ReviewJournal of cellular biochemistry2008
Single-molecule analysis of chromatin: changing the view of genomes one molecule at a time.
Review in Journal of cellular biochemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed, 18 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
- Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data.Bioinformatics (Oxford, England) · 2021Article
- CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing.Bioinformatics (Oxford, England) · 2017Article
- Mechanisms underlying epigenetic and transcriptional heterogeneity in Chinese hamster ovary (CHO) cell lines.BMC biotechnology · 2016Article
- Rapid deamination of cyclobutane pyrimidine dimer photoproducts at TCG sites in a translationally and rotationally positioned nucleosome in vivo.The Journal of biological chemistry · 2015Article
- DNA methylation and nucleosome occupancy regulate the cancer germline antigen gene MAGEA11.Epigenetics · 2013Article
- Epigenetic diversity of Kaposi's sarcoma-associated herpesvirus.Nucleic acids research · 2013Article
- Dissecting epigenetic silencing complexity in the mouse lung cancer suppressor gene Cadm1.PloS one · 2012Article
- DNA methyltransferase accessibility protocol for individual templates by deep sequencing.Methods in enzymology · 2012Article
- WIF1 is a frequent target for epigenetic silencing in squamous cell carcinoma of the cervix.Carcinogenesis · 2011Article
- 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
- 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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Wrapping DNA into chromatin provides a wealth of regulatory mechanisms that ensure normal growth and development in eukaryotes. Our understanding of chromatin structure, including nucleosomes and non-histone protein-DNA interactions, has benefited immensely from nuclease and chemical digestion techniques. DNA-bound proteins, such as histones or site-specific factors, protect DNA against nuclease cleavage and generate large nucleosomal or small regulatory factor footprints. Chromatin subject to distinct modes of regulation often coincides with sites of nuclease hypersensitivity or nucleosome positioning. An inherent limitation of cleavage-based analyses has been the inability to reliably analyze regions of interest when levels of digestion depart from single-hit kinetics. Moreover, cleavage-based techniques provide views that are averaged over all the molecules in a sample population. Therefore, in cases of occupancy of multiple regulatory elements by factors, one cannot define whether the factors are bound to the same or different molecules in the population. The recent development of DNA methyltransferase-based, single-molecule MAP-IT technology overcomes limitations of ensemble approaches and has opened numerous new avenues in chromatin research. Here, we review the strengths, limitations, applications and future prospects of MAP-IT ranging from structural issues to mechanistic questions in eukaryotic chromatin regulation.
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What 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.