ArticleJournal of molecular biology2001
Quantification of DNaseI-sensitivity by real-time PCR: quantitative analysis of DNaseI-hypersensitivity of the mouse beta-globin LCR.
Article in Journal of molecular biology, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 86 citations in OpenAlex.
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- Transcription factor SOX9 plays a key role in the regulation of visual cycle gene expression in the retinal pigment epithelium.The Journal of biological chemistry · 2014Article
- The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription.Nucleic acids research · 2014Article
- Measuring Arabidopsis chromatin accessibility using DNase I-polymerase chain reaction and DNase I-chip assays.Plant physiology · 2013Article
- Causes and consequences of chromatin variation between inbred mice.PLoS genetics · 2013Article
- Epigenetic expansion of VHL-HIF signal output drives multiorgan metastasis in renal cancer.Nature medicine · 2013Article
- DNase I digestion of isolated nulcei for genome-wide mapping of DNase hypersensitivity sites in chromatin.Methods in molecular biology (Clifton, N.J.) · 2013Article
- Epigenetic modifications unlock the milk protein gene loci during mouse mammary gland development and differentiation.PloS one · 2013Article
- Novel evolutionary-conserved role for the activity-dependent neuroprotective protein (ADNP) family that is important for erythropoiesis.The Journal of biological chemistry · 2012Article
- High-resolution mapping of open chromatin in the rice genome.Genome research · 2012Article
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- Epigenetic priors for identifying active transcription factor binding sites.Bioinformatics (Oxford, England) · 2012Article
- The distinctive roles of erythroid specific activator GATA-1 and NF-E2 in transcription of the human fetal γ-globin genes.Nucleic acids research · 2011Article
- NF-κB and BRG1 bind a distal regulatory element in the IL-3/GM-CSF locus.Molecular immunology · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
We employ real-time PCR to allow us to quantify the sensitivity of chromatin to digestion by DNaseI. This approach has three clear advantages over the more conventional use of the Southern hybridization assay: the accuracy of quantification is improved; the resolution of the assay is enhanced, by designing primers to amplify small amplicons it is possible to analyze sequences both co-incident and proximal to sites of DNaseI-hypersensitivity; less material is needed, as little as 5 ng of treated genomic DNA. We applied this method in an analysis of the chromatin structure of the previously described mouse beta-globin locus control region (LCR) using fetal liver cells. The four hypersensitive sites of the canonical mouse LCR, HS1 to HS4, are shown to have kinetics of digestion consistent with these sequences being nucleosome-free in vivo. A different pattern was seen for HS6, a recently described "weak" hypersensitive site. The site was also rapidly lost but more of the sites proved resistant, we interpreted this to show that this hypersensitive was only forming in a portion of the erythroid cells. This finding implies that in vivo the LCR is structurally heterogeneous. Sequences proximal to the hypersensitive sites show a third pattern of intermediate sensitivity, consistent with the chromatin being unfolded but the sites still bound by a continual nucleosomal array. Our results demonstrate that this method has the potential to achieve accurate and detailed mapping of chromatin structure from small amounts of tissue samples.
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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.