Journal article
Formaldehyde-assisted isolation of regulatory elements
Wiley interdisciplinary reviews. Systems biology and medicine, Vol.1(3), pp.400-406
11/2009
DOI: 10.1002/wsbm.36
PMCID: PMC2800794
PMID: 20046543
Abstract
Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) is based on locus-specific variations in the ability of protein components of chromatin to trap genomic DNA following formaldehyde treatment. This variation is mostly due to uneven nucleosome distribution since histones are the most abundant and highly crosslinkable components of chromatin. The method can identify and enrich for physically accessible DNA segments of the eukaryotic genome corresponding to known regulatory regions and regions that might have thus far unidentified structural role in the nuclear organization of chromatin. The enrichment patterns are cell type specific and thus might provide information about how transcriptional systems are organized and regulated in various tissues and how they might be disrupted in disease states. Analysis of a 268 kb region of chromosome 19 in human fibroblasts shown here demonstrates that while most DNA fragments detected by FAIRE correspond to sites of DNaseI hypersensitivity in active regions of chromatin, some are found in otherwise repressed chromatin domains and at other sites that are not found with other methods used to probe chromatin structure. Further exploration of FAIRE is warrented due to the simplicity of the protocol and recent advancements in massively parallel sequencing.
Details
- Title: Subtitle
- Formaldehyde-assisted isolation of regulatory elements
- Creators
- Peter L Nagy - Departments of Pathology, Biochemistry and Pediatrics, University of Iowa, Iowa City, IA 52242, USADavid H Price - Departments of Pathology, Biochemistry and Pediatrics, University of Iowa, Iowa City, IA 52242, USA
- Resource Type
- Journal article
- Publication Details
- Wiley interdisciplinary reviews. Systems biology and medicine, Vol.1(3), pp.400-406
- DOI
- 10.1002/wsbm.36
- PMID
- 20046543
- PMCID
- PMC2800794
- NLM abbreviation
- Wiley Interdiscip Rev Syst Biol Med
- ISSN
- 1939-5094
- eISSN
- 1939-005X
- Publisher
- United States
- Grant note
- NS064253 / NINDS NIH HHS R01 NS064253-02 / NINDS NIH HHS GM35500 / NIGMS NIH HHS R01 NS064253 / NINDS NIH HHS R01 GM035500 / NIGMS NIH HHS
- Language
- English
- Date published
- 11/2009
- Academic Unit
- Biochemistry and Molecular Biology
- Record Identifier
- 9984024538902771
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