSBs in G1 phase. Using a combinatorial approach of END-seq, SAR-seq, and RPA ChIP-seq, we directly assessed the extent of resection, DNA synthesis, and ssDNA, respectively, at AsiSI-induced DSBs. We show that in the presence of 53BP1, Polα-dependent DNA synthesis reduces the fraction of resected DSBs and the resection lengths. However, in the absence of 53BP1, Polα activity is sustained on ssDNA yet does not substantially counter resection. In contrast, Exo1 nuclease activity is essential for hyperresection in the absence of 53BP1. Thus, 53BP1 inhibits resection mainly through end-protection rather than by promoting fill-in.
2021-09-10 | GSE181667 | GEO
Project description:Double-strand break (DSB) repair choice is greatly influenced by the initial processing of DNA ends. 53BP1 limits the formation of recombinogenic single strand DNA (ssDNA) in BRCA1-deficient cells leading to defects in homologous recombination (HR). However, the exact mechanisms by which 53BP1 inhibits DSB resection remain unclear. Previous studies have identified two potential pathways: protection against exonucleases presumably through the Shieldin (SHLD) complex binding to ssDNA, and localized DNA synthesis through the (CTC1-STN1-TEN1) CST and DNA polymerase alpha (Polα) to counteract resection. We present evidence here that 53BP1-mediated exonuclease protection plays a more significant role than CST/Polα synthesis in countering hyper-resection at DSBs in G1 phase. Using a combinatorial approach of END-seq, SAR-seq, and RPA ChIP-seq, we directly assessed the extent of resection, DNA synthesis, and ssDNA, respectively, at AsiSI-induced DSBs. We show that in the presence of 53BP1, Polα-dependent DNA synthesis reduces the fraction of resected DSBs and the resection lengths. However, in the absence of 53BP1, Polα activity is sustained on ssDNA yet does not substantially counter resection. In contrast, Exo1 nuclease activity is essential for hyperresection in the absence of 53BP1. Thus, 53BP1 inhibits resection mainly through end-protection rather than by promoting fill-in.
2021-09-10 | GSE181668 | GEO
Project description:Role of 53BP1 in End Protection and DNA synthesis at DNA breaks
| PRJNA752898 | ENA
Project description:Role of 53BP1 in End Protection and DNA synthesis at DNA breaks [END-seq]
| PRJNA752903 | ENA
Project description:Role of 53BP1 in End Protection and DNA synthesis at DNA breaks [SAR-seq]
| PRJNA752901 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2021-09-10 | GSE181670 | GEO
Project description:53BP1 regulates DNA end-joining in lymphocytes, diversifying immune antigen receptors. This involves nucleosome-bound 53BP1 at DNA double-stranded breaks (DSBs) recruiting RIF1 and shieldin, a poorly understood DNA-binding complex. The 53BP1-RIF1-shieldin axis is pathological in BRCA1-mutated cancers, blocking homologous recombination (HR) and driving illegitimate non-homologous end-joining (NHEJ). However, how this axis regulates DNA end-joining and HR suppression remains unresolved. We investigated shieldin and its interplay with CST, a complex recently implicated in 53BP1-dependent activities. Immunophenotypically, mice lacking shieldin or CST are equivalent, with class-switch recombination co-reliant on both complexes. DNA damage-responsive signalling promotes shieldin-CST interaction, demonstrating shieldin as a DSB-specific CST adaptor. Furthermore, DNA polymerase ζ functions downstream of shieldin, establishing DNA fill-in synthesis as the physiological function of shieldin-CST. Lastly, 53BP1 suppresses HR and promotes NHEJ in BRCA1-deficient cells independently of shieldin. These findings showcase the resilience of the 53BP1 pathway, achieved through the collaboration of chromatin-bound 53BP1 complexes and DNA end-processing effector proteins.
2024-08-27 | PXD045534 | Pride
Project description:DNA double-strand breaks (DSBs) represent a threat to the genome because they can lead to loss of genetic information and chromosome rearrangements. The DNA repair protein p53 binding protein 1 (53BP1) protects the genome by limiting nucleolytic processing of DSBs by a mechanism that requires its phosphorylation, but whether it does so directly is not known. Here we identify Rapl-interacting factor 1 (Rif1) as an Ataxia-Telangiectasia Mutated (ATM) phosphorylation-dependent interactor of 53BP1, and show that absence of Rif1 results in 5M-bM-^@M-^Y-3M-bM-^@M-^Y DNA end resection in mice. Consistent with enhanced DNA resection, Rif1 deficiency impairs DNA repair in the G1 and S phases of the cell cycle, interferes with class switch recombination (CSR) in B lymphocytes, and leads to accumulation of chromosome DSBs. Study of Rif1 DNA-end protection activity against resection via analysis of single-stranded DNA binding protein RPA and Rad51 accumulation at sites of AID-induced DNA damage by ChIP-seq. All samples shown in Fig. 4 are included (controls and test samples, 7 samples in total).
2013-03-01 | E-GEOD-42298 | biostudies-arrayexpress
Project description:The structure of broken DNA ends is a critical determinant of the pathway used for DNA double strand break (DSB) repair. Here, we develop an approach, hairpin capture of DNA end structures (HCoDES), which elucidates chromosomal DNA end structures at single nucleotide resolution. HCoDES defines structures of physiologic DSBs generated by the RAG endonuclease, as well as those generated by nucleases widely used for genome editing. Analysis of G1-phase cells deficient in H2AX or 53BP1 reveals DNA ends that are frequently resected to form long single-stranded overhangs that can be repaired by mutagenic pathways. In addition to 3’ overhangs, many of these DNA ends unexpectedly form long 5’ single-stranded overhangs. The divergence in DNA end structures resolved by HCoDES suggests that H2AX and 53BP1 may have distinct activities in end protection. Thus, the high-resolution end structures obtained by HCoDES identify new features of DNA end processing during DSB repair. Single stranded DNA ligation of genomic DNA isolated from G1 arrested LigaseIV-/-, LigaseIV-/- 53BP1-/- and LigaseIV-/- H2AX-/- Abelson pre-B cells harboring site specific DSBs generated by the RAG recombinase, Cas9 endonuclease or Zinc Finger Endonuclease.
2014-12-03 | E-GEOD-62534 | biostudies-arrayexpress