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The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of DNA. To investigate how DNA mismatches affect the mechanical stability and the exposure of nucleosomal DNA, we used an optical trap combined with single-molecule FRET and a single-molecule FRET cyclization assay. We found that a single base-pair C-C mismatch enhances DNA bendability and nucleosome mechanical stability for the 601-nucleosome positioning sequence. An increase in force required for DNA unwrapping from the histone core is observed for single base-pair C-C mismatches placed at three tested positions: at the inner turn, at the outer turn, or at the junction of the inner and outer turn of the nucleosome. The results support a model where nucleosomal DNA accessibility is reduced by mismatches, potentially explaining the preferred accumulation of single-nucleotide substitutions in the nucleosome core and serving as the source of genetic variation during evolution and cancer progression. Mechanical stability of an intact nucleosome, that is mismatch-free, is also dependent on the species as we find that yeast nucleosomes are mechanically less stable and more symmetrical in the outer turn unwrapping compared to Xenopus nucleosomes.
Basu,
Measuring DNA mechanics on the genome scale.
2021, Pubmed
Basu,
Measuring DNA mechanics on the genome scale.
2021,
Pubmed
Basu,
Deciphering the mechanical code of the genome and epigenome.
2022,
Pubmed
Blosser,
Dynamics of nucleosome remodelling by individual ACF complexes.
2009,
Pubmed
Chen,
Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes.
2012,
Pubmed
Chen,
Structures and Functions of Chromatin Fibers.
2021,
Pubmed
Chen,
Prime editing for precise and highly versatile genome manipulation.
2023,
Pubmed
Díaz-Celis,
Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products.
2022,
Pubmed
Dyer,
Reconstitution of nucleosome core particles from recombinant histones and DNA.
2004,
Pubmed
Fazal,
Real-time observation of the initiation of RNA polymerase II transcription.
2015,
Pubmed
Fields,
Euler buckling and nonlinear kinking of double-stranded DNA.
2013,
Pubmed
Galburt,
Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner.
2007,
Pubmed
Hanahan,
Hallmarks of cancer: the next generation.
2011,
Pubmed
Hara,
DNA damage in the nucleosome core is refractory to repair by human excision nuclease.
2000,
Pubmed
Hohng,
Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction.
2007,
Pubmed
Huang,
DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy.
2021,
Pubmed
Isaacs,
A model for initial DNA lesion recognition by NER and MMR based on local conformational flexibility.
2004,
Pubmed
Jeong,
Single-molecule fluorescence studies on DNA looping.
2016,
Pubmed
Jeong,
Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking.
2019,
Pubmed
Jo,
Determination of single-molecule loading rate during mechanotransduction in cell adhesion.
2024,
Pubmed
Kim,
Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers.
2024,
Pubmed
Kornberg,
Chromatin structure: a repeating unit of histones and DNA.
1974,
Pubmed
Lancrey,
Nucleosome Positioning on Large Tandem DNA Repeats of the '601' Sequence Engineered in Saccharomyces cerevisiae.
2022,
Pubmed
LeGresley,
DNA damage may drive nucleosomal reorganization to facilitate damage detection.
2014,
Pubmed
Li,
Mechanisms and functions of DNA mismatch repair.
2008,
Pubmed
Li,
Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome.
2020,
Pubmed
Luger,
New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?
2012,
Pubmed
Maffeo,
A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.
2014,
Pubmed
McBurney,
Divergent Residues Within Histone H3 Dictate a Unique Chromatin Structure in Saccharomyces cerevisiae.
2016,
Pubmed
Mertz,
APOBEC-Induced Mutagenesis in Cancer.
2022,
Pubmed
Ngo,
Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility.
2015,
Pubmed
,
Xenbase
Ngo,
Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability.
2016,
Pubmed
Park,
Bi-directional nucleosome sliding by the Chd1 chromatin remodeler integrates intrinsic sequence-dependent and ATP-dependent nucleosome positioning.
2023,
Pubmed
Perales,
Histone occupancy in vivo at the 601 nucleosome binding element is determined by transcriptional history.
2011,
Pubmed
Rees,
Base editing: precision chemistry on the genome and transcriptome of living cells.
2018,
Pubmed
Sabarinathan,
Nucleotide excision repair is impaired by binding of transcription factors to DNA.
2016,
Pubmed
Sasaki,
Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites.
2009,
Pubmed
Schweikhard,
Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms.
2014,
Pubmed
Semple,
Molecular biology. The structure of change.
2009,
Pubmed
Tokuda,
The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome.
2018,
Pubmed
Tolstorukov,
Impact of chromatin structure on sequence variability in the human genome.
2011,
Pubmed
Vafabakhsh,
Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization.
2012,
Pubmed
Wang,
DNA bending and unbending by MutS govern mismatch recognition and specificity.
2003,
Pubmed
Wang,
Comment on "A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme".
2016,
Pubmed
Warnecke,
The impact of the nucleosome code on protein-coding sequence evolution in yeast.
2008,
Pubmed
Washietl,
Evolutionary footprints of nucleosome positions in yeast.
2008,
Pubmed
White,
Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions.
2001,
Pubmed
,
Xenbase
Yazdi,
Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact.
2015,
Pubmed
Yoo,
DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.
2021,
Pubmed
Zhou,
SSB functions as a sliding platform that migrates on DNA via reptation.
2011,
Pubmed
