Mapping Open Chromatin with Formaldehyde-Assisted Isolation of Regulatory Elements (original) (raw)

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.

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References

  1. Henikoff S.(2008) Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet 9,15–26.
    Article PubMed CAS Google Scholar
  2. Segal E, Widom J.(2009) What controls nucleosome positions? Trends Genet 25,335–343.
    Article PubMed CAS Google Scholar
  3. 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.
    PubMed CAS Google Scholar
  4. Elgin SC.(1988) The formation and function of DNase I hypersensitive sites in the process of gene activation. J Biol Chem 263,19259–19262.
    PubMed CAS Google Scholar
  5. 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.
    Article PubMed CAS Google Scholar
  6. 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.
    Article PubMed CAS Google Scholar
  7. 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.
    Article PubMed CAS Google Scholar
  8. 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.
    Article PubMed CAS Google Scholar
  9. 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.
    Article PubMed CAS Google Scholar
  10. 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.
    Article PubMed CAS Google Scholar
  11. Gaulton KJ, Nammo T, Pasquali L et al.(2010) A map of open chromatin in human pancreatic islets. Nat Genet 42,255–259.
    Article PubMed CAS Google Scholar
  12. 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.
    Article PubMed CAS Google Scholar
  13. Boyle AP, Guinney J, Crawford GE, Furey TS.(2008) F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24,2537–2538.
    Article PubMed CAS Google Scholar

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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.

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Authors and Affiliations

  1. Genomic Programming of Beta Cells, Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
    Takao Nammo, Santiago A. Rodríguez-Seguí & Jorge Ferrer

Authors

  1. Takao Nammo
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  2. Santiago A. Rodríguez-Seguí
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  3. Jorge Ferrer
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Corresponding author

Correspondence toJorge Ferrer .

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Editors and Affiliations

  1. Dept. Biology, University of Alabama, Birmingham, University Blvd. 1300, Birmingham, 35294-1170, Alabama, USA
    Trygve O. Tollefsbol

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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

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