ArticlePloS one2009
Impact of chromatin structures on DNA processing for genomic analyses.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
86 citing papers in PubMed, 123 citations in OpenAlex.
- A step-by-step guide for isolating soluble and insoluble chromatin followed by next-generation sequencing library preparation.STAR protocols · 2026Article
- CUT&Tag overcomes biases of ChIP and establishes chromatin patterns for repetitive genomic loci.iScience · 2025Article
- Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility.Nature genetics · 2024Article
- Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis.Nature genetics · 2023Article
- A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples.Bio-protocol · 2022Article
- Biomimetic mimicry of formaldehyde-induced DNA-protein crosslinks in the confined space of a metal-organic framework.Chemical science · 2022Article
- Chromatin structure can introduce systematic biases in genome-wide analyses ofOpen research Europe · 2022Article
- FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers.Nucleic acids research · 2021Article
- Bayesian Markov models improve the prediction of binding motifs beyond first order.NAR genomics and bioinformatics · 2021Article
- Article
- Genome-Wide Profiling of Protein-DNA Interactions with Chromatin Endogenous Cleavage and High-Throughput Sequencing (ChEC-Seq ).Methods in molecular biology (Clifton, N.J.) · 2021Article
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
- Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications.Nature protocols · 2019Article
- Fermentation innovation through complex hybridization of wild and domesticated yeasts.Nature ecology & evolution · 2019Article
- Quantitative MNase-seq accurately maps nucleosome occupancy levels.Genome biology · 2019Article
- Defining the regulon of genes controlled by σMolecular microbiology · 2019Article
- Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes.Scientific reports · 2019Article
- ChIPulate: A comprehensive ChIP-seq simulation pipeline.PLoS computational biology · 2019Article
- Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells.Biochimica et biophysica acta. Gene regulatory mechanisms · 2018Article
- Cavitation Enhancement Increases the Efficiency and Consistency of Chromatin Fragmentation from Fixed Cells for Downstream Quantitative Applications.Biochemistry · 2018Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results of chromatin immunoprecipitation (ChIP) experiments. We initially discovered this effect at the Saccharomyces cerevisiae HMR locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. Using input samples from ChIP-Seq studies, we detected a similar bias throughout the heterochromatic portions of the yeast genome. We also observed significant chromatin-related effects at telomeres, protein binding sites, and genes, reflected in the variation of input-Seq coverage. Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects. Our results suggested that assays relying on immunoprecipitation of chromatin will be biased by intrinsic differences between regions packaged into different chromatin structures - biases which have been largely ignored to date. These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.