ArticleMethods in molecular biology (Clifton, N.J.)2012
Quantitative analysis of genome-wide chromatin remodeling.
Article in Methods in molecular biology (Clifton, N.J.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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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.
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Who cites it
24 citing papers in PubMed.
- Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response.Nature communications · 2021Article
- Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction.Nature genetics · 2020Article
- Computational Methods for Assessing Chromatin Hierarchy.Computational and structural biotechnology journal · 2018Review
- Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis.The FEBS journal · 2017Article
- Anti-Inflammatory Chromatinscape Suggests Alternative Mechanisms of Glucocorticoid Receptor Action.Immunity · 2017Article
- Genome-Wide Identification of Basic Helix-Loop-Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus.Endocrinology · 2017Article
- ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data.Bioinformatics (Oxford, England) · 2017Article
- Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response.Genome research · 2017Article
- Genome-wide footprinting: ready for prime time?Nature methods · 2016Article
- Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation.PloS one · 2016Article
- Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes.Methods in molecular biology (Clifton, N.J.) · 2016Article
- Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome.PloS one · 2016Article
- Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale.Nucleic acids research · 2015Article
- Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling.Nature communications · 2015Article
- A comparison of peak callers used for DNase-Seq data.PloS one · 2014Article
- Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions.Nature structural & molecular biology · 2014Article
- Chromatin accessibility: a window into the genome.Epigenetics & chromatin · 2014Review
- Article
- Reprogramming the chromatin landscape: interplay of the estrogen and glucocorticoid receptors at the genomic level.Cancer research · 2013Article
- C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements.The EMBO journal · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Recent high-throughput sequencing technologies have opened the door for genome-wide characterization of chromatin features at an unprecedented resolution. Chromatin accessibility is an important property that regulates protein binding and other nuclear processes. Here, we describe computational methods to analyze chromatin accessibility using DNaseI hypersensitivity by sequencing (DNaseI-seq). Although there are numerous bioinformatic tools to analyze ChIP-seq data, our statistical algorithm was developed specifically to identify significantly accessible genomic regions by handling features of DNaseI hypersensitivity. Without prior knowledge of relevant protein factors, one can discover genome-wide chromatin remodeling events associated with specific conditions or differentiation stages from quantitative analysis of DNaseI hypersensitivity. By performing appropriate subsequent computational analyses on a select subset of remodeled sites, it is also possible to extract information about putative factors that may bind to specific DNA elements within DNaseI hypersensitive sites. These approaches enabled by DNaseI-seq represent a powerful new methodology that reveals mechanisms of transcriptional regulation.
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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.