title: Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq).
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.
authors.affiliation: Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, Canada, J1K 2R1.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Bianco
authors.affiliation: Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, Canada, J1K 2R1.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Rodrigue
authors.affiliation: Centre de Recherche en Reproduction Animale, Faculté de Médecine Vétérinaire, Université de Montréal, Saint Hyacinthe, QC, Canada, J2S 7C6.
authors.forename: Bruce D
authors.initials: BD
authors.lastname: Murphy
authors.affiliation: Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, Canada, J1K 2R1. nicolas.gevry@usherbrooke.ca.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Gévry
mesh_terms: D002843:Chromatin / Q000737:chemistry / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D005557:Formaldehyde / Q000737:chemistry; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D038101:Insulator Elements / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D037941:Silencer Elements, Transcriptional / Q000235:genetics
chemical_list: D002843:Chromatin; D011506:Proteins; D005557:Formaldehyde; D004247:DNA
keywords: Chromatin; Chromatin accessibility; Epigenetics; Formaldehyde; Next-generation sequencing; Nucleosome-depleted regions; Protein–DNA interaction; Regulatory elements