Abstract
Noncoding regulatory genomic elements are central for cellular function, differentiation, and disease, but remain poorly characterized. FAIRE (formaldehyde-assisted isolation of regulatory elements) has emerged as a simple method to identify and analyze active regulatory sequences based on their decreased nucleosomal content. More recently FAIRE was combined with high-throughput sequencing (FAIRE-seq) to locate tissue-specific regulatory elements at a genome scale in purified human pancreatic islets. Here we describe the implementation of the FAIRE method in human pancreatic islet cells.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Henikoff S.(2008) Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet 9,15–26.
Segal E, Widom J.(2009) What controls nucleosome positions? Trends Genet 25,335–343.
Almer A, Horz W.(1986) Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus in yeast. EMBO J 5,2681–2687.
Elgin SC.(1988) The formation and function of DNase I hypersensitive sites in the process of gene activation. J Biol Chem 263,19259–19262.
Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD.(2007) FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 17,877–885.
Nagy PL, Cleary ML, Brown PO, Lieb JD.(2003) Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. Proc Natl Acad Sci U S A 100,6364–6369.
Giresi PG, Lieb JD.(2009) Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48,233–239.
Ponts N, Harris EY, Prudhomme J et al.(2010) Nucleosome landscape and control of transcription in the human malaria parasite. Genome Res 20,228–238.
Eeckhoute J, Lupien M, Meyer CA et al.(2009) Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res 19,372–380.
Berchowitz LE, Hanlon SE, Lieb JD, Copenhaver GP.(2009) A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae. Genome Res 19,2245–2257.
Gaulton KJ, Nammo T, Pasquali L et al.(2010) A map of open chromatin in human pancreatic islets. Nat Genet 42,255–259.
Street CN, Lakey JR, Shapiro AM et al.(2004) Islet graft assessment in the Edmonton Protocol: implications for predicting long-term clinical outcome. Diabetes 53,3107–3114.
Boyle AP, Guinney J, Crawford GE, Furey TS.(2008) F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24,2537–2538.
Acknowledgments
The authors would like to thank Jason D. Lieb and Paul G. Giresi for advice and support in the adaptation of the FAIRE protocol for human islets. Work in the authors’ laboratory has been funded by Ministerio de Ciencia e Innovación and Centro de Investigación Biomédica en Red (CIBER) de Diabetes y Enfermedades Metabólicas.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Nammo, T., Rodríguez-Seguí, S.A., Ferrer, J. (2011). Mapping Open Chromatin with Formaldehyde-Assisted Isolation of Regulatory Elements. In: Tollefsbol, T. (eds) Epigenetics Protocols. Methods in Molecular Biology, vol 791. Humana Press. https://doi.org/10.1007/978-1-61779-316-5_21
Download citation
DOI: https://doi.org/10.1007/978-1-61779-316-5_21
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-315-8
Online ISBN: 978-1-61779-316-5
eBook Packages: Springer Protocols