Precision Kinetic High-Resolution Analysis of DNA Damage Patterns
Keywords:
53BP1, p53fluorescence microscopy; image analysis; image cytometry, “DNA damage response;”Abstract
53BP1, a protein known to interact with p53, has been isolated in vitro, but its critical role in supporting the p53-driven transcriptional program in the DNA Damage Response (DDR) is often overlooked. This is evident even when assessing different reactions to DNA Double-Strand Breaks (DSBs) caused by ionizing radiation. Inhibiting 53BP1 is key to optimizing both mental and physical performance by easing their interaction. This study introduces advanced image cytometry to track DDR progression, highlighting 53BP1 translocation from damage sites where it regulates DDR. By analyzing cell cycle deficiencies, we provide a quantitative framework of molecular interactions and their spatial-temporal constraints. We offer a detailed quantitative analysis of the processes following DSBs, validated through rigorous testing. Using Single-Molecule Localization Microscopy (SMLM), we confirm the p53-53BP1 interaction at critical DDR stages, offering new insights into their coordination.
References
Palmer SA, Smith O, Allaby RG. 2012 The blossoming of plant archaeogenetics. Ann. Anat.194, 146–156.
Allentoft MEet al.2012 The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils.Proc. R. Soc. B 279, 4724–4733.
Shapiro B, Hofreiter M. 2014 A paleogenomic perspective on evolution and gene function: new insights from ancient DNA.Science343, 1236573.
Poinar HN et al.2006 Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.Science311, 392–394.
Paabo Set al.2004 Genetic analyses from ancient DNA. Annu. Rev. Genet.38, 645–679.
Dabney J, Meyer M, Paabo S. 2013 Ancient DNA damage.Cold Spring Harb. Perspect. Biol.5, a012567.
Lindahl T, Andersson A. 1972 Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry 11, 3618–3623.
Lindahl T, Nyberg B. 1972 Rate of depurination of native deoxyribonucleic acid. Biochemistry 11, 3610–3618.
Briggs AWet al.2007 Patterns of damage in genomic DNA sequences from a Neandertal.Proc. Natl Acad. Sci. USA 104, 14 616–14 621.
Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, Cooper A. 2007 Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res.35, 5717–5728.
Sawyer S, Krause J, Guschanski K, Savolainen V, Paabo S. 2012 Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA.PLoS ONE 7, e34131.
Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, Paabo S. 2010 A complete mtDNA genome of an early modern human from Kostenki, Russia.Curr. Biol.20, 231–236.
Pruvost M, Schwarz R, Correia VB, Champlot S, Braguier S, Morel N, Fernandez-Jalvo Y, Grange T, Geigl EM. 2007 Freshly excavated fossil bones are best for amplification of ancient DNA.Proc. Natl Acad. Sci. USA 104, 739–744.
Lindahl T. 1993 Instability and decay of the primary structure of DNA. Nature362, 709–715.
Yoshida K et al.2013 The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine.eLife2, e00731.
Kistler L. 2012 Ancient DNA extraction from plants. Methods Mol. Biol. 840, 71–79.
Deagle BE, Eveson JP, Jarman SN. 2006 Quantification of damage in DNA recovered from highly degraded samples—a case study on DNA in faeces.Front. Zool.3, 11.
Rogers SO, Bendich AJ. 1985 Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues.Plant Mol. Biol.5, 69–76.
Martin MD et al.2013 Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat. Commun. 4, 2172.
Staats M, Erkens RH, van de Vossenberg B, Wieringa JJ, Kraaijeveld K, Stielow B, Geml J, Richardson JE, Bakker FT. 2013 Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.PLoS ONE 8, e69189.
