ArticleProceedings of the National Academy of Sciences of the United States of America2007
Ribonucleoprotein-masked nicks at 50-kbp intervals in the eukaryotic genomic DNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 24 citations in OpenAlex.
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- Doxorubicin impacts chromatin binding of HMGB1, Histone H1 and retinoic acid receptor.Scientific reports · 2022Article
- Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae.Nucleic acids research · 2018Article
- Nucleosome stability measured in situ by automated quantitative imaging.Scientific reports · 2017Article
- RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases.Genome research · 2017Article
- The monoclonal S9.6 antibody exhibits highly variable binding affinities towards different R-loop sequences.PloS one · 2017Article
- Temporal activation of XRCC1-mediated DNA repair is essential for muscle differentiation.Cell discovery · 2016Article
- The THO complex component Thp2 counteracts telomeric R-loops and telomere shortening.The EMBO journal · 2013Article
- The sub-nanomolar binding of DNA-RNA hybrids by the single-chain Fv fragment of antibody S9.6.Journal of molecular recognition : JMR · 2013Article
- Anti-DNA:RNA antibodies and silicon photonic microring resonators: increased sensitivity for multiplexed microRNA detection.Analytical chemistry · 2011Article
- The TFIIB tip domain couples transcription initiation to events involved in RNA processing.The Journal of biological chemistry · 2010Article
- A structural basis for cellular senescence.Aging · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
By using a microscopic approach, field inversion single-cell gel electrophoresis, we show that preformed single-strand discontinuities are present in the chromatin of resting and proliferating mammalian and yeast cells. These single-strand breaks are primarily nicks positioned at approximately 50-kbp intervals throughout the entire genome that could be efficiently labeled in situ by DNA polymerase I holoenzyme but not by Klenow fragment and terminal transferase unless after ribonucleolytic treatments. The RNA molecules involved appear to comprise R-loops, recognized by the S9.6 RNA/DNA hybrid-specific antibody. By using the breakpoint cluster region of the Mixed Lineage Leukemia (MLL) gene as a model, we have found that the number of manifest nicks detected by FISH performed after field inversion single-cell gel electrophoresis depends on epigenetic context, but the difference between germ-line and translocated MLL alleles is abolished by protease treatment. Our data imply that the double-stranded genomic DNA is composed of contiguous rather than continuous single strands and reveal an aspect of higher-order chromatin organization with ribonucleoprotein-associated persistent nicks defining approximately 50-kbp domains.
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