Int. J. Dev. Biol. 60: 141 - 150 (2016)

https://doi.org/10.1387/ijdb.160108jb

Vol 60, Issue 4-5-6

Genome-wide identification of enhancer elements

Developmental Expression Pattern | Published: 6 July 2016

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