Int. J. Dev. Biol. 60: 141 - 150 (2016)
doi: 10.1387/ijdb.160108jb
© UPV/EHU Press

Genome-wide identification of enhancer elements

Sarah Tulin1, Julius C. Barsi*,2, Carlo Bocconcelli1 and Joel Smith1

1Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA and 2Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA

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.

Keywords:

GRIP-seq, chromatin conformation capture, anti-Pol-II, sea urchin development

*Corresponding author e-mail: barsi@caltech.edu