ArticleThe EMBO journal1996
Direct study of DNA-protein interactions in repressed and active chromatin in living cells.
Article in The EMBO journal, 1996. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
33 citing papers in PubMed, 85 citations in OpenAlex.
- FENGC: Targeted, Multiplexed, and Integrated Single-Molecule Profiling of Chromatin Accessibility and DNA Methylation.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Beyond assembly: the increasing flexibility of single-molecule sequencing technology.Nature reviews. Genetics · 2023Review
- Partitioned usage of chromatin remodelers by nucleosome-displacing factors.Cell reports · 2022Article
- Chromatin accessibility profiling methods.Nature reviews. Methods primers · 2021Article
- Review
- Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma.Genome research · 2014Article
- Epigenetic diversity of Kaposi's sarcoma-associated herpesvirus.Nucleic acids research · 2013Article
- DNA methyltransferase accessibility protocol for individual templates by deep sequencing.Methods in enzymology · 2012Article
- Simultaneous single-molecule mapping of protein-DNA interactions and DNA methylation by MAPit.Current protocols in molecular biology · 2011Article
- MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects.Nucleic acids research · 2011Article
- A yeast one-hybrid system to screen for methylated DNA-binding proteins.Nucleic acids research · 2010Article
- Bisulfite sequencing of DNA.Current protocols in molecular biology · 2010Article
- SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes.Molecular cell · 2010Article
- Single-molecule analysis of chromatin: changing the view of genomes one molecule at a time.Journal of cellular biochemistry · 2008Review
- A nucleosome positioned by alpha2/Mcm1 prevents Hap1 activator binding in vivo.Biochemical and biophysical research communications · 2007Article
- Article
- Single-molecule and population probing of chromatin structure using DNA methyltransferases.Methods (San Diego, Calif.) · 2007Article
- Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting.PLoS genetics · 2006Article
- Effectors of lysine 4 methylation of histone H3 in Saccharomyces cerevisiae are negative regulators of PHO5 and GAL1-10.The Journal of biological chemistry · 2004Article
- Cloning of CviPII nicking and modification system from chlorella virus NYs-1 and application of Nt.CviPII in random DNA amplification.Nucleic acids research · 2004Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Current methods for analysis of chromatin architecture are invasive, utilizing chemicals or nucleases that damage DNA, making detection of labile constituents and conclusions about true in vivo structure problematic. We describe a sensitive assay of chromatin structure which is performed in intact, living yeast. The approach utilizes expression of SssI DNA methyltransferase (MTase) in Saccharomyces cerevisiae to provide an order-of-magnitude increase in resolution over previously introduced MTases. Combining this resolution increase with the novel application of a PCR-based, positive chemical display of modified cytosines provides a significant advance in the direct study of DNA-protein interactions in growing cells that enables quantitative footprinting. The validity and efficacy of the strategy are demonstrated in mini-chromosomes, where positioned nucleosomes and a labile, operator-bound repressor are detected. Also, using a heterologous system to study gene activation, we show that in vivo hormone occupancy of the estrogen receptor is required for maximal site-specific DNA binding, whereas, at very high receptor-expression levels, hormone-independent partial occupancy of an estrogen-responsive element was observed. Receptor binding to a palindromic estrogen-responsive element leads to a footprint with strand-specific asymmetry, which is explicable by known structural information.
Indexed as
Identifiers
8947052PMC452452W1732318706What OpenQuestion holds
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.