Strand-specific ChIP-seq at DNA breaks distinguishes ssDNA versus dsDNA binding and refutes single-stranded nucleosomes. 2021

Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.

In a first step of DNA double-strand break (DSB) repair by homologous recombination, DNA ends are resected such that single-stranded DNA (ssDNA) overhangs are generated. ssDNA is specifically bound by RPA and other factors, which constitutes a ssDNA-domain on damaged chromatin. The molecular organization of this ssDNA and the adjacent dsDNA domain is crucial during DSB signaling and repair. However, data regarding the presence of nucleosomes, the most basic chromatin components, in the ssDNA domain have been contradictory. Here, we use site-specific induction of DSBs and chromatin immunoprecipitation followed by strand-specific sequencing to analyze in vivo binding of key DSB repair and signaling proteins to either the ssDNA or dsDNA domain. In the case of nucleosomes, we show that recently proposed ssDNA nucleosomes are not a major, persistent species, but that nucleosome eviction and DNA end resection are intrinsically coupled. These results support a model of separated dsDNA-nucleosome and ssDNA-RPA domains during DSB repair.

UI MeSH Term Description Entries
D009707 Nucleosomes The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4. Dinucleosomes,Polynucleosomes,Dinucleosome,Nucleosome,Polynucleosome
D004247 DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D004260 DNA Repair The removal of DNA LESIONS and/or restoration of intact DNA strands without BASE PAIR MISMATCHES, intrastrand or interstrand crosslinks, or discontinuities in the DNA sugar-phosphate backbones. DNA Damage Response
D004277 DNA, Single-Stranded A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle. Single-Stranded DNA,DNA, Single Stranded,Single Stranded DNA
D000081204 Chromatin Immunoprecipitation Sequencing A technique for identifying the BINDING SITES on nucleic acid sequences that are associated with binding proteins. ATAC-Seq,Assay for Transposase-Accessible Chromatin Using Sequencing,CLIP-Seq,ChIA-PET,ChIP Sequencing,ChIP-Chip,ChIP-Exo,ChIP-Exonuclease,ChIP-PET,ChIP-Seq,Chromatin Immuno-Precipitation Paired-End Tag,Chromatin Immuno-precipitation Sequencing,Chromatin Immunoprecipitation Paired-End Tag,Chromatin Immunoprecipitation Sequencing-Chip,Cross-Linking and Immunoprecipitation Followed by Deep Sequencing,HITS-CLIP,High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation,Assay for Transposase Accessible Chromatin Using Sequencing,ChIP Exonuclease,Chromatin Immuno Precipitation Paired End Tag,Chromatin Immuno precipitation Sequencing,Chromatin Immunoprecipitation Paired End Tag,Chromatin Immunoprecipitation Sequencing Chip,Chromatin Immunoprecipitation Sequencing-Chips,Cross Linking and Immunoprecipitation Followed by Deep Sequencing,High Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation,Sequencing, ChIP,Sequencing, Chromatin Immuno-precipitation,Sequencing, Chromatin Immunoprecipitation
D053903 DNA Breaks, Double-Stranded Interruptions in the sugar-phosphate backbone of DNA, across both strands adjacently. Double-Stranded DNA Breaks,Double-Strand DNA Breaks,Double-Stranded DNA Break,Break, Double-Strand DNA,Break, Double-Stranded DNA,Breaks, Double-Strand DNA,Breaks, Double-Stranded DNA,DNA Break, Double-Strand,DNA Break, Double-Stranded,DNA Breaks, Double Stranded,DNA Breaks, Double-Strand,Double Strand DNA Breaks,Double Stranded DNA Break,Double Stranded DNA Breaks,Double-Strand DNA Break
D059765 Homologous Recombination An exchange of DNA between matching or similar sequences. Homologous Recombinations,Recombination, Homologous,Recombinations, Homologous

Related Publications

Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
August 2019, Bio-protocol,
Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
April 2013, Genome research,
Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
January 1971, International journal of radiation biology and related studies in physics, chemistry, and medicine,
Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
May 2017, Biology of reproduction,
Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
August 1995, Virology,
Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
March 1991, Cell,
Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
July 1983, Journal of molecular biology,
Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
June 2020, Nature methods,
Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
January 2004, DNA repair,
Martina Peritore, and Karl-Uwe Reusswig, and Susanne C S Bantele, and Tobias Straub, and Boris Pfander
January 2017, Methods in molecular biology (Clifton, N.J.),
Copied contents to your clipboard!