title: Genome-wide identification of enhancer elements.
abstract: We present a prospective genome-wide regulatory element database for the sea urchin embryo and the modified chromosome capture-related methodology used to create it. The method we developed is termed GRIP-seq for genome-wide regulatory element immunoprecipitation and combines features of chromosome conformation capture, chromatin immunoprecipitation, and paired-end next-generation sequencing with molecular steps that enrich for active cis-regulatory elements associated with basal transcriptional machinery. The first GRIP-seq database, available to the community, comes from S. purpuratus 24 hpf embryos and takes advantage of the extremely well-characterized cis-regulatory elements in this system for validation. In addition, using the GRIP-seq database, we identify and experimentally validate a novel, intronic cis-regulatory element at the onecut locus. We find GRIP-seq signal sensitively identifies active cis-regulatory elements with a high signal-to-noise ratio for both distal and intronic elements. This promising GRIP-seq protocol has the potential to address a rate-limiting step in resolving comprehensive, predictive network models in all systems.
authors.affiliation: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Tulin
authors.forename: Julius C
authors.initials: JC
authors.lastname: Barsi
authors.forename: Carlo
authors.initials: C
authors.lastname: Bocconcelli
authors.forename: Joel
authors.initials: J
authors.lastname: Smith
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D030541:Databases, Genetic; D004742:Enhancer Elements, Genetic; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing