ArticlePLoS genetics2006
Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting.
Article in PLoS genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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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
35 citing papers in PubMed, 70 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
- Stress-induced translocation of the endoplasmic reticulum chaperone GRP78/BiP and its impact on human disease and therapy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo.Molecular cell · 2021Article
- Current Insights into Oral Cancer Epigenetics.International journal of molecular sciences · 2018Review
- Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters.Molecular cell · 2017Article
- Mechanisms underlying epigenetic and transcriptional heterogeneity in Chinese hamster ovary (CHO) cell lines.BMC biotechnology · 2016Article
- Regulation of the transcriptome by ER stress: non-canonical mechanisms and physiological consequences.Frontiers in genetics · 2013Review
- Functional DNA demethylation is accompanied by chromatin accessibility.Nucleic acids research · 2013Article
- Epigenetic diversity of Kaposi's sarcoma-associated herpesvirus.Nucleic acids research · 2013Article
- Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.Genome research · 2012Article
- Functions of DNA methylation: islands, start sites, gene bodies and beyond.Nature reviews. Genetics · 2012Review
- Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to methylated nucleosomes and maintenance of DNA methylation in somatic cells.Epigenetics & chromatin · 2012Article
- DNA methyltransferase accessibility protocol for individual templates by deep sequencing.Methods in enzymology · 2012Article
- Dissecting epigenetic silencing complexity in the mouse lung cancer suppressor gene Cadm1.PloS one · 2012Article
- Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells.Molecular and cellular biology · 2011Article
- DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter.Human molecular genetics · 2011Article
- 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
- H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes.Molecular cell · 2010Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Chromatin organization and transcriptional regulation are interrelated processes. A shortcoming of current experimental approaches to these complex events is the lack of methods that can capture the activation process on single promoters. We have recently described a method that combines methyltransferase M.SssI treatment of intact nuclei and bisulfite sequencing allowing the representation of replicas of single promoters in terms of protected and unprotected footprint modules. Here we combine this method with computational analysis to study single molecule dynamics of transcriptional activation in the stress inducible GRP78 promoter. We show that a 350-base pair region upstream of the transcription initiation site is constitutively depleted of nucleosomes, regardless of the induction state of the promoter, providing one of the first examples for such a promoter in mammals. The 350-base pair nucleosome-free region can be dissected into modules, identifying transcription factor binding sites and their combinatorial organization during endoplasmic reticulum stress. The interaction of the transcriptional machinery with the GRP78 core promoter is highly organized, represented by six major combinatorial states. We show that the TATA box is frequently occupied in the noninduced state, that stress induction results in sequential loading of the endoplasmic reticulum stress response elements, and that a substantial portion of these elements is no longer occupied following recruitment of factors to the transcription initiation site. Studying the positioning of nucleosomes and transcription factors at the single promoter level provides a powerful tool to gain novel insights into the transcriptional process in eukaryotes.
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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.