Abstract
Genetic information is organized in a complex structure composed of DNA and proteins together designated chromatin. Chromatin plays a dynamic role in transcriptional processes in that alteration of the interaction between its components results in the deregulation of cellular transcriptional program. Modification of epigenetic marks, variation in the precise positioning of nucleosomes, and consequent mobilization of nucleosomes regulate the access of various transcriptional factors to its underlying DNA template. Nucleosome-depleted regions, also designated open chromatin domains, are associated with active DNA regulatory elements, including promoters, enhancers, silencers, and insulators. Here, we describe the protocol of a rapid and simple technique entitled FAIRE (formaldehyde-assisted isolation of regulatory elements). Combined with high-throughput sequencing (FAIRE-seq), this procedure allows isolation of nucleosome-free regions and their mapping along the genome, thereby providing a global view of cell-specific regulatory elements.
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
Hogan C, Varga-Weisz P (2007) The regulation of ATP-dependent nucleosome remodelling factors. Mutat Res 618(1-2):41–51
Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21(3):381–395
Jin J, Cai Y, Li B et al (2005) In and out: histone variant exchange in chromatin. Trends Biochem Sci 30(12):680–687
Cockerill PN (2011) Structure and function of active chromatin and DNase I hypersensitive sites. FEBS J 278(13):2182–2210
Rizzo JM, Sinha S (2014) Analyzing the global chromatin structure of keratinocytes by MNase-Seq. Methods Mol Biol 1195:49–59
Gaulton KJ, Nammo T, Pasquali L et al (2010) A map of open chromatin in human pancreatic islets. Nat Genet 42(3):255–259
Paul DS, Albers CA, Rendon A et al (2013) Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci. Genome Res 23(7):1130–1141
Song L, Zhang Z, Grasfeder LL et al (2011) Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 21(10):1757–1767
Waki H, Nakamura M, Yamauchi T et al (2011) Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation. PLoS Genet 7(10), e1002311
Rodrigue S, Materna AC, Timberlake SC et al (2010) Unlocking short read sequencing for metagenomics. PLoS One 5(7), e11840
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760
Lassmann T, Hayashizaki Y, Daub CO (2011) SAMStat: monitoring biases in next generation sequencing data. Bioinformatics 27(1):130–131
Zhang Y, Liu T, Meyer CA et al (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9(9):R137
Boyle AP, Guinney J, Crawford GE et al (2008) F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24(21):2537–2538
Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14(2):178–192
Acknowledgement
We thank Alain Lavigueur and Maïka Jangal for critical comments on the manuscript.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Bianco, S., Rodrigue, S., Murphy, B.D., Gévry, N. (2015). Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq). In: Leblanc, B., Rodrigue, S. (eds) DNA-Protein Interactions. Methods in Molecular Biology, vol 1334. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2877-4_17
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2877-4_17
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2876-7
Online ISBN: 978-1-4939-2877-4
eBook Packages: Springer Protocols