ArticlePloS one2012
Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 35 citations in OpenAlex.
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- Genetic variants of NEUROD1 target genes are associated with clinical outcomes of small-cell lung cancer patients.Thoracic cancer · 2023Article
- CALN1 hypomethylation as a biomarker for high-risk bladder cancer.BMC urology · 2022Article
- Genome-Wide Study of Colocalization between Genomic Stretches: A Method and Applications to the Regulation of Gene Expression.Biology · 2022Article
- Epigenetic alterations of CXCL5 in Cr(VI)-induced carcinogenesis.The Science of the total environment · 2022Article
- Systematic identification of silencers in human cells.Nature genetics · 2020Article
- EnhancerDB: a resource of transcriptional regulation in the context of enhancers.Database : the journal of biological databases and curation · 2019Article
- Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana.Molecular biology and evolution · 2018Article
- Computational Methods for Assessing Chromatin Hierarchy.Computational and structural biotechnology journal · 2018Review
- Genome-wide Identification and Characterization of Enhancers Across 10 Human Tissues.International journal of biological sciences · 2018Article
- Chromatin accessibility dynamics reveal novel functional enhancers inGenome research · 2017Article
- Recognition but no repair of abasic site in single-stranded DNA by human ribosomal uS3 protein residing within intact 40S subunit.Nucleic acids research · 2017Article
- RGmatch: matching genomic regions to proximal genes in omics data integration.BMC bioinformatics · 2016Article
- The histone deacetylase inhibitor Entinostat enhances polymer-mediated transgene expression in cancer cell lines.Biotechnology and bioengineering · 2016Article
- Modeling co-occupancy of transcription factors using chromatin features.Nucleic acids research · 2016Article
- Chromatin accessibility: a window into the genome.Epigenetics & chromatin · 2014Review
- Genome-wide mapping of DNase I hypersensitive sites and association analysis with gene expression in MSB1 cells.Frontiers in genetics · 2014Article
- A comparison of peak callers used for DNase-Seq data.PloS one · 2014Article
- Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells.PloS one · 2014Article
- Bioinformatics analysis of the factors controlling type I IFN gene expression in autoimmune disease and virus-induced immunity.Frontiers in immunology · 2013Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mapping DNase I hypersensitive sites (DHSs) within nuclear chromatin is a traditional and powerful method of identifying genetic regulatory elements. DHSs have been mapped by capturing the ends of long DNase I-cut fragments (>100,000 bp), or 100-1200 bp DNase I-double cleavage fragments (also called double-hit fragments). But next generation sequencing requires a DNA library containing DNA fragments of 100-500 bp. Therefore, we used short DNA fragments released by DNase I digestion to generate DNA libraries for next generation sequencing. The short segments are 100-300 bp and can be directly cloned and used for high-throughput sequencing. We identified 83,897 DHSs in 2,343,479 tags across the human genome. Our results indicate that the DHSs identified by this DHS assay are consistent with those identified by longer fragments in previous studies. We also found: (1) the distribution of DHSs in promoter and other gene regions of similarly expressed genes differs among different chromosomes; (2) silenced genes had a more open chromatin structure than previously thought; (3) DHSs in 3'untranslated regions (3'UTRs) are negatively correlated with level of gene expression.
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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.