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Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq)

  • Stéphanie Bianco
  • Sébastien Rodrigue
  • Bruce D. Murphy
  • Nicolas GévryEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1334)

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.

Key words

Chromatin Formaldehyde Regulatory elements Next-generation sequencing Protein–DNA interaction Epigenetics Chromatin accessibility Nucleosome-depleted regions 

Notes

Acknowledgement

We thank Alain Lavigueur and Maïka Jangal for critical comments on the manuscript.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Stéphanie Bianco
    • 1
  • Sébastien Rodrigue
    • 1
  • Bruce D. Murphy
    • 2
  • Nicolas Gévry
    • 1
    Email author
  1. 1.Département de Biologie, Faculté des SciencesUniversité de SherbrookeSherbrookeCanada
  2. 2.Centre de Recherche en Reproduction Animale, Faculté de Médecine VétérinaireUniversité de MontréalSaint HyacintheCanada

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