ArticleProceedings of the National Academy of Sciences of the United States of America2004
Discovery of functional noncoding elements by digital analysis of chromatin structure.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers, 3 of them syntheses that pooled it.
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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
92 citing papers in PubMed, 3 syntheses or guidelines pooled it, 139 citations in OpenAlex.
- Meta-analyses identify DNA methylation associated with kidney function and damage.Nature communications · 2021Pooled it
- On the presence and role of human gene-body DNA methylation.Oncotarget · 2012Pooled it
- Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains.Nucleic acids research · 2011Pooled it
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- The cistrome response to hypoxia in human umbilical vein endothelial cells.bioRxiv : the preprint server for biology · 2026Article
- Preferential formation of NUP98-KDM5A condensates at specific H3K4me3-rich loci drives leukemogenic gene expression.bioRxiv : the preprint server for biology · 2026Article
- Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity.Cell systems · 2025Article
- GFI1-Dependent Repression ofCancers · 2022Article
- Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations.Genome biology · 2022Article
- Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus.Nature communications · 2021Article
- Characterization of universal features of partially methylated domains across tissues and species.Epigenetics & chromatin · 2020Article
- Enhancer Predictions and Genome-Wide Regulatory Circuits.Annual review of genomics and human genetics · 2020Review
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- Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance.Genome biology · 2020Article
- A framework for transcriptome-wide association studies in breast cancer in diverse study populations.Genome biology · 2020Article
- Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules.Frontiers in genetics · 2020Article
- Article
- RNA element discovery from germ cell to blastocyst.Nucleic acids research · 2019Article
- Soluble TREM2 and biomarkers of central and peripheral inflammation in neurodegenerative disease.Journal of neuroimmunology · 2018Article
32 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
12 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We developed a quantitative methodology, digital analysis of chromatin structure (DACS), for high-throughput, automated mapping of DNase I-hypersensitive sites and associated cis-regulatory sequences in the human and other complex genomes. We used 19/20-bp genomic DNA tags to localize individual DNase I cutting events in nuclear chromatin and produced approximately 257,000 tags from erythroid cells. Tags were mapped to the human genome, and a quantitative algorithm was applied to discriminate statistically significant clusters of independent DNase I cutting events. We show that such clusters identify both known regulatory sequences and previously unrecognized functional elements across the genome. We used in silico simulation to demonstrate that DACS is capable of efficient and accurate localization of the majority of DNase I-hypersensitive sites in the human genome without requiring an independent validation step. A unique feature of DACS is that it permits unbiased evaluation of the chromatin state of regulatory sequences from widely separated genomic loci. We found surprisingly large differences in the accessibility of distant regulatory sequences, suggesting the existence of a hierarchy of nuclear organization that escapes detection by conventional chromatin assays.
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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.